[med-svn] [picard-tools] 01/03: Imported Upstream version 1.113
Olivier Sallou
osallou at debian.org
Fri Jun 6 21:35:22 UTC 2014
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch master
in repository picard-tools.
commit db975eec8cfe47577ed127e842c5e088c92bd909
Author: Olivier Sallou <olivier.sallou at debian.org>
Date: Fri Jun 6 23:33:41 2014 +0200
Imported Upstream version 1.113
---
.gitignore | 11 +
build.xml | 5 +-
.../net/sf/picard/analysis/CollectWgsMetrics.java | 274 ++++
.../net/sf/picard/cmdline/CommandLineParser.java | 18 +-
.../sf/picard/filter/SecondaryAlignmentFilter.java | 20 +
.../sf/picard/illumina/CheckIlluminaDirectory.java | 78 +-
.../picard/illumina/ClusterDataToSamConverter.java | 22 +-
.../picard/illumina/ExtractIlluminaBarcodes.java | 5 +-
.../illumina/IlluminaBasecallsConverter.java | 83 +-
.../picard/illumina/IlluminaBasecallsToFastq.java | 1 +
.../sf/picard/illumina/IlluminaBasecallsToSam.java | 1 +
.../sf/picard/illumina/MarkIlluminaAdapters.java | 23 +-
.../net/sf/picard/illumina/parser/BclData.java | 30 +
.../net/sf/picard/illumina/parser/BclParser.java | 239 ++-
.../net/sf/picard/illumina/parser/CifParser.java | 79 -
.../net/sf/picard/illumina/parser/CnfParser.java | 67 -
.../illumina/parser/CycleIlluminaFileMap.java | 177 +--
.../illumina/parser/IlluminaDataProvider.java | 69 +-
.../parser/IlluminaDataProviderFactory.java | 167 +-
.../picard/illumina/parser/IlluminaDataType.java | 2 +-
.../sf/picard/illumina/parser/IlluminaFileMap.java | 27 +-
.../picard/illumina/parser/IlluminaFileUtil.java | 1345 +---------------
.../illumina/parser/IlluminaIntensityParser.java | 132 --
.../sf/picard/illumina/parser/IlluminaParser.java | 16 +-
.../parser/MultiTileBclCycleFilesIterator.java | 40 -
.../illumina/parser/MultiTileBclFileUtil.java | 115 ++
.../picard/illumina/parser/MultiTileBclParser.java | 112 +-
.../picard/illumina/parser/MultiTileFileUtil.java | 120 ++
.../illumina/parser/MultiTileFilterParser.java | 6 +
.../illumina/parser/MultiTileLocsParser.java | 5 +
.../illumina/parser/ParameterizedFileUtil.java | 174 +++
.../picard/illumina/parser/PerTileCycleParser.java | 203 +++
.../sf/picard/illumina/parser/PerTileFileUtil.java | 78 +
.../illumina/parser/PerTilePerCycleFileUtil.java | 268 ++++
.../illumina/parser/PerTilePerCycleParser.java | 197 ---
.../net/sf/picard/illumina/parser/QseqParser.java | 592 --------
.../net/sf/picard/illumina/parser/TileIndex.java | 12 +-
.../illumina/parser/fakers/BclFileFaker.java | 15 +-
.../illumina/parser/fakers/CifFileFaker.java | 31 -
.../illumina/parser/fakers/CnfFileFaker.java | 31 -
.../picard/illumina/parser/fakers/FileFaker.java | 26 +-
.../illumina/parser/fakers/QSeqFileFaker.java | 25 -
.../picard/illumina/parser/readers/BclReader.java | 467 +++---
src/java/net/sf/picard/io/IoUtil.java | 22 +-
src/java/net/sf/picard/metrics/MetricsFile.java | 22 +-
.../reference/AbstractFastaSequenceFile.java | 4 +-
.../sf/picard/reference/FastaSequenceIndex.java | 1 +
.../sf/picard/reference/ReferenceSequenceFile.java | 4 +
.../reference/ReferenceSequenceFileWalker.java | 5 +
.../net/sf/picard/sam/AbstractAlignmentMerger.java | 28 +-
src/java/net/sf/picard/sam/AddCommentsToBam.java | 57 +
src/java/net/sf/picard/sam/BuildBamIndex.java | 2 +-
src/java/net/sf/picard/sam/FilterSamReads.java | 7 +-
src/java/net/sf/picard/sam/FixMateInformation.java | 38 +-
src/java/net/sf/picard/sam/GatherBamFiles.java | 97 ++
src/java/net/sf/picard/sam/MarkDuplicates.java | 2 +-
src/java/net/sf/picard/sam/MergeBamAlignment.java | 7 +-
src/java/net/sf/picard/sam/ReplaceSamHeader.java | 60 +-
...RevertOriginalBaseQualitiesAndAddMateCigar.java | 22 +-
src/java/net/sf/picard/sam/SamAlignmentMerger.java | 7 +-
src/java/net/sf/picard/sam/SamFileValidator.java | 30 +-
src/java/net/sf/picard/util/AdapterMarker.java | 341 +++++
src/java/net/sf/picard/util/BasicInputParser.java | 4 +
src/java/net/sf/picard/util/IlluminaUtil.java | 45 +-
src/java/net/sf/picard/util/IntervalList.java | 402 ++++-
src/java/net/sf/picard/util/IntervalListTools.java | 142 +-
src/java/net/sf/picard/util/MathUtil.java | 11 +-
src/java/net/sf/picard/util/SamLocusIterator.java | 16 +-
src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java | 16 +-
src/java/net/sf/picard/vcf/MergeVcfs.java | 12 +-
src/java/net/sf/picard/vcf/SplitVcfs.java | 12 +-
src/java/net/sf/picard/vcf/VcfFormatConverter.java | 14 +-
.../net/sf/samtools/AbstractSAMHeaderRecord.java | 5 +
src/java/net/sf/samtools/BAMFileReader.java | 77 +-
src/java/net/sf/samtools/BAMFileWriter.java | 81 +-
src/java/net/sf/samtools/BamFileIoUtils.java | 155 ++
src/java/net/sf/samtools/Defaults.java | 15 +
src/java/net/sf/samtools/SAMFileWriterFactory.java | 2 +-
src/java/net/sf/samtools/SAMRecord.java | 264 +---
src/java/net/sf/samtools/SAMRecordSetBuilder.java | 19 +-
src/java/net/sf/samtools/SAMTag.java | 2 +-
src/java/net/sf/samtools/SAMUtils.java | 295 ++++
src/java/net/sf/samtools/SAMValidationError.java | 8 +-
src/java/net/sf/samtools/SamPairUtil.java | 62 +-
.../StreamInflatingIndexingOutputStream.java | 80 +
.../sf/samtools/TagValueAndUnsignedArrayFlag.java | 2 +-
src/java/net/sf/samtools/TextTagCodec.java | 10 +-
.../samtools/util/BlockCompressedInputStream.java | 7 +
.../net/sf/samtools/util/CloseableIterator.java | 6 +-
src/java/net/sf/samtools/util/IOUtil.java | 31 +
src/java/net/sf/samtools/util/LineReader.java | 4 +-
.../org/broad/tribble/AbstractFeatureReader.java | 31 +-
src/java/org/broad/tribble/index/IndexFactory.java | 5 +
.../java/org/broad/tribble/util/ftp/.gitignore | 0
.../writer/VariantContextWriterBuilder.java | 466 ++++++
.../writer/VariantContextWriterFactory.java | 14 +-
.../variant/vcf/AbstractVCFCodec.java | 31 +
.../variant/vcf/VCFCompoundHeaderLine.java | 7 +-
.../org/broadinstitute/variant/vcf/VCFEncoder.java | 4 +-
src/scripts/release_picard.sh | 5 +-
.../tests/java/net/sf/picard/fastq/.gitignore | 0
.../illumina/CheckIlluminaDirectoryTest.java | 84 +-
.../illumina/ExtractIlluminaBarcodesTest.java | 211 ++-
.../illumina/IlluminaBasecallsToFastqTest.java | 32 +-
.../IlluminaBasecallsToSamAdapterClippingTest.java | 32 +-
.../illumina/IlluminaBasecallsToSamTest.java | 29 +-
.../sf/picard/illumina/parser/BclParserTest.java | 443 +++---
.../net/sf/picard/illumina/parser/BinTdUtil.java | 473 ++----
.../parser/ClusterIntensityFileReaderTest.java | 102 --
.../illumina/parser/CycleIlluminaFileMapTest.java | 46 +-
.../picard/illumina/parser/FilterParserTest.java | 141 +-
.../illumina/parser/IlluminaDataProviderTest.java | 420 ++---
.../illumina/parser/IlluminaFileUtilTest.java | 684 +++------
.../parser/IlluminaIntensityParserTest.java | 147 --
.../illumina/parser/PerTilePerCycleParserTest.java | 185 +--
.../sf/picard/illumina/parser/PosParserTest.java | 2 +
.../net/sf/picard/illumina/parser/QSeqTdUtil.java | 707 ---------
.../sf/picard/illumina/parser/QseqParserTest.java | 356 -----
.../illumina/parser/fakers/BclFileFakerTest.java | 59 +
.../illumina/parser/readers/BclReaderTest.java | 45 +-
.../illumina/parser/readers/PosFileReaderTest.java | 50 +-
.../picard/reference/FastaSequenceIndexTest.java | 1 +
.../reference/IndexedFastaSequenceFileTest.java | 33 +
.../reference/ReferenceSequenceFileWalkerTest.java | 11 +-
.../net/sf/picard/sam/AddCommentsToBamTest.java | 63 +
src/tests/java/net/sf/picard/sam/CleanSamTest.java | 19 +-
.../net/sf/picard/sam/MergeBamAlignmentTest.java | 5 +-
.../java/net/sf/picard/sam/MergeSamFilesTest.java | 3 +-
.../net/sf/picard/sam/ValidateSamFileTest.java | 45 +
.../net/sf/picard/sam/testers/CleanSamTester.java | 18 +-
.../net/sf/picard/sam/testers/SamFileTester.java | 25 +-
.../net/sf/picard/util/ClippingUtilityTest.java | 386 ++++-
.../java/net/sf/picard/util/IntervalListTest.java | 387 +++++
.../net/sf/picard/util/IntervalListToolsTest.java | 21 +
.../java/net/sf/picard/vcf/SplitVcfsTest.java | 11 +-
.../net/sf/picard/vcf/VcfFormatConverterTest.java | 3 +-
.../java/net/sf/samtools/BAMFileIndexTest.java | 6 +-
.../java/net/sf/samtools/BAMFileWriterTest.java | 2 +-
.../java/net/sf/samtools/BamFileIoUtilsTest.java | 83 +
.../net/sf/samtools/SAMFileWriterFactoryTest.java | 6 +-
.../java/net/sf/samtools/SamPairUtilTest.java | 73 +-
.../tests/java/net/sf/samtools/apps/.gitignore | 0
src/tests/java/net/sf/samtools/util/IupacTest.java | 2 +-
.../tests/java/org/broad/tribble/source/.gitignore | 0
.../writer/TabixOnTheFlyIndexCreationTest.java | 10 +-
.../variantcontext/writer/VCFWriterUnitTest.java | 17 +-
.../VariantContextWriterBuilderUnitTest.java | 343 +++++
.../writer/VariantContextWritersUnitTest.java | 12 +-
.../variant/vcf/IndexFactoryUnitTest.java | 9 +-
.../variant/vcf/VCFCompoundHeaderLineUnitTest.java | 46 +
.../variant/vcf/VCFHeaderUnitTest.java | 40 +
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.../Intensities/BaseCalls/L001/C41.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C42.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C42.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C43.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C43.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C44.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C44.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C45.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C45.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C46.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C46.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C47.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C47.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C48.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C48.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C49.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C49.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C5.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C5.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C50.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C50.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C51.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C51.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C52.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C52.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C53.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C53.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C54.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C54.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C55.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C55.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C56.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C56.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C57.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C57.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C58.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C58.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C6.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C6.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C7.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C7.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C8.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C8.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C9.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C9.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/s_1_1101.filter | Bin 0 -> 72 bytes
.../Intensities/BaseCalls/L001/s_1_1201.filter | Bin 0 -> 72 bytes
.../Intensities/BaseCalls/L001/s_1_2101.filter | Bin 0 -> 72 bytes
.../Intensities/BaseCalls/s_1_1101_barcode.txt.gz | Bin 0 -> 429 bytes
.../Intensities/BaseCalls/s_1_1201_barcode.txt.gz | Bin 0 -> 391 bytes
.../Intensities/BaseCalls/s_1_2101_barcode.txt.gz | Bin 0 -> 428 bytes
.../25T8B25T/Data/Intensities/L001/s_1_1101.clocs | Bin 0 -> 455 bytes
.../25T8B25T/Data/Intensities/L001/s_1_1201.clocs | Bin 0 -> 455 bytes
.../25T8B25T/Data/Intensities/L001/s_1_2101.clocs | Bin 0 -> 455 bytes
.../fastq/AAAAAAAA.1.fastq} | 0
.../fastq/AAAAAAAA.2.fastq} | 0
.../fastq/AAAAAAAA.barcode_1.fastq} | 0
.../fastq/AAAAGAAG.1.fastq} | 0
.../fastq/AAAAGAAG.2.fastq} | 0
.../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 +
.../fastq/ACAAAATT.1.fastq} | 0
.../fastq/ACAAAATT.2.fastq} | 0
.../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 +
.../fastq/ACCAGTTG.1.fastq} | 0
.../fastq/ACCAGTTG.2.fastq} | 0
.../fastq/ACCAGTTG.barcode_1.fastq} | 0
.../fastq/ACGAAATC.1.fastq} | 0
.../fastq/ACGAAATC.2.fastq} | 0
.../fastq/ACGAAATC.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/ACTAAGAC.1.fastq | 16 +
.../illumina/25T8B25T/fastq/ACTAAGAC.2.fastq | 16 +
.../25T8B25T/fastq/ACTAAGAC.barcode_1.fastq | 16 +
.../fastq/ACTGTACC.1.fastq} | 0
.../fastq/ACTGTACC.2.fastq} | 0
.../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 +
.../fastq/AGAAAAGA.1.fastq} | 0
.../fastq/AGAAAAGA.2.fastq} | 0
.../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 +
.../fastq/CAATAGAC.1.fastq} | 0
.../fastq/CAATAGAC.2.fastq} | 0
.../fastq/CAATAGAC.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/CAATAGTC.1.fastq | 28 +
.../illumina/25T8B25T/fastq/CAATAGTC.2.fastq | 28 +
.../25T8B25T/fastq/CAATAGTC.barcode_1.fastq | 28 +
.../fastq/CAGCGGAT.1.fastq} | 0
.../fastq/CAGCGGAT.2.fastq} | 0
.../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 +
.../fastq/CCATGCGT.1.fastq} | 0
.../fastq/CCATGCGT.2.fastq} | 0
.../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 +
.../N-N-N.sam => 25T8B25T/fastq/CTATGCGC.1.fastq} | 0
.../N-N.sam => 25T8B25T/fastq/CTATGCGC.2.fastq} | 0
.../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 +
.../fastq/GAAAAAAA.1.fastq} | 0
.../s_1_1.bcl => 25T8B25T/fastq/GAAAAAAA.2.fastq} | 0
.../fastq/GAAAAAAA.barcode_1.fastq} | 0
.../fastq/GAACGAT..1.fastq} | 0
.../fastq/GAACGAT..2.fastq} | 0
.../fastq/GAACGAT..barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/GAAGGAAG.1.fastq | 12 +
.../illumina/25T8B25T/fastq/GAAGGAAG.2.fastq | 12 +
.../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 +
.../fastq/GACCAGGC.1.fastq} | 0
.../fastq/GACCAGGC.2.fastq} | 0
.../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 +
.../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 +
.../fastq/TACCGTCT.1.fastq} | 0
.../fastq/TACCGTCT.2.fastq} | 0
.../fastq/TACCGTCT.barcode_1.fastq} | 0
.../fastq/TAGCGGTA.1.fastq} | 0
.../fastq/TAGCGGTA.2.fastq} | 0
.../fastq/TAGCGGTA.barcode_1.fastq} | 0
.../fastq/TATCAGCC.1.fastq} | 0
.../fastq/TATCAGCC.2.fastq} | 0
.../fastq/TATCAGCC.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/TATCCAGG.1.fastq | 16 +
.../illumina/25T8B25T/fastq/TATCCAGG.2.fastq | 16 +
.../25T8B25T/fastq/TATCCAGG.barcode_1.fastq | 16 +
.../fastq/TATCCATG.1.fastq} | 0
.../fastq/TATCCATG.2.fastq} | 0
.../fastq/TATCCATG.barcode_1.fastq} | 0
.../fastq/TATCTCGG.1.fastq} | 0
.../fastq/TATCTCGG.2.fastq} | 0
.../fastq/TATCTCGG.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/TATCTGCC.1.fastq | 28 +
.../illumina/25T8B25T/fastq/TATCTGCC.2.fastq | 28 +
.../25T8B25T/fastq/TATCTGCC.barcode_1.fastq | 28 +
.../fastq/TCCGTCTA.1.fastq} | 0
.../fastq/TCCGTCTA.2.fastq} | 0
.../fastq/TCCGTCTA.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/TCGCTAGA.1.fastq | 20 +
.../illumina/25T8B25T/fastq/TCGCTAGA.2.fastq | 20 +
.../25T8B25T/fastq/TCGCTAGA.barcode_1.fastq | 20 +
.../illumina/25T8B25T/fastq/TCTGCAAG.1.fastq | 4 +
.../illumina/25T8B25T/fastq/TCTGCAAG.2.fastq | 4 +
.../25T8B25T/fastq/TCTGCAAG.barcode_1.fastq | 4 +
.../illumina/25T8B25T/fastq/TGCAAGTA.1.fastq | 8 +
.../illumina/25T8B25T/fastq/TGCAAGTA.2.fastq | 8 +
.../25T8B25T/fastq/TGCAAGTA.barcode_1.fastq | 8 +
.../illumina/25T8B25T/fastq/TGCTGCTG.1.fastq | 16 +
.../illumina/25T8B25T/fastq/TGCTGCTG.2.fastq | 16 +
.../25T8B25T/fastq/TGCTGCTG.barcode_1.fastq | 16 +
.../illumina/25T8B25T/fastq/TGTAACTC.1.fastq | 4 +
.../illumina/25T8B25T/fastq/TGTAACTC.2.fastq | 4 +
.../25T8B25T/fastq/TGTAACTC.barcode_1.fastq | 4 +
.../illumina/25T8B25T/fastq/TGTAATCA.1.fastq | 12 +
.../illumina/25T8B25T/fastq/TGTAATCA.2.fastq | 12 +
.../25T8B25T/fastq/TGTAATCA.barcode_1.fastq | 12 +
.../illumina/25T8B25T/fastq/TTGTCTAT.1.fastq | 16 +
.../illumina/25T8B25T/fastq/TTGTCTAT.2.fastq | 16 +
.../25T8B25T/fastq/TTGTCTAT.barcode_1.fastq | 16 +
.../picard/illumina/25T8B25T/fastq/barcode.params | 63 +
.../illumina/25T8B25T/fastq/mp_barcode.params | 63 +
.../illumina/25T8B25T/fastq/nonBarcoded.1.fastq | 720 +++++++++
.../illumina/25T8B25T/fastq/nonBarcoded.2.fastq | 720 +++++++++
.../illumina/25T8B25T/fastq/testMultiplex.1.fastq | 720 +++++++++
.../25T8B25T/fastq/testMultiplex.barcode_1.fastq | 720 +++++++++
.../25T8B25T/fastq/testMultiplexRH.1.fastq | 720 +++++++++
.../25T8B25T/fastq/testMultiplexRH.2.fastq | 720 +++++++++
.../25T8B25T/fastq/testMultiplexRH.barcode_1.fastq | 720 +++++++++
.../sf/picard/illumina/25T8B25T/sams/AAAAAAAA.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/AAAAGAAG.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/AACAATGG.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/AACGCATT.sam | 16 +
.../sf/picard/illumina/25T8B25T/sams/ACAAAATT.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/ACAGGTAT.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/ACAGTTGA.sam | 6 +
.../sf/picard/illumina/25T8B25T/sams/ACCAGTTG.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/ACGAAATC.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/ACTAAGAC.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/ACTGTACC.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/ACTGTATC.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/AGAAAAGA.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/AGCATGGA.sam | 8 +
.../sf/picard/illumina/25T8B25T/sams/AGGTAAGG.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/AGGTCGCA.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/ATTATCAA.sam | 12 +
.../sf/picard/illumina/25T8B25T/sams/ATTCCTCT.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/CAACTCTC.sam | 12 +
.../sf/picard/illumina/25T8B25T/sams/CAATAGAC.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/CAATAGTC.sam | 16 +
.../sf/picard/illumina/25T8B25T/sams/CAGCGGAT.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/CAGCGGTA.sam | 12 +
.../sf/picard/illumina/25T8B25T/sams/CCAACATT.sam | 16 +
.../sf/picard/illumina/25T8B25T/sams/CCAGCACC.sam | 8 +
.../sf/picard/illumina/25T8B25T/sams/CCATGCGT.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/CGCCTTCC.sam | 6 +
.../sf/picard/illumina/25T8B25T/sams/CGCTATGT.sam | 12 +
.../sf/picard/illumina/25T8B25T/sams/CTAACTCG.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/CTATGCGC.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/CTATGCGT.sam | 16 +
.../sf/picard/illumina/25T8B25T/sams/CTGCGGAT.sam | 8 +
.../sf/picard/illumina/25T8B25T/sams/CTGTAATC.sam | 14 +
.../sf/picard/illumina/25T8B25T/sams/GAAAAAAA.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/GAACGAT..sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/GAAGGAAG.sam | 8 +
.../sf/picard/illumina/25T8B25T/sams/GACCAGGA.sam | 16 +
.../sf/picard/illumina/25T8B25T/sams/GACCAGGC.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/GACCGTTG.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/GACCTAAC.sam | 4 +
.../sf/picard/illumina/25T8B25T/sams/GATATCCA.sam | 8 +
.../sf/picard/illumina/25T8B25T/sams/GCCGTCGA.sam | 12 +
.../sf/picard/illumina/25T8B25T/sams/GCCTAGCC.sam | 12 +
.../sf/picard/illumina/25T8B25T/sams/GTAACATC.sam | 6 +
.../sf/picard/illumina/25T8B25T/sams/GTCCACAG.sam | 6 +
.../net/sf/picard/illumina/25T8B25T/sams/N.sam | 34 +
.../sf/picard/illumina/25T8B25T/sams/TAAGCACA.sam | 6 +
.../sf/picard/illumina/25T8B25T/sams/TACCGTCT.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/TAGCGGTA.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/TATCAGCC.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/TATCCAGG.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/TATCCATG.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/TATCTCGG.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/TATCTGCC.sam | 16 +
.../sf/picard/illumina/25T8B25T/sams/TCCGTCTA.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/TCGCTAGA.sam | 12 +
.../sf/picard/illumina/25T8B25T/sams/TCTGCAAG.sam | 4 +
.../sf/picard/illumina/25T8B25T/sams/TGCAAGTA.sam | 6 +
.../sf/picard/illumina/25T8B25T/sams/TGCTGCTG.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/TGTAACTC.sam | 4 +
.../sf/picard/illumina/25T8B25T/sams/TGTAATCA.sam | 8 +
.../sf/picard/illumina/25T8B25T/sams/TTGTCTAT.sam | 10 +
.../picard/illumina/25T8B25T/sams/barcode.params | 63 +
.../sams/multiplexed_positive_rgtags.params | 63 +
.../picard/illumina/25T8B25T/sams/nonBarcoded.sam | 182 +++
.../Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C59.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C60.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C61.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C62.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C63.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C64.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C65.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C66.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/s_1_1101.filter | Bin 0 -> 72 bytes
.../Intensities/BaseCalls/s_1_1101_barcode.txt | 60 +
.../25T8B8B25T/Data/Intensities/L001/s_1_1101.locs | Bin 0 -> 492 bytes
.../25T8B8B25T/fastq/AACTTGACGCTCTCTT.1.fastq | 4 +
.../25T8B8B25T/fastq/AACTTGACGCTCTCTT.2.fastq | 4 +
.../fastq/AACTTGACGCTCTCTT.barcode_1.fastq | 4 +
.../fastq/AACTTGACGCTCTCTT.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/AAGACACTAGTCACCT.1.fastq | 4 +
.../25T8B8B25T/fastq/AAGACACTAGTCACCT.2.fastq | 4 +
.../fastq/AAGACACTAGTCACCT.barcode_1.fastq | 4 +
.../fastq/AAGACACTAGTCACCT.barcode_2.fastq | 4 +
.../fastq/AAGACACTAGTCTCCT.1.fastq} | 0
.../fastq/AAGACACTAGTCTCCT.2.fastq} | 0
.../fastq/AAGACACTAGTCTCCT.barcode_1.fastq} | 0
.../fastq/AAGACACTAGTCTCCT.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/ACAGGTATCACTTCAT.1.fastq | 4 +
.../25T8B8B25T/fastq/ACAGGTATCACTTCAT.2.fastq | 4 +
.../fastq/ACAGGTATCACTTCAT.barcode_1.fastq | 4 +
.../fastq/ACAGGTATCACTTCAT.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/ACAGTTGAATCTTCTC.1.fastq | 8 +
.../25T8B8B25T/fastq/ACAGTTGAATCTTCTC.2.fastq | 8 +
.../fastq/ACAGTTGAATCTTCTC.barcode_1.fastq | 8 +
.../fastq/ACAGTTGAATCTTCTC.barcode_2.fastq | 8 +
.../25T8B8B25T/fastq/ACCAACTGCATCACTT.1.fastq | 4 +
.../25T8B8B25T/fastq/ACCAACTGCATCACTT.2.fastq | 4 +
.../fastq/ACCAACTGCATCACTT.barcode_1.fastq | 4 +
.../fastq/ACCAACTGCATCACTT.barcode_2.fastq | 4 +
.../fastq/ACCTACTGCTTCCCTT.1.fastq} | 0
.../fastq/ACCTACTGCTTCCCTT.2.fastq} | 0
.../fastq/ACCTACTGCTTCCCTT.barcode_1.fastq} | 0
.../fastq/ACCTACTGCTTCCCTT.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/ACTAAGACGTCCTCAT.1.fastq | 4 +
.../25T8B8B25T/fastq/ACTAAGACGTCCTCAT.2.fastq | 4 +
.../fastq/ACTAAGACGTCCTCAT.barcode_1.fastq | 4 +
.../fastq/ACTAAGACGTCCTCAT.barcode_2.fastq | 4 +
.../fastq/AGGTCGCATTCCTTTC.1.fastq} | 0
.../fastq/AGGTCGCATTCCTTTC.2.fastq} | 0
.../fastq/AGGTCGCATTCCTTTC.barcode_1.fastq} | 0
.../fastq/AGGTCGCATTCCTTTC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/AGGTGCGAGACATTAA.1.fastq | 4 +
.../25T8B8B25T/fastq/AGGTGCGAGACATTAA.2.fastq | 4 +
.../fastq/AGGTGCGAGACATTAA.barcode_1.fastq | 4 +
.../fastq/AGGTGCGAGACATTAA.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/AGGTTATCTTAGCCAG.1.fastq | 4 +
.../25T8B8B25T/fastq/AGGTTATCTTAGCCAG.2.fastq | 4 +
.../fastq/AGGTTATCTTAGCCAG.barcode_1.fastq | 4 +
.../fastq/AGGTTATCTTAGCCAG.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/AGTTGCTTTGACTTGG.1.fastq | 4 +
.../25T8B8B25T/fastq/AGTTGCTTTGACTTGG.2.fastq | 4 +
.../fastq/AGTTGCTTTGACTTGG.barcode_1.fastq | 4 +
.../fastq/AGTTGCTTTGACTTGG.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.1.fastq | 4 +
.../25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.2.fastq | 4 +
.../fastq/ATAGCGTCTTGGTCTG.barcode_1.fastq | 4 +
.../fastq/ATAGCGTCTTGGTCTG.barcode_2.fastq | 4 +
.../fastq/ATTATCAACACCATAC.1.fastq} | 0
.../fastq/ATTATCAACACCATAC.2.fastq} | 0
.../fastq/ATTATCAACACCATAC.barcode_1.fastq} | 0
.../fastq/ATTATCAACACCATAC.barcode_2.fastq} | 0
.../fastq/ATTGTCTGGATTCACA.1.fastq} | 0
.../fastq/ATTGTCTGGATTCACA.2.fastq} | 0
.../fastq/ATTGTCTGGATTCACA.barcode_1.fastq} | 0
.../fastq/ATTGTCTGGATTCACA.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/CAATAGTCCGACTCTC.1.fastq | 4 +
.../25T8B8B25T/fastq/CAATAGTCCGACTCTC.2.fastq | 4 +
.../fastq/CAATAGTCCGACTCTC.barcode_1.fastq | 4 +
.../fastq/CAATAGTCCGACTCTC.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/CAGCAAGGGCGATATT.1.fastq | 4 +
.../25T8B8B25T/fastq/CAGCAAGGGCGATATT.2.fastq | 4 +
.../fastq/CAGCAAGGGCGATATT.barcode_1.fastq | 4 +
.../fastq/CAGCAAGGGCGATATT.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/CAGCGGTAAGTACTGC.1.fastq | 4 +
.../25T8B8B25T/fastq/CAGCGGTAAGTACTGC.2.fastq | 4 +
.../fastq/CAGCGGTAAGTACTGC.barcode_1.fastq | 4 +
.../fastq/CAGCGGTAAGTACTGC.barcode_2.fastq | 4 +
.../fastq/CAGCGGTATGTACTGC.1.fastq} | 0
.../fastq/CAGCGGTATGTACTGC.2.fastq} | 0
.../fastq/CAGCGGTATGTACTGC.barcode_1.fastq} | 0
.../fastq/CAGCGGTATGTACTGC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/CATGCTTATAGCATTG.1.fastq | 8 +
.../25T8B8B25T/fastq/CATGCTTATAGCATTG.2.fastq | 8 +
.../fastq/CATGCTTATAGCATTG.barcode_1.fastq | 8 +
.../fastq/CATGCTTATAGCATTG.barcode_2.fastq | 8 +
.../fastq/CATGCTTATAGCATTT.1.fastq} | 0
.../fastq/CATGCTTATAGCATTT.2.fastq} | 0
.../fastq/CATGCTTATAGCATTT.barcode_1.fastq} | 0
.../fastq/CATGCTTATAGCATTT.barcode_2.fastq} | 0
.../fastq/CATGCTTTTAGCATTG.1.fastq} | 0
.../fastq/CATGCTTTTAGCATTG.2.fastq} | 0
.../fastq/CATGCTTTTAGCATTG.barcode_1.fastq} | 0
.../fastq/CATGCTTTTAGCATTG.barcode_2.fastq} | 0
.../fastq/CATGTTCGCGCCTTTT.1.fastq} | 0
.../fastq/CATGTTCGCGCCTTTT.2.fastq} | 0
.../fastq/CATGTTCGCGCCTTTT.barcode_1.fastq} | 0
.../fastq/CATGTTCGCGCCTTTT.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/CCAGAGCTCAACTGAT.1.fastq | 8 +
.../25T8B8B25T/fastq/CCAGAGCTCAACTGAT.2.fastq | 8 +
.../fastq/CCAGAGCTCAACTGAT.barcode_1.fastq | 8 +
.../fastq/CCAGAGCTCAACTGAT.barcode_2.fastq | 8 +
.../fastq/CCCGATTTTCTCTCCC.1.fastq} | 0
.../fastq/CCCGATTTTCTCTCCC.2.fastq} | 0
.../fastq/CCCGATTTTCTCTCCC.barcode_1.fastq} | 0
.../fastq/CCCGATTTTCTCTCCC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/CCTATGCCAATTGGCC.1.fastq | 4 +
.../25T8B8B25T/fastq/CCTATGCCAATTGGCC.2.fastq | 4 +
.../fastq/CCTATGCCAATTGGCC.barcode_1.fastq | 4 +
.../fastq/CCTATGCCAATTGGCC.barcode_2.fastq | 4 +
.../fastq/CCTATTCTTCGTTTTC.1.fastq} | 0
.../fastq/CCTATTCTTCGTTTTC.2.fastq} | 0
.../fastq/CCTATTCTTCGTTTTC.barcode_1.fastq} | 0
.../fastq/CCTATTCTTCGTTTTC.barcode_2.fastq} | 0
.../fastq/CCTCTTCTCTCGCTTT.1.fastq} | 0
.../fastq/CCTCTTCTCTCGCTTT.2.fastq} | 0
.../fastq/CCTCTTCTCTCGCTTT.barcode_1.fastq} | 0
.../fastq/CCTCTTCTCTCGCTTT.barcode_2.fastq} | 0
.../fastq/CCTCTTTCTTCTGCTC.1.fastq} | 0
.../fastq/CCTCTTTCTTCTGCTC.2.fastq} | 0
.../fastq/CCTCTTTCTTCTGCTC.barcode_1.fastq} | 0
.../fastq/CCTCTTTCTTCTGCTC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/CCTTCGCAGAATCGAC.1.fastq | 4 +
.../25T8B8B25T/fastq/CCTTCGCAGAATCGAC.2.fastq | 4 +
.../fastq/CCTTCGCAGAATCGAC.barcode_1.fastq | 4 +
.../fastq/CCTTCGCAGAATCGAC.barcode_2.fastq | 4 +
.../fastq/CCTTCTTTTATCATTT.1.fastq} | 0
.../fastq/CCTTCTTTTATCATTT.2.fastq} | 0
.../fastq/CCTTCTTTTATCATTT.barcode_1.fastq} | 0
.../fastq/CCTTCTTTTATCATTT.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/CGCTATGTTTCACCTT.1.fastq | 4 +
.../25T8B8B25T/fastq/CGCTATGTTTCACCTT.2.fastq | 4 +
.../fastq/CGCTATGTTTCACCTT.barcode_1.fastq | 4 +
.../fastq/CGCTATGTTTCACCTT.barcode_2.fastq | 4 +
.../fastq/CGCTATGTTTCTCCTT.1.fastq} | 0
.../fastq/CGCTATGTTTCTCCTT.2.fastq} | 0
.../fastq/CGCTATGTTTCTCCTT.barcode_1.fastq} | 0
.../fastq/CGCTATGTTTCTCCTT.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/CTACCAGGTTCTTGGC.1.fastq | 4 +
.../25T8B8B25T/fastq/CTACCAGGTTCTTGGC.2.fastq | 4 +
.../fastq/CTACCAGGTTCTTGGC.barcode_1.fastq | 4 +
.../fastq/CTACCAGGTTCTTGGC.barcode_2.fastq | 4 +
.../fastq/CTCCCTCTTCCTTCTT.1.fastq} | 0
.../fastq/CTCCCTCTTCCTTCTT.2.fastq} | 0
.../fastq/CTCCCTCTTCCTTCTT.barcode_1.fastq} | 0
.../fastq/CTCCCTCTTCCTTCTT.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/CTGTAATCCTATTAGC.1.fastq | 4 +
.../25T8B8B25T/fastq/CTGTAATCCTATTAGC.2.fastq | 4 +
.../fastq/CTGTAATCCTATTAGC.barcode_1.fastq | 4 +
.../fastq/CTGTAATCCTATTAGC.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/GACCAGGACCATCACA.1.fastq | 4 +
.../25T8B8B25T/fastq/GACCAGGACCATCACA.2.fastq | 4 +
.../fastq/GACCAGGACCATCACA.barcode_1.fastq | 4 +
.../fastq/GACCAGGACCATCACA.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/GCCGTCGAAGGTACCA.1.fastq | 8 +
.../25T8B8B25T/fastq/GCCGTCGAAGGTACCA.2.fastq | 8 +
.../fastq/GCCGTCGAAGGTACCA.barcode_1.fastq | 8 +
.../fastq/GCCGTCGAAGGTACCA.barcode_2.fastq | 8 +
.../fastq/GCCGTCGAAGGTACCC.1.fastq} | 0
.../fastq/GCCGTCGAAGGTACCC.2.fastq} | 0
.../fastq/GCCGTCGAAGGTACCC.barcode_1.fastq} | 0
.../fastq/GCCGTCGAAGGTACCC.barcode_2.fastq} | 0
.../fastq/GCCGTCGATGGTACCC.1.fastq} | 0
.../fastq/GCCGTCGATGGTACCC.2.fastq} | 0
.../fastq/GCCGTCGATGGTACCC.barcode_1.fastq} | 0
.../fastq/GCCGTCGATGGTACCC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/GCCTAGCCCTTGAATC.1.fastq | 4 +
.../25T8B8B25T/fastq/GCCTAGCCCTTGAATC.2.fastq | 4 +
.../fastq/GCCTAGCCCTTGAATC.barcode_1.fastq | 4 +
.../fastq/GCCTAGCCCTTGAATC.barcode_2.fastq | 4 +
.../fastq/GCTATCCACCTCCCCC.1.fastq} | 0
.../fastq/GCTATCCACCTCCCCC.2.fastq} | 0
.../fastq/GCTATCCACCTCCCCC.barcode_1.fastq} | 0
.../fastq/GCTATCCACCTCCCCC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/GTATAACAAATTCAAC.1.fastq | 4 +
.../25T8B8B25T/fastq/GTATAACAAATTCAAC.2.fastq | 4 +
.../fastq/GTATAACAAATTCAAC.barcode_1.fastq | 4 +
.../fastq/GTATAACAAATTCAAC.barcode_2.fastq | 4 +
.../fastq/GTATAACATATTCAAC.1.fastq} | 0
.../fastq/GTATAACATATTCAAC.2.fastq} | 0
.../fastq/GTATAACATATTCAAC.barcode_1.fastq} | 0
.../fastq/GTATAACATATTCAAC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/GTCTGATGGAACTTCG.1.fastq | 4 +
.../25T8B8B25T/fastq/GTCTGATGGAACTTCG.2.fastq | 4 +
.../fastq/GTCTGATGGAACTTCG.barcode_1.fastq | 4 +
.../fastq/GTCTGATGGAACTTCG.barcode_2.fastq | 4 +
.../fastq/GTCTGATGTCACTTCC.1.fastq} | 0
.../fastq/GTCTGATGTCACTTCC.2.fastq} | 0
.../fastq/GTCTGATGTCACTTCC.barcode_1.fastq} | 0
.../fastq/GTCTGATGTCACTTCC.barcode_2.fastq} | 0
.../sf/picard/illumina/25T8B8B25T/fastq/NN.1.fastq | 76 +
.../sf/picard/illumina/25T8B8B25T/fastq/NN.2.fastq | 76 +
.../illumina/25T8B8B25T/fastq/NN.barcode_1.fastq | 76 +
.../illumina/25T8B8B25T/fastq/NN.barcode_2.fastq | 76 +
.../25T8B8B25T/fastq/TACTTAGCGTCTGCAC.1.fastq | 8 +
.../25T8B8B25T/fastq/TACTTAGCGTCTGCAC.2.fastq | 8 +
.../fastq/TACTTAGCGTCTGCAC.barcode_1.fastq | 8 +
.../fastq/TACTTAGCGTCTGCAC.barcode_2.fastq | 8 +
.../fastq/TCCCCGTTCCAACTTC.1.fastq} | 0
.../fastq/TCCCCGTTCCAACTTC.2.fastq} | 0
.../fastq/TCCCCGTTCCAACTTC.barcode_1.fastq} | 0
.../fastq/TCCCCGTTCCAACTTC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/TCCTTGGTGCTGCACT.1.fastq | 4 +
.../25T8B8B25T/fastq/TCCTTGGTGCTGCACT.2.fastq | 4 +
.../fastq/TCCTTGGTGCTGCACT.barcode_1.fastq | 4 +
.../fastq/TCCTTGGTGCTGCACT.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/TCGCCTTGCCAACGCT.1.fastq | 4 +
.../25T8B8B25T/fastq/TCGCCTTGCCAACGCT.2.fastq | 4 +
.../fastq/TCGCCTTGCCAACGCT.barcode_1.fastq | 4 +
.../fastq/TCGCCTTGCCAACGCT.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/TGCAAGTACGAACTTC.1.fastq | 8 +
.../25T8B8B25T/fastq/TGCAAGTACGAACTTC.2.fastq | 8 +
.../fastq/TGCAAGTACGAACTTC.barcode_1.fastq | 8 +
.../fastq/TGCAAGTACGAACTTC.barcode_2.fastq | 8 +
.../25T8B8B25T/fastq/TGCTCGACTTCACAGA.1.fastq | 4 +
.../25T8B8B25T/fastq/TGCTCGACTTCACAGA.2.fastq | 4 +
.../fastq/TGCTCGACTTCACAGA.barcode_1.fastq | 4 +
.../fastq/TGCTCGACTTCACAGA.barcode_2.fastq | 4 +
.../fastq/TGCTCGACTTCACAGT.1.fastq} | 0
.../fastq/TGCTCGACTTCACAGT.2.fastq} | 0
.../fastq/TGCTCGACTTCACAGT.barcode_1.fastq} | 0
.../fastq/TGCTCGACTTCACAGT.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/TGTAATCACCTCTAAC.1.fastq | 4 +
.../25T8B8B25T/fastq/TGTAATCACCTCTAAC.2.fastq | 4 +
.../fastq/TGTAATCACCTCTAAC.barcode_1.fastq | 4 +
.../fastq/TGTAATCACCTCTAAC.barcode_2.fastq | 4 +
.../fastq/TGTATCTCTTACTCTT.1.fastq} | 0
.../fastq/TGTATCTCTTACTCTT.2.fastq} | 0
.../fastq/TGTATCTCTTACTCTT.barcode_1.fastq} | 0
.../fastq/TGTATCTCTTACTCTT.barcode_2.fastq} | 0
.../fastq/TGTCGGTTTTTTGCTT.1.fastq} | 0
.../fastq/TGTCGGTTTTTTGCTT.2.fastq} | 0
.../fastq/TGTCGGTTTTTTGCTT.barcode_1.fastq} | 0
.../fastq/TGTCGGTTTTTTGCTT.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/TGTTCCGAAACCTCTT.1.fastq | 4 +
.../25T8B8B25T/fastq/TGTTCCGAAACCTCTT.2.fastq | 4 +
.../fastq/TGTTCCGAAACCTCTT.barcode_1.fastq | 4 +
.../fastq/TGTTCCGAAACCTCTT.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/TTAATCAGCTGGTATT.1.fastq | 4 +
.../25T8B8B25T/fastq/TTAATCAGCTGGTATT.2.fastq | 4 +
.../fastq/TTAATCAGCTGGTATT.barcode_1.fastq | 4 +
.../fastq/TTAATCAGCTGGTATT.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/TTATATCTTCATGTCT.1.fastq | 4 +
.../25T8B8B25T/fastq/TTATATCTTCATGTCT.2.fastq | 4 +
.../fastq/TTATATCTTCATGTCT.barcode_1.fastq | 4 +
.../fastq/TTATATCTTCATGTCT.barcode_2.fastq | 4 +
.../fastq/TTCCCCAGTGCTTTTA.1.fastq} | 0
.../fastq/TTCCCCAGTGCTTTTA.2.fastq} | 0
.../fastq/TTCCCCAGTGCTTTTA.barcode_1.fastq} | 0
.../fastq/TTCCCCAGTGCTTTTA.barcode_2.fastq} | 0
.../fastq/TTCCTCCTCACCATCC.1.fastq} | 0
.../fastq/TTCCTCCTCACCATCC.2.fastq} | 0
.../fastq/TTCCTCCTCACCATCC.barcode_1.fastq} | 0
.../fastq/TTCCTCCTCACCATCC.barcode_2.fastq} | 0
.../fastq/TTCTCATCTTCCTTCC.1.fastq} | 0
.../fastq/TTCTCATCTTCCTTCC.2.fastq} | 0
.../fastq/TTCTCATCTTCCTTCC.barcode_1.fastq} | 0
.../fastq/TTCTCATCTTCCTTCC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/TTGAATAGATATCCGA.1.fastq | 4 +
.../25T8B8B25T/fastq/TTGAATAGATATCCGA.2.fastq | 4 +
.../fastq/TTGAATAGATATCCGA.barcode_1.fastq | 4 +
.../fastq/TTGAATAGATATCCGA.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/barcode_double.params | 65 +
.../sf/picard/illumina/25T8B8B25T/library.params | 65 +
.../picard/illumina/25T8B8B25T/sams/AACTTGAC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/AAGACACT.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/ACAGGTAT.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/ACAGTTGA.sam | 6 +
.../picard/illumina/25T8B8B25T/sams/ACCAACTG.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/ACCTACTG.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/ACTAAGAC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/AGGTCGCA.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/AGGTGCGA.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/AGGTTATC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/AGTTGCTT.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/ATAGCGTC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/ATTATCAA.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/ATTGTCTG.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CAATAGTC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/CAGCAAGG.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/CAGCGGTA.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/CATGCTTA.sam | 6 +
.../picard/illumina/25T8B8B25T/sams/CATGCTTT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CATGTTCG.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CCAGAGCT.sam | 6 +
.../picard/illumina/25T8B8B25T/sams/CCCGATTT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CCTATGCC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/CCTATTCT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CCTCTTCT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CCTCTTTC.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CCTTCGCA.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/CCTTCTTT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CGCTATGT.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/CTACCAGG.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/CTCCCTCT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CTGTAATC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/GACCAGGA.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/GCCGTCGA.sam | 6 +
.../picard/illumina/25T8B8B25T/sams/GCCTAGCC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/GCTATCCA.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/GTATAACA.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/GTCTGATG.sam | 4 +
.../net/sf/picard/illumina/25T8B8B25T/sams/N.sam | 40 +
.../picard/illumina/25T8B8B25T/sams/TACTTAGC.sam | 6 +
.../picard/illumina/25T8B8B25T/sams/TCCCCGTT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/TCCTTGGT.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/TCGCCTTG.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/TGCAAGTA.sam | 6 +
.../picard/illumina/25T8B8B25T/sams/TGCTCGAC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/TGTAATCA.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/TGTATCTC.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/TGTCGGTT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/TGTTCCGA.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/TTAATCAG.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/TTATATCT.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/TTCCCCAG.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/TTCCTCCT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/TTCTCATC.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/TTGAATAG.sam | 4 +
.../illumina/25T8B8B25T/sams/barcode_double.params | 65 +
.../Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C1.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C1.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C10.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C10.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C11.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C11.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C12.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C12.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C13.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C13.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C14.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C14.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C15.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C15.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C16.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C16.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C17.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C17.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C18.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C18.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C19.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C19.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C2.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C2.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C20.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C20.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C21.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C21.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C22.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C22.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C23.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C23.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C24.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C24.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C25.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C25.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C26.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C26.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C27.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C27.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C28.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C28.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C29.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C29.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C3.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C3.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C30.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C30.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C31.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C31.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C32.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C32.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C33.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C33.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C34.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C34.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C35.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C35.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C36.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C36.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C37.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C37.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C38.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C38.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C39.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C39.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C4.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C4.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C40.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C40.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C41.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C41.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl | Bin 24 -> 0 bytes
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.../ExtractIlluminaBarcodes/s_2_1_0002_qseq.txt | 23 -
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.../IlluminaBasecallsToFastqTest/AACTTGAC.1.fastq | 52 -
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.../IlluminaBasecallsToFastqTest/AAGGATGT.1.fastq | 52 -
.../AAGGATGT.barcode_1.fastq | 52 -
.../AAGGATGTTTCGCTGA.1.fastq | 52 -
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.../AAGGATGTTTCGCTGA.barcode_2.fastq | 52 -
.../IlluminaBasecallsToFastqTest/ACCAACTG.1.fastq | 36 -
.../ACCAACTG.barcode_1.fastq | 36 -
.../ACCAACTGTGTCGGAT.1.fastq | 36 -
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.../IlluminaBasecallsToFastqTest/AGCAATTC.1.fastq | 32 -
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.../AGCAATTCTGCTCGAC.barcode_2.fastq | 32 -
.../IlluminaBasecallsToFastqTest/AGTTGCTT.1.fastq | 32 -
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.../AGTTGCTTTCTGGCGA.barcode_1.fastq | 32 -
.../AGTTGCTTTCTGGCGA.barcode_2.fastq | 32 -
.../IlluminaBasecallsToFastqTest/ATTATGTT.1.fastq | 12 -
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.../IlluminaBasecallsToFastqTest/CACATCCT.1.fastq | 36 -
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.../IlluminaBasecallsToFastqTest/CAGGAGCC.1.fastq | 36 -
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.../IlluminaBasecallsToFastqTest/CATAGCGA.1.fastq | 48 -
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.../CATAGCGAGGTCCAGA.barcode_2.fastq | 48 -
.../IlluminaBasecallsToFastqTest/CATGCTTA.1.fastq | 20 -
.../CATGCTTA.barcode_1.fastq | 20 -
.../CATGCTTAGCACATCT.1.fastq | 20 -
.../CATGCTTAGCACATCT.barcode_1.fastq | 20 -
.../CATGCTTAGCACATCT.barcode_2.fastq | 20 -
.../IlluminaBasecallsToFastqTest/CCAGTTAG.1.fastq | 44 -
.../CCAGTTAG.barcode_1.fastq | 44 -
.../CCAGTTAGGCACACGA.1.fastq | 44 -
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.../IlluminaBasecallsToFastqTest/CTACCAGG.1.fastq | 24 -
.../CTACCAGG.barcode_1.fastq | 24 -
.../CTACCAGGCCTACCAT.1.fastq | 24 -
.../CTACCAGGCCTACCAT.barcode_1.fastq | 24 -
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.../IlluminaBasecallsToFastqTest/GCACACGA.1.fastq | 36 -
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.../GCACACGACCAGTTAG.barcode_2.fastq | 36 -
.../IlluminaBasecallsToFastqTest/GCACATCT.1.fastq | 12 -
.../GCACATCT.barcode_1.fastq | 12 -
.../GCACATCTCATGCTTA.1.fastq | 12 -
.../GCACATCTCATGCTTA.barcode_1.fastq | 12 -
.../GCACATCTCATGCTTA.barcode_2.fastq | 12 -
.../IlluminaBasecallsToFastqTest/GGTCCAGA.1.fastq | 28 -
.../GGTCCAGA.barcode_1.fastq | 28 -
.../GGTCCAGACATAGCGA.1.fastq | 28 -
.../GGTCCAGACATAGCGA.barcode_1.fastq | 28 -
.../GGTCCAGACATAGCGA.barcode_2.fastq | 28 -
.../IlluminaBasecallsToFastqTest/GTATAACA.1.fastq | 40 -
.../GTATAACA.barcode_1.fastq | 40 -
.../GTATAACACAGGAGCC.1.fastq | 40 -
.../GTATAACACAGGAGCC.barcode_1.fastq | 40 -
.../GTATAACACAGGAGCC.barcode_2.fastq | 40 -
.../IlluminaBasecallsToFastqTest/N.1.fastq | 892 -----------
.../IlluminaBasecallsToFastqTest/N.barcode_1.fastq | 892 -----------
.../IlluminaBasecallsToFastqTest/NN.1.fastq | 892 -----------
.../NN.barcode_1.fastq | 892 -----------
.../NN.barcode_2.fastq | 892 -----------
.../IlluminaBasecallsToFastqTest/TACTTAGC.1.fastq | 32 -
.../TACTTAGC.barcode_1.fastq | 32 -
.../TACTTAGCCACATCCT.1.fastq | 32 -
.../TACTTAGCCACATCCT.barcode_1.fastq | 32 -
.../TACTTAGCCACATCCT.barcode_2.fastq | 32 -
.../IlluminaBasecallsToFastqTest/TCGGAATG.1.fastq | 28 -
.../TCGGAATG.barcode_1.fastq | 28 -
.../TCGGAATGATTATGTT.1.fastq | 28 -
.../TCGGAATGATTATGTT.barcode_1.fastq | 28 -
.../TCGGAATGATTATGTT.barcode_2.fastq | 28 -
.../IlluminaBasecallsToFastqTest/TCTGGCGA.1.fastq | 20 -
.../TCTGGCGA.barcode_1.fastq | 20 -
.../TCTGGCGAAGTTGCTT.1.fastq | 20 -
.../TCTGGCGAAGTTGCTT.barcode_1.fastq | 20 -
.../TCTGGCGAAGTTGCTT.barcode_2.fastq | 20 -
.../IlluminaBasecallsToFastqTest/TGCTCGAC.1.fastq | 20 -
.../TGCTCGAC.barcode_1.fastq | 20 -
.../TGCTCGACAGCAATTC.1.fastq | 20 -
.../TGCTCGACAGCAATTC.barcode_1.fastq | 20 -
.../TGCTCGACAGCAATTC.barcode_2.fastq | 20 -
.../IlluminaBasecallsToFastqTest/TGTCGGAT.1.fastq | 16 -
.../TGTCGGAT.barcode_1.fastq | 16 -
.../TGTCGGATACCAACTG.1.fastq | 16 -
.../TGTCGGATACCAACTG.barcode_1.fastq | 16 -
.../TGTCGGATACCAACTG.barcode_2.fastq | 16 -
.../IlluminaBasecallsToFastqTest/TTCGCTGA.1.fastq | 20 -
.../TTCGCTGA.barcode_1.fastq | 20 -
.../TTCGCTGAAAGGATGT.1.fastq | 20 -
.../TTCGCTGAAAGGATGT.barcode_1.fastq | 20 -
.../TTCGCTGAAAGGATGT.barcode_2.fastq | 20 -
.../IlluminaBasecallsToFastqTest/TTGAGCCT.1.fastq | 24 -
.../TTGAGCCT.barcode_1.fastq | 24 -
.../TTGAGCCTAACTTGAC.1.fastq | 24 -
.../TTGAGCCTAACTTGAC.barcode_1.fastq | 24 -
.../TTGAGCCTAACTTGAC.barcode_2.fastq | 24 -
.../IlluminaBasecallsToFastqTest/barcode.params | 26 -
.../barcode_double.params | 26 -
.../nonBarcoded.1.fastq | 240 ---
.../nonBarcoded.2.fastq | 240 ---
.../testMultiplex.1.fastq | 1600 --------------------
.../testMultiplex.barcode_1.fastq | 1600 --------------------
.../IlluminaBasecallsToSamTest/AACTTGAC.sam | 15 -
.../AACTTGACTTGAGCCT.sam | 15 -
.../IlluminaBasecallsToSamTest/AAGGATGT.sam | 15 -
.../AAGGATGTTTCGCTGA.sam | 15 -
.../IlluminaBasecallsToSamTest/ACCAACTG.sam | 11 -
.../ACCAACTGTGTCGGAT.sam | 11 -
.../IlluminaBasecallsToSamTest/AGCAATTC.sam | 10 -
.../AGCAATTCTGCTCGAC.sam | 10 -
.../IlluminaBasecallsToSamTest/AGTTGCTT.sam | 10 -
.../AGTTGCTTTCTGGCGA.sam | 10 -
.../IlluminaBasecallsToSamTest/ATTATGTT.sam | 5 -
.../ATTATGTTTCGGAATG.sam | 5 -
.../IlluminaBasecallsToSamTest/CACATCCT.sam | 11 -
.../CACATCCTTACTTAGC.sam | 11 -
.../IlluminaBasecallsToSamTest/CAGGAGCC.sam | 11 -
.../CAGGAGCCGTATAACA.sam | 11 -
.../IlluminaBasecallsToSamTest/CATAGCGA.sam | 14 -
.../CATAGCGAGGTCCAGA.sam | 14 -
.../IlluminaBasecallsToSamTest/CATGCTTA.sam | 7 -
.../CATGCTTAGCACATCT.sam | 7 -
.../IlluminaBasecallsToSamTest/CCAGTTAG.sam | 13 -
.../CCAGTTAGGCACACGA.sam | 13 -
.../IlluminaBasecallsToSamTest/CCTACCAT.sam | 4 -
.../CCTACCATCTACCAGG.sam | 4 -
.../IlluminaBasecallsToSamTest/CTACCAGG.sam | 8 -
.../CTACCAGGCCTACCAT.sam | 8 -
.../IlluminaBasecallsToSamTest/GCACACGA.sam | 11 -
.../GCACACGACCAGTTAG.sam | 11 -
.../IlluminaBasecallsToSamTest/GCACATCT.sam | 5 -
.../GCACATCTCATGCTTA.sam | 5 -
.../IlluminaBasecallsToSamTest/GGTCCAGA.sam | 9 -
.../GGTCCAGACATAGCGA.sam | 9 -
.../IlluminaBasecallsToSamTest/GTATAACA.sam | 12 -
.../GTATAACACAGGAGCC.sam | 12 -
.../illumina/IlluminaBasecallsToSamTest/N.sam | 225 ---
.../illumina/IlluminaBasecallsToSamTest/NN.sam | 225 ---
.../IlluminaBasecallsToSamTest/TACTTAGC.sam | 10 -
.../TACTTAGCCACATCCT.sam | 10 -
.../IlluminaBasecallsToSamTest/TCGGAATG.sam | 9 -
.../TCGGAATGATTATGTT.sam | 9 -
.../IlluminaBasecallsToSamTest/TCTGGCGA.sam | 7 -
.../TCTGGCGAAGTTGCTT.sam | 7 -
.../IlluminaBasecallsToSamTest/TGCTCGAC.sam | 7 -
.../TGCTCGACAGCAATTC.sam | 7 -
.../IlluminaBasecallsToSamTest/TGTCGGAT.sam | 6 -
.../TGTCGGATACCAACTG.sam | 6 -
.../IlluminaBasecallsToSamTest/TTCGCTGA.sam | 7 -
.../TTCGCTGAAAGGATGT.sam | 7 -
.../IlluminaBasecallsToSamTest/TTGAGCCT.sam | 8 -
.../TTGAGCCTAACTTGAC.sam | 8 -
.../IlluminaBasecallsToSamTest/barcode.params | 26 -
.../barcode_double.params | 26 -
.../barcode_single.params | 26 -
.../barcode_triple.params | 26 -
.../multiplexed_positive_rgtags.params | 26 -
.../negative_test.params | 25 -
.../IlluminaBasecallsToSamTest/nonBarcoded.sam | 122 --
.../nonMatchingBarcoded.sam | 225 ---
.../IlluminaBasecallsToSamTest/singleBarcoded.sam | 8 -
.../IlluminaTests/BasecallsDir/s_1_1_0001_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_1_1_0002_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_1_1_0003_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_1_2_0001_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_1_2_0002_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_1_2_0003_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_2_1_0001_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_4_1_0001_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_4_1_0002_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_4_1_0003_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_4_2_0001_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_4_2_0002_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_4_2_0003_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_5_1_0001_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_6_1_0001_qseq.txt | 10 -
.../IlluminaTests/BasecallsDir/s_6_2_0001_qseq.txt | 10 -
.../IlluminaTests/BasecallsDir/s_6_3_0001_qseq.txt | 10 -
.../BasecallsDir/s_7_0001_barcode.txt | 200 ---
.../BasecallsDir/s_7_0002_barcode.txt | 200 ---
.../IlluminaTests/BasecallsDir/s_7_1_0001_qseq.txt | 200 ---
.../IlluminaTests/BasecallsDir/s_7_1_0002_qseq.txt | 200 ---
.../IlluminaTests/BasecallsDir/s_7_2_0001_qseq.txt | 200 ---
.../IlluminaTests/BasecallsDir/s_7_2_0002_qseq.txt | 200 ---
.../IlluminaTests/BasecallsDir/s_8_1_0001_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_8_2_0001_qseq.txt | 20 -
.../BasecallsDir/s_9_0001_barcode.txt | 200 ---
.../BasecallsDir/s_9_0002_barcode.txt | 200 ---
.../IlluminaTests/BasecallsDir/s_9_1_0001_qseq.txt | 200 ---
.../IlluminaTests/BasecallsDir/s_9_1_0002_qseq.txt | 200 ---
.../IlluminaTests/BasecallsDir/s_9_2_0001_qseq.txt | 200 ---
.../IlluminaTests/BasecallsDir/s_9_2_0002_qseq.txt | 200 ---
.../IlluminaTests/BasecallsDir/s_9_3_0001_qseq.txt | 200 ---
.../IlluminaTests/BasecallsDir/s_9_3_0002_qseq.txt | 200 ---
.../illumina/IlluminaTests/L001/C1.1/s_1_1.cif | Bin 1224093 -> 0 bytes
.../illumina/IlluminaTests/L001/C1.1/s_1_1.cnf | Bin 612053 -> 0 bytes
.../illumina/IlluminaTests/L001/C1.1/s_1_2.cif | Bin 1199213 -> 0 bytes
.../illumina/IlluminaTests/L001/C1.1/s_1_2.cnf | Bin 599613 -> 0 bytes
.../illumina/IlluminaTests/L001/C2.1/s_1_1.cif | Bin 1224093 -> 0 bytes
.../illumina/IlluminaTests/L001/C2.1/s_1_1.cnf | Bin 612053 -> 0 bytes
.../illumina/IlluminaTests/L001/C2.1/s_1_2.cif | Bin 1199213 -> 0 bytes
.../illumina/IlluminaTests/L001/C2.1/s_1_2.cnf | Bin 599613 -> 0 bytes
.../illumina/IlluminaTests/L001/C3.1/s_1_1.cif | Bin 1224093 -> 0 bytes
.../illumina/IlluminaTests/L001/C3.1/s_1_1.cnf | Bin 612053 -> 0 bytes
.../illumina/IlluminaTests/L001/C3.1/s_1_2.cif | Bin 1199213 -> 0 bytes
.../illumina/IlluminaTests/L001/C3.1/s_1_2.cnf | Bin 599613 -> 0 bytes
.../illumina/IlluminaTests/L001/C4.1/s_1_1.cif | Bin 1224093 -> 0 bytes
.../illumina/IlluminaTests/L001/C4.1/s_1_1.cnf | Bin 612053 -> 0 bytes
.../illumina/IlluminaTests/L001/C4.1/s_1_2.cif | Bin 1199213 -> 0 bytes
.../illumina/IlluminaTests/L001/C4.1/s_1_2.cnf | Bin 599613 -> 0 bytes
.../illumina/IlluminaTests/L008/C1.1/s_8_1.cif | Bin 173 -> 0 bytes
.../illumina/IlluminaTests/L008/C1.1/s_8_1.cnf | Bin 93 -> 0 bytes
.../illumina/IlluminaTests/L008/C2.1/s_8_1.cif | Bin 173 -> 0 bytes
.../illumina/IlluminaTests/L008/C2.1/s_8_1.cnf | Bin 93 -> 0 bytes
.../illumina/IlluminaTests/L008/C3.1/s_8_1.cif | Bin 173 -> 0 bytes
.../illumina/IlluminaTests/L008/C3.1/s_8_1.cnf | Bin 93 -> 0 bytes
.../illumina/IlluminaTests/L008/C4.1/s_8_1.cif | Bin 173 -> 0 bytes
.../illumina/IlluminaTests/L008/C4.1/s_8_1.cnf | Bin 93 -> 0 bytes
.../illumina/IlluminaTests/L008/C5.1/s_8_1.cif | Bin 173 -> 0 bytes
.../illumina/IlluminaTests/L008/C5.1/s_8_1.cnf | Bin 93 -> 0 bytes
.../illumina/IlluminaTests/L008/C6.1/s_8_1.cif | Bin 173 -> 0 bytes
.../illumina/IlluminaTests/L008/C6.1/s_8_1.cnf | Bin 93 -> 0 bytes
.../illumina/IlluminaTests/L008/C7.1/s_8_1.cif | Bin 173 -> 0 bytes
.../illumina/IlluminaTests/L008/C7.1/s_8_1.cnf | Bin 93 -> 0 bytes
.../illumina/IlluminaTests/L008/C8.1/s_8_1.cif | Bin 173 -> 0 bytes
.../illumina/IlluminaTests/L008/C8.1/s_8_1.cnf | Bin 93 -> 0 bytes
.../rta/BasecallsDir/s_1_1_0001_qseq.txt | 20 -
.../rta/BasecallsDir/s_2_1_0001_qseq.txt | 20 -
.../Homerus_Simpsonus_assembly18.fasta.0.2bpb | 1 -
.../Homerus_Simpsonus_assembly18.fasta.1.2bpb | 1 -
.../MakeSquashedMap/Map_to_genomic_coordinates.txt | 3 -
.../sf/picard/illumina/MakeSquashedMap/test.dict | 3 -
.../picard/illumina/Map_to_genomic_coordinates.txt | 45 -
.../sf/picard/illumina/s_1_1_eland_extended.txt | 9 -
.../net/sf/picard/illumina/s_1_1_eland_query.txt | 1 -
testdata/net/sf/picard/illumina/s_1_1_export.txt | 9 -
.../sf/picard/illumina/s_1_2_eland_extended.txt | 9 -
.../net/sf/picard/illumina/s_1_2_eland_query.txt | 1 -
testdata/net/sf/picard/illumina/s_1_2_export.txt | 9 -
.../net/sf/picard/illumina/s_2_eland_extended.txt | 3 -
testdata/net/sf/picard/illumina/s_2_export.txt | 3 -
.../sf/picard/illumina/s_4_1_eland_extended.txt | 9 -
.../net/sf/picard/illumina/s_4_1_eland_query.txt | 1 -
testdata/net/sf/picard/illumina/s_4_1_export.txt | 9 -
.../sf/picard/illumina/s_4_2_eland_extended.txt | 9 -
.../net/sf/picard/illumina/s_4_2_eland_query.txt | 1 -
testdata/net/sf/picard/illumina/s_4_2_export.txt | 9 -
.../net/sf/picard/illumina/s_5_eland_extended.txt | 3 -
testdata/net/sf/picard/illumina/s_5_export.txt | 3 -
.../IntervalListchr123_empty.interval_list | 4 +
.../sf/picard/sam/CompareSAMs/bigger_seq_dict.sam | 4 +-
testdata/net/sf/picard/sam/CompareSAMs/chr21.sam | 4 +-
.../net/sf/picard/sam/CompareSAMs/diff_coords.sam | 4 +-
.../net/sf/picard/sam/CompareSAMs/example2.sam | 4 +-
.../sf/picard/sam/CompareSAMs/genomic_sorted.sam | 4 +-
.../sf/picard/sam/CompareSAMs/genomic_sorted_5.sam | 4 +-
.../sam/CompareSAMs/genomic_sorted_5_plus.sam | 4 +-
.../sf/picard/sam/CompareSAMs/group_same_coord.sam | 4 +-
.../CompareSAMs/group_same_coord_diff_order.sam | 4 +-
.../sf/picard/sam/CompareSAMs/has_non_primary.sam | 4 +-
.../sf/picard/sam/CompareSAMs/unmapped_first.sam | 4 +-
.../sf/picard/sam/CompareSAMs/unmapped_second.sam | 4 +-
.../net/sf/picard/sam/CompareSAMs/unsorted.sam | 4 +-
.../net/sf/picard/sam/MarkDuplicates/merge1.sam | 2 +-
.../net/sf/picard/sam/MarkDuplicates/merge2.sam | 2 +-
.../net/sf/picard/sam/MarkDuplicates/merge3.sam | 2 +-
.../sam/MergeBamAlignment/aligned.badorder.sam | 2 +-
.../sam/MergeBamAlignment/aligned.supplement.sam | 2 +-
.../MergeBamAlignment/allread1.trimmed.aligned.sam | 2 +-
.../MergeBamAlignment/allread2.trimmed.aligned.sam | 2 +-
.../sam/MergeBamAlignment/cliptest.unmapped.sam | 2 +-
.../firsthalf.read1.trimmed.aligned.sam | 2 +-
.../firsthalf.read2.trimmed.aligned.sam | 2 +-
.../sam/MergeBamAlignment/multihit.aligned.sam | 2 +-
.../multihit.filter.fragment.unmapped.sam | 2 +-
.../MergeBamAlignment/multihit.filter.unmapped.sam | 2 +-
.../sam/MergeBamAlignment/multihit.unmapped.sam | 2 +-
.../secondhalf.read1.trimmed.aligned.sam | 2 +-
.../secondhalf.read2.trimmed.aligned.sam | 2 +-
.../sam/MergeBamAlignment/unmapped.badorder.sam | 2 +-
.../sf/picard/sam/MergeBamAlignment/unmapped.sam | 2 +-
.../sam/MergeSamFiles/case1/chr11sub_file1.sam | 2 +-
.../sam/MergeSamFiles/case1/chr11sub_file2.sam | 2 +-
.../sam/MergeSamFiles/case1/expected_output.sam | 2 +-
.../sam/MergeSamFiles/case2/chr11sub_file1.sam | 2 +-
.../sam/MergeSamFiles/case2/chr11sub_file2.sam | 2 +-
.../sam/MergeSamFiles/case2/chr11sub_file3.sam | 2 +-
.../sam/MergeSamFiles/case2/chr11sub_file4.sam | 2 +-
.../sam/MergeSamFiles/case2/expected_output.sam | 6 +-
.../picard/sam/MergeSamFiles/unsorted_input/1.sam | 2 +-
.../picard/sam/MergeSamFiles/unsorted_input/2.sam | 2 +-
.../sam/ValidateSamFileTest/duplicate_rg.sam | 11 +
.../ValidateSamFileTest/missing_platform_unit.sam | 10 +
.../sf/picard/sam/ValidateSamFileTest/valid.sam | 21 +
testdata/net/sf/picard/sam/aligned.sam | 2 +-
.../net/sf/picard/sam/aligned_queryname_sorted.bam | Bin 0 -> 725 bytes
.../net/sf/picard/sam/aligned_queryname_sorted.sam | 2 +-
.../bam2fastq/nonpaired/.gitignore} | 0
.../bam2fastq/paired/bad/grouped-unpaired-mate.sam | 4 +-
.../sam/bam2fastq/paired/bad/unpaired-mate.sam | 2 +-
.../sam/bam2fastq/paired/ok/clipping_test.sam | 2 +-
.../paired/ok/first-mate-bof-last-mate-eof.sam | 2 +-
.../paired/ok/grouped-last-pair-mates-flipped.sam | 4 +-
.../paired/ok/last-pair-mates-flipped.sam | 2 +-
.../picard/sam/bam2fastq/paired/ok/sorted-pair.sam | 2 +-
testdata/net/sf/picard/sam/onehalfaligned.sam | 2 +-
testdata/net/sf/picard/sam/otherhalfaligned.sam | 2 +-
testdata/net/sf/picard/sam/readWithBadRname.sam | 4 +-
testdata/net/sf/picard/sam/revert_sam_basic.sam | 6 +-
testdata/net/sf/picard/sam/revert_sam_negative.sam | 6 +-
testdata/net/sf/picard/sam/samHeaderProvider.sam | 15 +
testdata/net/sf/picard/sam/sequenceWithSpace.sam | 4 +-
.../sam/summary_alignment_bisulfite_test.sam | 2 +-
.../sf/picard/sam/summary_alignment_stats_test.sam | 2 +-
.../sam/summary_alignment_stats_test_multiple.sam | 8 +-
testdata/net/sf/picard/sam/unmapped.sam | 2 +-
.../tmp/.gitignore} | 0
2818 files changed, 17280 insertions(+), 24585 deletions(-)
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..879b2f2
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,11 @@
+. - Picard-public.iws
+.command_tmp
+classes
+testclasses
+javadoc
+dist
+contracts
+atlassian-ide-plugin.xml
+intellij.testclasses
+intellij.classes
+
diff --git a/build.xml b/build.xml
index b942ca7..f7337a2 100755
--- a/build.xml
+++ b/build.xml
@@ -43,7 +43,7 @@
<!-- Get SVN revision, if available, otherwise leave it blank. -->
<exec executable="svnversion" outputproperty="repository.revision" failifexecutionfails="false"/>
<property name="repository.revision" value=""/>
- <property name="sam-version" value="1.110"/>
+ <property name="sam-version" value="1.113"/>
<property name="picard-version" value="${sam-version}"/>
<property name="tribble-version" value="${sam-version}"/>
<property name="variant-version" value="${sam-version}"/>
@@ -285,6 +285,7 @@
<!-- The order of these elements determines the order they appear in the on-line help -->
<!-- If you don't want to generate on-line doc for a command, use package-command instead of package-and-document-command -->
+ <package-and-document-command title="AddCommentsToBam" main-class="net.sf.picard.sam.AddCommentsToBam"/>
<package-and-document-command title="AddOrReplaceReadGroups" main-class="net.sf.picard.sam.AddOrReplaceReadGroups"/>
<package-and-document-command title="BamToBfq" main-class="net.sf.picard.fastq.BamToBfq"/>
<package-and-document-command title="BamIndexStats" main-class="net.sf.picard.sam.BamIndexStats"/>
@@ -297,6 +298,7 @@
<package-and-document-command title="CollectMultipleMetrics" main-class="net.sf.picard.analysis.CollectMultipleMetrics"/>
<package-and-document-command title="CollectTargetedPcrMetrics" main-class="net.sf.picard.analysis.directed.CollectTargetedPcrMetrics"/>
<package-and-document-command title="CollectRnaSeqMetrics" main-class="net.sf.picard.analysis.CollectRnaSeqMetrics"/>
+ <package-and-document-command title="CollectWgsMetrics" main-class="net.sf.picard.analysis.CollectWgsMetrics"/>
<package-and-document-command title="CompareSAMs" main-class="net.sf.picard.sam.CompareSAMs"/>
<package-and-document-command title="CreateSequenceDictionary" main-class="net.sf.picard.sam.CreateSequenceDictionary"/>
<package-and-document-command title="DownsampleSam" main-class="net.sf.picard.sam.DownsampleSam"/>
@@ -305,6 +307,7 @@
<package-and-document-command title="FastqToSam" main-class="net.sf.picard.sam.FastqToSam"/>
<package-and-document-command title="FilterSamReads" main-class="net.sf.picard.sam.FilterSamReads"/>
<package-and-document-command title="FixMateInformation" main-class="net.sf.picard.sam.FixMateInformation"/>
+ <package-and-document-command title="GatherBamFiles" main-class="net.sf.picard.sam.GatherBamFiles"/>
<package-and-document-command title="IlluminaBasecallsToFastq" main-class="net.sf.picard.illumina.IlluminaBasecallsToFastq"/>
<package-and-document-command title="IlluminaBasecallsToSam" main-class="net.sf.picard.illumina.IlluminaBasecallsToSam"/>
<package-and-document-command title="CheckIlluminaDirectory" main-class="net.sf.picard.illumina.CheckIlluminaDirectory"/>
diff --git a/src/java/net/sf/picard/analysis/CollectWgsMetrics.java b/src/java/net/sf/picard/analysis/CollectWgsMetrics.java
new file mode 100644
index 0000000..9cf4888
--- /dev/null
+++ b/src/java/net/sf/picard/analysis/CollectWgsMetrics.java
@@ -0,0 +1,274 @@
+package net.sf.picard.analysis;
+
+import net.sf.picard.cmdline.CommandLineProgram;
+import net.sf.picard.cmdline.Option;
+import net.sf.picard.cmdline.StandardOptionDefinitions;
+import net.sf.picard.cmdline.Usage;
+import net.sf.picard.filter.SamRecordFilter;
+import net.sf.picard.filter.SecondaryAlignmentFilter;
+import net.sf.picard.io.IoUtil;
+import net.sf.picard.metrics.MetricBase;
+import net.sf.picard.metrics.MetricsFile;
+import net.sf.picard.reference.ReferenceSequence;
+import net.sf.picard.reference.ReferenceSequenceFileWalker;
+import net.sf.picard.util.Histogram;
+import net.sf.picard.util.Log;
+import net.sf.picard.util.MathUtil;
+import net.sf.picard.util.ProgressLogger;
+import net.sf.picard.util.SamLocusIterator;
+import net.sf.samtools.AlignmentBlock;
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMRecord;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+
+/**
+ * Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
+ *
+ * @author tfennell
+ */
+public class CollectWgsMetrics extends CommandLineProgram {
+
+ @Usage
+ public final String usage = "Computes a number of metrics that are useful for evaluating coverage and performance of " +
+ "whole genome sequencing experiments.";
+
+ @Option(shortName=StandardOptionDefinitions.INPUT_SHORT_NAME, doc="Input SAM or BAM file.")
+ public File INPUT;
+
+ @Option(shortName=StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc="Output metrics file.")
+ public File OUTPUT;
+
+ @Option(shortName=StandardOptionDefinitions.REFERENCE_SHORT_NAME, doc="The reference sequence fasta aligned to.")
+ public File REFERENCE_SEQUENCE;
+
+ @Option(shortName="MQ", doc="Minimum mapping quality for a read to contribute coverage.")
+ public int MINIMUM_MAPPING_QUALITY = 20;
+
+ @Option(shortName="Q", doc="Minimum base quality for a base to contribute coverage.")
+ public int MINIMUM_BASE_QUALITY = 20;
+
+ @Option(shortName="CAP", doc="Treat bases with coverage exceeding this value as if they had coverage at this value.")
+ public int COVERAGE_CAP = 250;
+
+ @Option(doc="For debugging purposes, stop after processing this many genomic bases.")
+ public long STOP_AFTER = -1;
+
+ private final Log log = Log.getInstance(CollectWgsMetrics.class);
+
+ /** Metrics for evaluating the performance of whole genome sequencing experiments. */
+ public static class WgsMetrics extends MetricBase {
+ /** The number of non-N bases in the genome reference over which coverage will be evaluated. */
+ public long GENOME_TERRITORY;
+ /** The mean coverage in bases of the genome territory, after all filters are applied. */
+ public double MEAN_COVERAGE;
+ /** The standard deviation of coverage of the genome after all filters are applied. */
+ public double SD_COVERAGE;
+ /** The median coverage in bases of the genome territory, after all filters are applied. */
+ public double MEDIAN_COVERAGE;
+ /** The median absolute deviation of coverage of the genome after all filters are applied. */
+ public double MAD_COVERAGE;
+
+ /** The fraction of aligned bases that were filtered out because they were in reads with low mapping quality (default is < 20). */
+ public double PCT_EXC_MAPQ;
+ /** The fraction of aligned bases that were filtered out because they were in reads marked as duplicates. */
+ public double PCT_EXC_DUPE;
+ /** The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair. */
+ public double PCT_EXC_UNPAIRED;
+ /** The fraction of aligned bases that were filtered out because they were of low base quality (default is < 20). */
+ public double PCT_EXC_BASEQ;
+ /** The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads. */
+ public double PCT_EXC_OVERLAP;
+ /** The fraction of aligned bases that were filtered out because they would have raised coverage above the capped value (default cap = 250x). */
+ public double PCT_EXC_CAPPED;
+ /** The total fraction of aligned bases excluded due to all filters. */
+ public double PCT_EXC_TOTAL;
+
+ /** The fraction of bases that attained at least 5X sequence coverage in post-filtering bases. */
+ public double PCT_5X;
+ /** The fraction of bases that attained at least 10X sequence coverage in post-filtering bases. */
+ public double PCT_10X;
+ /** The fraction of bases that attained at least 20X sequence coverage in post-filtering bases. */
+ public double PCT_20X;
+ /** The fraction of bases that attained at least 30X sequence coverage in post-filtering bases. */
+ public double PCT_30X;
+ /** The fraction of bases that attained at least 40X sequence coverage in post-filtering bases. */
+ public double PCT_40X;
+ /** The fraction of bases that attained at least 50X sequence coverage in post-filtering bases. */
+ public double PCT_50X;
+ /** The fraction of bases that attained at least 60X sequence coverage in post-filtering bases. */
+ public double PCT_60X;
+ /** The fraction of bases that attained at least 70X sequence coverage in post-filtering bases. */
+ public double PCT_70X;
+ /** The fraction of bases that attained at least 80X sequence coverage in post-filtering bases. */
+ public double PCT_80X;
+ /** The fraction of bases that attained at least 90X sequence coverage in post-filtering bases. */
+ public double PCT_90X;
+ /** The fraction of bases that attained at least 100X sequence coverage in post-filtering bases. */
+ public double PCT_100X;
+ }
+
+ public static void main(final String[] args) {
+ new CollectWgsMetrics().instanceMainWithExit(args);
+ }
+
+ @Override
+ protected int doWork() {
+ IoUtil.assertFileIsReadable(INPUT);
+ IoUtil.assertFileIsWritable(OUTPUT);
+ IoUtil.assertFileIsReadable(REFERENCE_SEQUENCE);
+
+ // Setup all the inputs
+ final ProgressLogger progress = new ProgressLogger(log, 10000000, "Processed", "loci");
+ final ReferenceSequenceFileWalker refWalker = new ReferenceSequenceFileWalker(REFERENCE_SEQUENCE);
+ final SAMFileReader in = new SAMFileReader(INPUT);
+
+ final SamLocusIterator iterator = new SamLocusIterator(in);
+ final List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
+ final CountingFilter dupeFilter = new CountingDuplicateFilter();
+ final CountingFilter mapqFilter = new CountingMapQFilter(MINIMUM_MAPPING_QUALITY);
+ final CountingPairedFilter pairFilter = new CountingPairedFilter();
+ filters.add(mapqFilter);
+ filters.add(dupeFilter);
+ filters.add(pairFilter);
+ filters.add(new SecondaryAlignmentFilter()); // Not a counting filter because we never want to count reads twice
+ iterator.setSamFilters(filters);
+ iterator.setEmitUncoveredLoci(true);
+ iterator.setMappingQualityScoreCutoff(0); // Handled separately because we want to count bases
+ iterator.setQualityScoreCutoff(0); // Handled separately because we want to count bases
+ iterator.setIncludeNonPfReads(false);
+
+ final int max = COVERAGE_CAP;
+ final long[] histogramArray = new long[max + 1];
+ final boolean usingStopAfter = STOP_AFTER > 0;
+ final long stopAfter = STOP_AFTER-1;
+ long counter = 0;
+
+ long basesExcludedByBaseq = 0;
+ long basesExcludedByOverlap = 0;
+ long basesExcludedByCapping = 0;
+
+ // Loop through all the loci
+ while (iterator.hasNext()) {
+ final SamLocusIterator.LocusInfo info = iterator.next();
+
+ // Check that the reference is not N
+ final ReferenceSequence ref = refWalker.get(info.getSequenceIndex());
+ final byte base = ref.getBases()[info.getPosition()-1];
+ if (base == 'N') continue;
+
+ // Figure out the coverage while not counting overlapping reads twice, and excluding various things
+ final HashSet<String> readNames = new HashSet<String>(info.getRecordAndPositions().size());
+ for (final SamLocusIterator.RecordAndOffset recs : info.getRecordAndPositions()) {
+ if (recs.getBaseQuality() < MINIMUM_BASE_QUALITY) { ++basesExcludedByBaseq; continue; }
+ if (!readNames.add(recs.getRecord().getReadName())) { ++basesExcludedByOverlap; continue; }
+ }
+
+ final int depth = Math.min(readNames.size(), max);
+ if (depth < readNames.size()) basesExcludedByCapping += readNames.size() - max;
+ histogramArray[depth]++;
+
+ // Record progress and perhaps stop
+ progress.record(info.getSequenceName(), info.getPosition());
+ if (usingStopAfter && ++counter > stopAfter) break;
+ }
+
+ // Construct and write the outputs
+ final Histogram<Integer> histo = new Histogram<Integer>("coverage", "count");
+ for (int i=0; i<histogramArray.length; ++i) {
+ histo.increment(i, histogramArray[i]);
+ }
+
+ final WgsMetrics metrics = new WgsMetrics();
+ metrics.GENOME_TERRITORY = (long) histo.getSumOfValues();
+ metrics.MEAN_COVERAGE = histo.getMean();
+ metrics.SD_COVERAGE = histo.getStandardDeviation();
+ metrics.MEDIAN_COVERAGE = histo.getMedian();
+ metrics.MAD_COVERAGE = histo.getMedianAbsoluteDeviation();
+
+ final long basesExcludedByDupes = dupeFilter.getFilteredBases();
+ final long basesExcludedByMapq = mapqFilter.getFilteredBases();
+ final long basesExcludedByPairing = pairFilter.getFilteredBases();
+ final double total = histo.getSum();
+ final double totalWithExcludes = total + basesExcludedByDupes + basesExcludedByMapq + basesExcludedByPairing + basesExcludedByBaseq + basesExcludedByOverlap + basesExcludedByCapping;
+ metrics.PCT_EXC_DUPE = basesExcludedByDupes / totalWithExcludes;
+ metrics.PCT_EXC_MAPQ = basesExcludedByMapq / totalWithExcludes;
+ metrics.PCT_EXC_UNPAIRED = basesExcludedByPairing / totalWithExcludes;
+ metrics.PCT_EXC_BASEQ = basesExcludedByBaseq / totalWithExcludes;
+ metrics.PCT_EXC_OVERLAP = basesExcludedByOverlap / totalWithExcludes;
+ metrics.PCT_EXC_CAPPED = basesExcludedByCapping / totalWithExcludes;
+ metrics.PCT_EXC_TOTAL = (totalWithExcludes - total) / totalWithExcludes;
+
+ metrics.PCT_5X = MathUtil.sum(histogramArray, 5, histogramArray.length) / (double) metrics.GENOME_TERRITORY;
+ metrics.PCT_10X = MathUtil.sum(histogramArray, 10, histogramArray.length) / (double) metrics.GENOME_TERRITORY;
+ metrics.PCT_20X = MathUtil.sum(histogramArray, 20, histogramArray.length) / (double) metrics.GENOME_TERRITORY;
+ metrics.PCT_30X = MathUtil.sum(histogramArray, 30, histogramArray.length) / (double) metrics.GENOME_TERRITORY;
+ metrics.PCT_40X = MathUtil.sum(histogramArray, 40, histogramArray.length) / (double) metrics.GENOME_TERRITORY;
+ metrics.PCT_50X = MathUtil.sum(histogramArray, 50, histogramArray.length) / (double) metrics.GENOME_TERRITORY;
+ metrics.PCT_60X = MathUtil.sum(histogramArray, 60, histogramArray.length) / (double) metrics.GENOME_TERRITORY;
+ metrics.PCT_70X = MathUtil.sum(histogramArray, 70, histogramArray.length) / (double) metrics.GENOME_TERRITORY;
+ metrics.PCT_80X = MathUtil.sum(histogramArray, 80, histogramArray.length) / (double) metrics.GENOME_TERRITORY;
+ metrics.PCT_90X = MathUtil.sum(histogramArray, 90, histogramArray.length) / (double) metrics.GENOME_TERRITORY;
+ metrics.PCT_100X = MathUtil.sum(histogramArray, 100, histogramArray.length) / (double) metrics.GENOME_TERRITORY;
+
+ final MetricsFile<WgsMetrics, Integer> out = getMetricsFile();
+ out.addMetric(metrics);
+ out.addHistogram(histo);
+ out.write(OUTPUT);
+
+ return 0;
+ }
+}
+
+/**
+ * A SamRecordFilter that counts the number of aligned bases in the reads which it filters out. Abstract and designed
+ * to be subclassed to implement the desired filter.
+ */
+abstract class CountingFilter implements SamRecordFilter {
+ private long filteredRecords = 0;
+ private long filteredBases = 0;
+
+ /** Gets the number of records that have been filtered out thus far. */
+ public long getFilteredRecords() { return this.filteredRecords; }
+
+ /** Gets the number of bases that have been filtered out thus far. */
+ public long getFilteredBases() { return this.filteredBases; }
+
+ @Override public final boolean filterOut(final SAMRecord record) {
+ final boolean filteredOut = reallyFilterOut(record);
+ if (filteredOut) {
+ ++filteredRecords;
+ for (final AlignmentBlock block : record.getAlignmentBlocks()) {
+ this.filteredBases += block.getLength();
+ }
+ }
+ return filteredOut;
+ }
+
+ abstract public boolean reallyFilterOut(final SAMRecord record);
+
+ @Override public boolean filterOut(final SAMRecord first, final SAMRecord second) {
+ throw new UnsupportedOperationException();
+ }
+}
+
+/** Counting filter that discards reads that have been marked as duplicates. */
+class CountingDuplicateFilter extends CountingFilter {
+ @Override public boolean reallyFilterOut(final SAMRecord record) { return record.getDuplicateReadFlag(); }
+}
+
+/** Counting filter that discards reads below a configurable mapping quality threshold. */
+class CountingMapQFilter extends CountingFilter {
+ private final int minMapq;
+ CountingMapQFilter(final int minMapq) { this.minMapq = minMapq; }
+ @Override public boolean reallyFilterOut(final SAMRecord record) { return record.getMappingQuality() < minMapq; }
+}
+
+/** Counting filter that discards reads that are unpaired in sequencing and paired reads who's mates are not mapped. */
+class CountingPairedFilter extends CountingFilter {
+ @Override public boolean reallyFilterOut(final SAMRecord record) { return !record.getReadPairedFlag() || record.getMateUnmappedFlag(); }
+}
+
diff --git a/src/java/net/sf/picard/cmdline/CommandLineParser.java b/src/java/net/sf/picard/cmdline/CommandLineParser.java
index 68a44fc..de98e17 100644
--- a/src/java/net/sf/picard/cmdline/CommandLineParser.java
+++ b/src/java/net/sf/picard/cmdline/CommandLineParser.java
@@ -755,13 +755,22 @@ public class CommandLineParser {
if (enumConstants == null && getUnderlyingType(optionDefinition.field) == Boolean.class) {
enumConstants = TRUE_FALSE_VALUES;
}
+
if (enumConstants != null) {
+ final Boolean isClpEnum=enumConstants.length>0 && (enumConstants[0] instanceof ClpEnum) ;
+
sb.append("Possible values: {");
+ if(isClpEnum) sb.append("\n");
+
for (int i = 0; i < enumConstants.length; ++i) {
- if (i > 0) {
+ if (i > 0 && ! isClpEnum) {
sb.append(", ");
}
sb.append(enumConstants[i].toString());
+
+ if(isClpEnum){
+ sb.append(" (" + ((ClpEnum)enumConstants[i]).getHelpDoc() + ")\n");
+ }
}
sb.append("} ");
}
@@ -1031,6 +1040,10 @@ public class CommandLineParser {
return argv;
}
+ public interface ClpEnum{
+ String getHelpDoc();
+ }
+
protected static class OptionDefinition {
final Field field;
final String name;
@@ -1063,7 +1076,8 @@ public class CommandLineParser {
if( isCollection && ((Collection) defaultValue).isEmpty()) {
//treat empty collections the same as uninitialized primitive types
this.defaultValue = "null";
- } else {
+ }
+ else {
//this is an intialized primitive type or a non-empty collection
this.defaultValue = defaultValue.toString();
}
diff --git a/src/java/net/sf/picard/filter/SecondaryAlignmentFilter.java b/src/java/net/sf/picard/filter/SecondaryAlignmentFilter.java
new file mode 100644
index 0000000..d971497
--- /dev/null
+++ b/src/java/net/sf/picard/filter/SecondaryAlignmentFilter.java
@@ -0,0 +1,20 @@
+package net.sf.picard.filter;
+
+import net.sf.samtools.SAMRecord;
+
+/**
+ * SamRecordFilter that filters out secondary alignments, but not supplemental alignments.
+ */
+public class SecondaryAlignmentFilter implements SamRecordFilter {
+ /**
+ * Returns true if the read is marked as secondary.
+ */
+ public boolean filterOut(final SAMRecord record) { return record.getNotPrimaryAlignmentFlag(); }
+
+ /**
+ * Returns true if either read is marked as secondary.
+ */
+ public boolean filterOut(final SAMRecord first, final SAMRecord second) {
+ return first.getNotPrimaryAlignmentFlag() || second.getNotPrimaryAlignmentFlag();
+ }
+}
diff --git a/src/java/net/sf/picard/illumina/CheckIlluminaDirectory.java b/src/java/net/sf/picard/illumina/CheckIlluminaDirectory.java
index 65aea3e..2b9b8a6 100644
--- a/src/java/net/sf/picard/illumina/CheckIlluminaDirectory.java
+++ b/src/java/net/sf/picard/illumina/CheckIlluminaDirectory.java
@@ -9,9 +9,11 @@ import net.sf.picard.illumina.parser.IlluminaDataProviderFactory;
import net.sf.picard.illumina.parser.IlluminaDataType;
import net.sf.picard.illumina.parser.IlluminaFileUtil;
import net.sf.picard.illumina.parser.OutputMapping;
+import net.sf.picard.illumina.parser.ParameterizedFileUtil;
import net.sf.picard.illumina.parser.ReadStructure;
import net.sf.picard.io.IoUtil;
import net.sf.picard.util.Log;
+import net.sf.picard.util.ProcessExecutor;
import net.sf.samtools.util.StringUtil;
import java.io.File;
@@ -32,33 +34,33 @@ public class CheckIlluminaDirectory extends CommandLineProgram {
// The following attributes define the command-line arguments
@Usage
public String USAGE = getStandardUsagePreamble() +
- "Check that the files to provide the data specified by DATA_TYPES are available, exist, and are reasonably sized for every tile/cycle. "
- +
- "Reasonably sized means non-zero sized for files that exist per tile and equal size for binary files that exist per cycle/per tile. "
- +
- "CheckIlluminaDirectory DOES NOT check that the individual records in a file are well-formed.\n";
+ "Check that the files to provide the data specified by DATA_TYPES are available, exist, and are reasonably sized for every tile/cycle. "
+ +
+ "Reasonably sized means non-zero sized for files that exist per tile and equal size for binary files that exist per cycle/per tile. "
+ +
+ "CheckIlluminaDirectory DOES NOT check that the individual records in a file are well-formed.\n";
@Option(doc = "The basecalls output directory. ", shortName = "B")
public File BASECALLS_DIR;
@Option(doc =
"The data types that should be checked for each tile/cycle. If no values are provided then the data types checked are those "
- +
- "required by IlluminaBaseCallsToSam (which is a superset of those used in ExtractIlluminaBarcodes). These data types vary slightly depending on"
- +
- "whether or not the run is barcoded so READ_STRUCTURE should be the same as that which will be passed to IlluminaBasecallsToSam. If this option "
- +
- "is left unspecified then both ExtractIlluminaBarcodes and IlluminaBaseCallsToSam should complete successfully UNLESS the "
- +
- "individual records of the files themselves are spurious. ",
+ +
+ "required by IlluminaBaseCallsToSam (which is a superset of those used in ExtractIlluminaBarcodes). These data types vary slightly depending on"
+ +
+ "whether or not the run is barcoded so READ_STRUCTURE should be the same as that which will be passed to IlluminaBasecallsToSam. If this option "
+ +
+ "is left unspecified then both ExtractIlluminaBarcodes and IlluminaBaseCallsToSam should complete successfully UNLESS the "
+ +
+ "individual records of the files themselves are spurious. ",
shortName = "DT",
optional = true)
public final Set<IlluminaDataType> DATA_TYPES = new TreeSet<IlluminaDataType>();
@Option(doc = ReadStructure.PARAMETER_DOC
- + " Note: If you want to check whether or not a future IlluminaBasecallsToSam or ExtractIlluminaBarcodes "
- +
- "run will fail then be sure to use the exact same READ_STRUCTURE that you would pass to these programs for this run.",
+ + " Note: If you want to check whether or not a future IlluminaBasecallsToSam or ExtractIlluminaBarcodes "
+ +
+ "run will fail then be sure to use the exact same READ_STRUCTURE that you would pass to these programs for this run.",
shortName = "RS")
public String READ_STRUCTURE;
@@ -73,6 +75,10 @@ public class CheckIlluminaDirectory extends CommandLineProgram {
optional = true)
public Boolean FAKE_FILES = false;
+ @Option(doc = "A flag to create symlinks to the loc file for the X Ten for each tile.", shortName = "X",
+ optional = true)
+ public Boolean LINK_LOCS = false;
+
/**
* Required main method implementation.
*/
@@ -97,12 +103,19 @@ public class CheckIlluminaDirectory extends CommandLineProgram {
log.info("Expected cycles: " + StringUtil.intValuesToString(expectedCycles));
for (final Integer lane : LANES) {
- final IlluminaFileUtil fileUtil = new IlluminaFileUtil(BASECALLS_DIR, lane);
+ IlluminaFileUtil fileUtil = new IlluminaFileUtil(BASECALLS_DIR, lane);
final List<Integer> expectedTiles = fileUtil.getExpectedTiles();
if (!TILE_NUMBERS.isEmpty()) {
expectedTiles.retainAll(TILE_NUMBERS);
}
+ if (LINK_LOCS) {
+ createLocFileSymlinks(fileUtil, lane);
+ //we need to create a new file util because it stores a cache to the files it found on
+ //construction and this doesn't inclue the recently created symlinks
+ fileUtil = new IlluminaFileUtil(BASECALLS_DIR, lane);
+ }
+
log.info("Checking lane " + lane);
log.info("Expected tiles: " + StringUtil.join(", ", expectedTiles));
@@ -129,6 +142,34 @@ public class CheckIlluminaDirectory extends CommandLineProgram {
return status;
}
+ private void createLocFileSymlinks(final IlluminaFileUtil fileUtil, final int lane) {
+ final File baseFile = new File(BASECALLS_DIR.getParentFile().getAbsolutePath() + File.separator + "s.locs");
+ final File newFileBase = new File(baseFile.getParent() + File.separator + IlluminaFileUtil
+ .longLaneStr(lane) + File.separator);
+ if (baseFile.exists()) {
+ boolean success = true;
+ if (!newFileBase.exists()) {
+ success = newFileBase.mkdirs();
+ }
+ if (success) {
+ for (final Integer tile : fileUtil.getExpectedTiles()) {
+ final String newName =
+ newFileBase + File.separator + String.format("s_%d_%d.locs", lane, tile);
+ final ProcessExecutor.ExitStatusAndOutput output =
+ ProcessExecutor.executeAndReturnInterleavedOutput(new String[]{"ln", "-fs", baseFile.getAbsolutePath(), newName});
+ if (output.exitStatus != 0) {
+ throw new PicardException("Could not create symlink: " + output.stdout);
+ }
+ }
+ } else {
+ throw new PicardException(String.format("Could not create lane directory: %s.", newFileBase.getAbsolutePath()));
+ }
+ } else {
+ throw new PicardException(String.format("Locations file %s does not exist.", baseFile.getAbsolutePath()));
+ }
+
+ }
+
/**
* Use fileUtil to find the data types that would be used by IlluminaDataProvider. Verify that for the expected
* tiles/cycles/data types that all the files needed to provide their data is present. This method logs every
@@ -138,7 +179,6 @@ public class CheckIlluminaDirectory extends CommandLineProgram {
* @param expectedTiles The tiles we expect to be available/well-formed
* @param cycles The cycles we expect to be available/well-formed
* @param dataTypes The data types we expect to be available/well-formed
- *
* @return The number of errors found/logged for this directory/lane
*/
private static final int verifyLane(final IlluminaFileUtil fileUtil, final List<Integer> expectedTiles,
@@ -177,7 +217,7 @@ public class CheckIlluminaDirectory extends CommandLineProgram {
}
for (final IlluminaFileUtil.SupportedIlluminaFormat format : formatToDataTypes.keySet()) {
- final IlluminaFileUtil.ParameterizedFileUtil util = fileUtil.getUtil(format);
+ final ParameterizedFileUtil util = fileUtil.getUtil(format);
final List<String> failures = util.verify(expectedTiles, cycles);
//if we have failures and we want to fake files then fake them now.
if (!failures.isEmpty() && fakeFiles) {
diff --git a/src/java/net/sf/picard/illumina/ClusterDataToSamConverter.java b/src/java/net/sf/picard/illumina/ClusterDataToSamConverter.java
index 8b2a9a6..fd1e3eb 100644
--- a/src/java/net/sf/picard/illumina/ClusterDataToSamConverter.java
+++ b/src/java/net/sf/picard/illumina/ClusterDataToSamConverter.java
@@ -31,10 +31,11 @@ import net.sf.picard.illumina.parser.ClusterData;
import net.sf.picard.illumina.parser.ReadData;
import net.sf.picard.illumina.parser.ReadStructure;
import net.sf.picard.sam.ReservedTagConstants;
+import net.sf.picard.util.AdapterMarker;
import net.sf.picard.util.AdapterPair;
-import net.sf.picard.util.ClippingUtility;
import net.sf.picard.util.IlluminaUtil;
import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMTag;
import java.util.List;
@@ -56,7 +57,7 @@ public class ClusterDataToSamConverter implements
private final boolean isBarcoded;
private final int [] templateIndices;
private final int [] barcodeIndices;
- private final AdapterPair[] adaptersToCheck;
+ private final AdapterMarker adapterMarker;
private final int outputRecordsPerCluster;
private final ReadNameEncoder readNameEncoder;
@@ -81,8 +82,11 @@ public class ClusterDataToSamConverter implements
this.isPairedEnd = readStructure.templates.length() == 2;
this.isBarcoded = !readStructure.barcodes.isEmpty();
- this.adaptersToCheck = new AdapterPair[adapters.size()];
- for (int i = 0; i < adapters.size(); i++) adaptersToCheck[i] = adapters.get(i);
+ if (adapters.isEmpty()) {
+ this.adapterMarker = null;
+ } else {
+ this.adapterMarker = new AdapterMarker(adapters.toArray(new AdapterPair[adapters.size()]));
+ }
this.templateIndices = readStructure.templates.getIndices();
this.barcodeIndices = readStructure.barcodes.getIndices();
@@ -114,13 +118,13 @@ public class ClusterDataToSamConverter implements
}
if (this.readGroupId != null) {
- sam.setAttribute("RG", readGroupId);
+ sam.setAttribute(SAMTag.RG.name(), readGroupId);
}
// If it's a barcoded run and the read isn't assigned to a barcode, then add the barcode
// that was read as an optional tag
if (unmatchedBarcode != null) {
- sam.setAttribute("BC", unmatchedBarcode);
+ sam.setAttribute(SAMTag.BC.name(), unmatchedBarcode);
}
return sam;
@@ -156,13 +160,13 @@ public class ClusterDataToSamConverter implements
ret.records[1] = secondOfPair;
}
- if (adaptersToCheck.length > 0) {
+ if (adapterMarker != null) {
// Clip the read
if (isPairedEnd) {
- ClippingUtility.adapterTrimIlluminaPairedReads(firstOfPair, secondOfPair, adaptersToCheck);
+ adapterMarker.adapterTrimIlluminaPairedReads(firstOfPair, secondOfPair);
}
else {
- ClippingUtility.adapterTrimIlluminaSingleRead(firstOfPair, adaptersToCheck);
+ adapterMarker.adapterTrimIlluminaSingleRead(firstOfPair);
}
}
return ret;
diff --git a/src/java/net/sf/picard/illumina/ExtractIlluminaBarcodes.java b/src/java/net/sf/picard/illumina/ExtractIlluminaBarcodes.java
index 6228179..beda46a 100644
--- a/src/java/net/sf/picard/illumina/ExtractIlluminaBarcodes.java
+++ b/src/java/net/sf/picard/illumina/ExtractIlluminaBarcodes.java
@@ -589,10 +589,13 @@ public class ExtractIlluminaBarcodes extends CommandLineProgram {
writer.newLine();
}
writer.close();
- } catch (Exception e) {
+ } catch (final Exception e) {
LOG.error(e, "Error processing tile ", this.tile);
this.exception = e;
}
+ finally{
+ provider.close();
+ }
}
/**
diff --git a/src/java/net/sf/picard/illumina/IlluminaBasecallsConverter.java b/src/java/net/sf/picard/illumina/IlluminaBasecallsConverter.java
index d79b0e8..2ace5db 100644
--- a/src/java/net/sf/picard/illumina/IlluminaBasecallsConverter.java
+++ b/src/java/net/sf/picard/illumina/IlluminaBasecallsConverter.java
@@ -24,7 +24,11 @@
package net.sf.picard.illumina;
import net.sf.picard.PicardException;
-import net.sf.picard.illumina.parser.*;
+import net.sf.picard.illumina.parser.ClusterData;
+import net.sf.picard.illumina.parser.IlluminaDataProvider;
+import net.sf.picard.illumina.parser.IlluminaDataProviderFactory;
+import net.sf.picard.illumina.parser.IlluminaDataType;
+import net.sf.picard.illumina.parser.ReadStructure;
import net.sf.picard.illumina.parser.readers.BclQualityEvaluationStrategy;
import net.sf.picard.util.FileChannelJDKBugWorkAround;
import net.sf.picard.util.Log;
@@ -33,7 +37,21 @@ import net.sf.samtools.util.PeekIterator;
import net.sf.samtools.util.SortingCollection;
import java.io.File;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.NoSuchElementException;
+import java.util.Queue;
+import java.util.Set;
+import java.util.Timer;
+import java.util.TimerTask;
+import java.util.TreeMap;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.PriorityBlockingQueue;
import java.util.concurrent.ThreadPoolExecutor;
@@ -45,6 +63,7 @@ import static java.util.concurrent.TimeUnit.MILLISECONDS;
* Manages the conversion of Illumina basecalls into some output format. Creates multiple threads to manage reading,
* sorting and writing efficiently. Output is written in queryname output. Optionally demultiplexes indexed reads
* into separate outputs by barcode.
+ *
* @param <CLUSTER_OUTPUT_RECORD> The class to which a ClusterData is converted in preparation for writing.
*/
public class IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> {
@@ -69,6 +88,7 @@ public class IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> {
public static final IlluminaDataType[] DATA_TYPES_NO_BARCODE =
{IlluminaDataType.BaseCalls, IlluminaDataType.QualityScores, IlluminaDataType.Position, IlluminaDataType.PF};
private static final IlluminaDataType[] DATA_TYPES_WITH_BARCODE = Arrays.copyOf(DATA_TYPES_NO_BARCODE, DATA_TYPES_NO_BARCODE.length + 1);
+
static {
DATA_TYPES_WITH_BARCODE[DATA_TYPES_WITH_BARCODE.length - 1] = IlluminaDataType.Barcodes;
}
@@ -112,29 +132,29 @@ public class IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> {
// ends, but for unit testing it is desirable to stop the task when done with this instance.
private final TimerTask gcTimerTask;
private List<Integer> tiles;
- private boolean includeNonPfReads;
+ private final boolean includeNonPfReads;
private final SortingCollection.Codec<CLUSTER_OUTPUT_RECORD> codecPrototype;
// Annoying that we need this.
private final Class<CLUSTER_OUTPUT_RECORD> outputRecordClass;
/**
- * @param basecallsDir Where to read basecalls from.
- * @param lane What lane to process.
- * @param readStructure How to interpret each cluster.
+ * @param basecallsDir Where to read basecalls from.
+ * @param lane What lane to process.
+ * @param readStructure How to interpret each cluster.
* @param barcodeRecordWriterMap Map from barcode to CLUSTER_OUTPUT_RECORD writer. If demultiplex is false, must contain
* one writer stored with key=null.
- * @param demultiplex If true, output is split by barcode, otherwise all are written to the same output stream.
- * @param maxReadsInRamPerTile Configures number of reads each tile will store in RAM before spilling to disk.
- * @param tmpDirs For SortingCollection spilling.
- * @param numProcessors Controls number of threads. If <= 0, the number of threads allocated is
- * available cores - numProcessors.
- * @param forceGc Force explicit GC periodically. This is good for causing memory maps to be released.
- * @param firstTile (For debugging) If non-null, start processing at this tile.
- * @param tileLimit (For debugging) If non-null, process no more than this many tiles.
+ * @param demultiplex If true, output is split by barcode, otherwise all are written to the same output stream.
+ * @param maxReadsInRamPerTile Configures number of reads each tile will store in RAM before spilling to disk.
+ * @param tmpDirs For SortingCollection spilling.
+ * @param numProcessors Controls number of threads. If <= 0, the number of threads allocated is
+ * available cores - numProcessors.
+ * @param forceGc Force explicit GC periodically. This is good for causing memory maps to be released.
+ * @param firstTile (For debugging) If non-null, start processing at this tile.
+ * @param tileLimit (For debugging) If non-null, process no more than this many tiles.
* @param outputRecordComparator For sorting output records within a single tile.
- * @param codecPrototype For spilling output records to disk.
- * @param outputRecordClass Inconveniently needed to create SortingCollections.
- * @param includeNonPfReads If true, will include ALL reads (including those which do not have PF set)
+ * @param codecPrototype For spilling output records to disk.
+ * @param outputRecordClass Inconveniently needed to create SortingCollections.
+ * @param includeNonPfReads If true, will include ALL reads (including those which do not have PF set)
*/
public IlluminaBasecallsConverter(final File basecallsDir, final int lane, final ReadStructure readStructure,
final Map<String, ? extends ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>> barcodeRecordWriterMap,
@@ -214,6 +234,7 @@ public class IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> {
/**
* Must be called before doTileProcessing. This is not passed in the ctor because often the
* IlluminaDataProviderFactory is needed in order to construct the converter.
+ *
* @param converter Converts ClusterData to CLUSTER_OUTPUT_RECORD
*/
public void setConverter(final ClusterDataConverter<CLUSTER_OUTPUT_RECORD> converter) {
@@ -246,22 +267,22 @@ public class IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> {
tileReadAggregator.submit();
try {
tileReadAggregator.awaitWorkComplete();
- } catch (InterruptedException e) {
+ } catch (final InterruptedException e) {
log.error(e, "Failure encountered in worker thread; attempting to shut down remaining worker threads and terminate ...");
throw new PicardException("Failure encountered in worker thread; see log for details.");
} finally {
tileReadAggregator.shutdown();
}
- for (Map.Entry<Byte, Integer> entry : bclQualityEvaluationStrategy.getPoorQualityFrequencies().entrySet()) {
+ for (final Map.Entry<Byte, Integer> entry : bclQualityEvaluationStrategy.getPoorQualityFrequencies().entrySet()) {
log.warn(String.format("Observed low quality of %s %s times.", entry.getKey(), entry.getValue()));
}
bclQualityEvaluationStrategy.assertMinimumQualities();
-
+
} finally {
try {
gcTimerTask.cancel();
- } catch (Throwable ex) {
+ } catch (final Throwable ex) {
log.warn(ex, "Ignoring exception stopping background GC thread.");
}
// Close the writers
@@ -450,6 +471,7 @@ public class IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> {
return this.getBarcodeRecords().keySet();
}
}
+
/**
* Reads the information from a tile via an IlluminaDataProvider and feeds red information into a processingRecord
* managed by the TileReadAggregator.
@@ -478,12 +500,13 @@ public class IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> {
readProgressLogger.record(null, 0);
// If this cluster is passing, or we do NOT want to ONLY emit passing reads, then add it to the next
if (cluster.isPf() || includeNonPfReads) {
- final String barcode = (demultiplex? cluster.getMatchedBarcode(): null);
+ final String barcode = (demultiplex ? cluster.getMatchedBarcode() : null);
this.processingRecord.addRecord(barcode, converter.convertClusterToOutputRecord(cluster));
}
}
this.handler.completeTile(this.tile);
+ dataProvider.close();
}
}
@@ -521,7 +544,8 @@ public class IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> {
// Higher priority items go earlier in the queue, so reverse the "natural" comparison.
return ((PriorityRunnable) o2).getPriority() - ((PriorityRunnable) o1).getPriority();
}
- }));
+ })
+ );
/**
* The object acting as a latch to notify when the aggregator completes its work.
@@ -575,7 +599,7 @@ public class IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> {
public void run() {
try {
reader.process();
- } catch (RuntimeException e) {
+ } catch (final RuntimeException e) {
/**
* In the event of an internal failure, signal to the parent thread that something has gone
* wrong. This is necessary because if an item of work fails to complete, the aggregator will
@@ -583,7 +607,7 @@ public class IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> {
*/
parentThread.interrupt();
throw e;
- } catch (Error e) {
+ } catch (final Error e) {
parentThread.interrupt();
throw e;
}
@@ -664,7 +688,7 @@ public class IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> {
* move to the next barcode.
*/
if (tileRecord.getState() != TileProcessingState.DONE_READING) {
- break NEXT_BARCODE;
+ break;
}
switch (tileRecord.getBarcodeState(barcode)) {
case NA:
@@ -683,7 +707,7 @@ public class IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> {
break NEXT_BARCODE;
case READ:
/**
- * This barcode has beenr read, and all of the earlier tiles have been written
+ * This barcode has been read, and all of the earlier tiles have been written
* for this barcode, so queue its writing.
*/
tileRecord.setBarcodeState(barcode, TileBarcodeProcessingState.QUEUED_FOR_WRITE);
@@ -754,7 +778,7 @@ public class IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> {
tileRecord.setBarcodeState(barcode, TileBarcodeProcessingState.WRITTEN);
findAndEnqueueWorkOrSignalCompletion();
- } catch (RuntimeException e) {
+ } catch (final RuntimeException e) {
/**
* In the event of an internal failure, signal to the parent thread that something has gone
* wrong. This is necessary because if an item of work fails to complete, the aggregator will
@@ -762,7 +786,7 @@ public class IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> {
*/
parentThread.interrupt();
throw e;
- } catch (Error e) {
+ } catch (final Error e) {
parentThread.interrupt();
throw e;
}
@@ -828,6 +852,7 @@ public class IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> {
public static interface ConvertedClusterDataWriter<OUTPUT_RECORD> {
void write(final OUTPUT_RECORD rec);
+
void close();
}
}
diff --git a/src/java/net/sf/picard/illumina/IlluminaBasecallsToFastq.java b/src/java/net/sf/picard/illumina/IlluminaBasecallsToFastq.java
index 511c584..fea549f 100644
--- a/src/java/net/sf/picard/illumina/IlluminaBasecallsToFastq.java
+++ b/src/java/net/sf/picard/illumina/IlluminaBasecallsToFastq.java
@@ -277,6 +277,7 @@ public class IlluminaBasecallsToFastq extends CommandLineProgram {
if (barcodeFastqWriterMap.isEmpty()) {
throw new PicardException("MULTIPLEX_PARAMS file " + MULTIPLEX_PARAMS + " does have any data rows.");
}
+ libraryParamsParser.close();
}
/**
diff --git a/src/java/net/sf/picard/illumina/IlluminaBasecallsToSam.java b/src/java/net/sf/picard/illumina/IlluminaBasecallsToSam.java
index 2603474..39423a8 100644
--- a/src/java/net/sf/picard/illumina/IlluminaBasecallsToSam.java
+++ b/src/java/net/sf/picard/illumina/IlluminaBasecallsToSam.java
@@ -335,6 +335,7 @@ public class IlluminaBasecallsToSam extends CommandLineProgram {
if (barcodeSamWriterMap.isEmpty()) {
throw new PicardException("LIBRARY_PARAMS(BARCODE_PARAMS) file " + LIBRARY_PARAMS + " does have any data rows.");
}
+ libraryParamsParser.close();
}
/**
diff --git a/src/java/net/sf/picard/illumina/MarkIlluminaAdapters.java b/src/java/net/sf/picard/illumina/MarkIlluminaAdapters.java
index d5f971d..3bf8072 100644
--- a/src/java/net/sf/picard/illumina/MarkIlluminaAdapters.java
+++ b/src/java/net/sf/picard/illumina/MarkIlluminaAdapters.java
@@ -96,6 +96,19 @@ public class MarkIlluminaAdapters extends CommandLineProgram {
@Option(doc="For specifying adapters other than standard Illumina", optional=true)
public String THREE_PRIME_ADAPTER;
+ @Option(doc="Adapters are truncated to this length to speed adapter matching. Set to a large number to effectively disable truncation.")
+ public int ADAPTER_TRUNCATION_LENGTH = AdapterMarker.DEFAULT_ADAPTER_LENGTH;
+
+ @Option(doc="If looking for multiple adapter sequences, then after having seen this many adapters, shorten the list of sequences. " +
+ "Keep the adapters that were found most frequently in the input so far. " +
+ "Set to -1 if the input has a heterogeneous mix of adapters so shortening is undesirable.",
+ shortName = "APT")
+ public int PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN = AdapterMarker.DEFAULT_PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN;
+
+ @Option(doc="If pruning the adapter list, keep only this many adapter sequences when pruning the list (plus any adapters that " +
+ "were tied with the adapters being kept).")
+ public int NUM_ADAPTERS_TO_KEEP = AdapterMarker.DEFAULT_NUM_ADAPTERS_TO_KEEP;
+
private static final Log log = Log.getInstance(MarkIlluminaAdapters.class);
// Stock main method
@@ -145,6 +158,12 @@ public class MarkIlluminaAdapters extends CommandLineProgram {
final ProgressLogger progress = new ProgressLogger(log, 1000000, "Read");
final SAMRecordIterator iterator = in.iterator();
+ final AdapterMarker adapterMarker = new AdapterMarker(ADAPTER_TRUNCATION_LENGTH, adapters).
+ setMaxPairErrorRate(MAX_ERROR_RATE_PE).setMinPairMatchBases(MIN_MATCH_BASES_PE).
+ setMaxSingleEndErrorRate(MAX_ERROR_RATE_SE).setMinSingleEndMatchBases(MIN_MATCH_BASES_SE).
+ setNumAdaptersToKeep(NUM_ADAPTERS_TO_KEEP).
+ setThresholdForSelectingAdaptersToKeep(PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN);
+
while (iterator.hasNext()) {
final SAMRecord rec = iterator.next();
final SAMRecord rec2 = rec.getReadPairedFlag() && iterator.hasNext() ? iterator.next() : null;
@@ -181,10 +200,10 @@ public class MarkIlluminaAdapters extends CommandLineProgram {
throw new PicardException("Two reads with same name but not correctly marked as 1st/2nd of pair: " + rec.getReadName());
}
- ClippingUtility.adapterTrimIlluminaPairedReads(first, second, MIN_MATCH_BASES_PE, MAX_ERROR_RATE_PE, adapters);
+ adapterMarker.adapterTrimIlluminaPairedReads(first, second);
}
else {
- ClippingUtility.adapterTrimIlluminaSingleRead(rec, MIN_MATCH_BASES_SE, MAX_ERROR_RATE_SE, adapters);
+ adapterMarker.adapterTrimIlluminaSingleRead(rec);
}
// Then output the records, update progress and metrics
diff --git a/src/java/net/sf/picard/illumina/parser/BclData.java b/src/java/net/sf/picard/illumina/parser/BclData.java
new file mode 100644
index 0000000..753dce0
--- /dev/null
+++ b/src/java/net/sf/picard/illumina/parser/BclData.java
@@ -0,0 +1,30 @@
+package net.sf.picard.illumina.parser;
+
+/** A class that implements the IlluminaData interfaces provided by this parser
+ * One BclData object is returned to IlluminaDataProvider per cluster and each
+ * first level array in bases and qualities represents a single read in that
+ * cluster */
+public class BclData implements BaseData, QualityData {
+ public final byte [][] bases;
+ public final byte [][] qualities;
+
+ public BclData(final int[] outputLengths) {
+ bases = new byte[outputLengths.length][];
+ qualities = new byte[outputLengths.length][];
+
+ for(int i = 0; i < outputLengths.length; i++) {
+ bases[i] = new byte[outputLengths[i]];
+ qualities[i] = new byte[outputLengths[i]];
+ }
+ }
+
+ @Override
+ public byte[][] getBases() {
+ return bases;
+ }
+
+ @Override
+ public byte[][] getQualities() {
+ return qualities;
+ }
+}
diff --git a/src/java/net/sf/picard/illumina/parser/BclParser.java b/src/java/net/sf/picard/illumina/parser/BclParser.java
index 81ba506..4c9941e 100644
--- a/src/java/net/sf/picard/illumina/parser/BclParser.java
+++ b/src/java/net/sf/picard/illumina/parser/BclParser.java
@@ -30,6 +30,7 @@ import net.sf.samtools.util.CloseableIterator;
import java.io.File;
import java.util.Collections;
+import java.util.List;
import java.util.NoSuchElementException;
import java.util.Set;
@@ -40,18 +41,19 @@ import static net.sf.samtools.util.CollectionUtil.makeSet;
* segmented based on these lengths. The only client of this class should be IlluminaDataProvider and an test classes. See BclReader for
* more information on BclFiles. BclParser provides support for reading BaseCalls and QualityScores.
*/
-class BclParser extends PerTilePerCycleParser<BclData>{
+class BclParser extends PerTileCycleParser<BclData> {
private static final int EAMSS_M2_GE_THRESHOLD = 30;
private static final int EAMSS_S1_LT_THRESHOLD = 15; //was 15
public static final byte MASKING_QUALITY = (byte) 0x02;
private static final Set<IlluminaDataType> SUPPORTED_TYPES = Collections.unmodifiableSet(makeSet(IlluminaDataType.BaseCalls, IlluminaDataType.QualityScores));
-
+
protected final BclQualityEvaluationStrategy bclQualityEvaluationStrategy;
private final boolean applyEamssFilter;
public BclParser(final File directory, final int lane, final CycleIlluminaFileMap tilesToCycleFiles, final OutputMapping outputMapping, final BclQualityEvaluationStrategy bclQualityEvaluationStrategy) {
this(directory, lane, tilesToCycleFiles, outputMapping, true, bclQualityEvaluationStrategy);
+ this.initialize();
}
public BclParser(final File directory, final int lane, final CycleIlluminaFileMap tilesToCycleFiles, final OutputMapping outputMapping, final boolean applyEamssFilter, final BclQualityEvaluationStrategy bclQualityEvaluationStrategy) {
@@ -61,56 +63,21 @@ class BclParser extends PerTilePerCycleParser<BclData>{
this.initialize();
}
- /** Create the BclData object segmented by the given outputLengths */
- @Override
- protected BclData makeData(final int[] outputLengths) {
- return new BclData(outputLengths);
- }
-
/**
- * Allow for overriding in derived classes.
- */
- protected CloseableIterator<BclReader.BclValue> makeReader(final File file, final int cycle, final int tileNumber) {
- return BclReader.make(file, bclQualityEvaluationStrategy);
- }
-
- /** Create a Bcl parser for an individual cycle and wrap it with the CycleFileParser interface which populates
+ * Create a Bcl parser for an individual cycle and wrap it with the CycleFilesParser interface which populates
* the correct cycle in BclData.
- * @param file The file to parse
- * @param cycle The cycle that file represents
- * @return A CycleFileParser that populates a BclData object with data for a single cycle
+ *
+ * @param files The files to parse.
+ * @return A CycleFilesParser that populates a BclData object with data for a single cycle
*/
@Override
- protected CycleFileParser<BclData> makeCycleFileParser(final File file, final int cycle, final int tileNumber) {
- return new CycleFileParser<BclData>(){
- final OutputMapping.TwoDIndex cycleOutputIndex = outputMapping.getOutputIndexForCycle(cycle);
- final CloseableIterator<BclReader.BclValue> reader = makeReader(file, cycle, tileNumber);
-
- final int majorIndex = cycleOutputIndex.majorIndex;
- final int minorIndex = cycleOutputIndex.minorIndex;
-
- @Override
- public void close() {
- reader.close();
- }
-
- @Override
- public void next(final BclData ild) {
- if(!hasNext()) {
- throw new NoSuchElementException();
- }
-
- final BclReader.BclValue value = reader.next();
- ild.bases[majorIndex][minorIndex] = value.base;
- ild.qualities[majorIndex][minorIndex] = value.quality;
- }
+ protected CycleFilesParser<BclData> makeCycleFileParser(final List<File> files) {
+ return new BclDataCycleFileParser(files);
+ }
- @Override
- public boolean hasNext() {
- try { return reader.hasNext(); }
- catch (final NullPointerException npe) { return false; }
- }
- };
+ @Override
+ public void initialize() {
+ seekToTile(currentTile);
}
@Override
@@ -118,17 +85,16 @@ class BclParser extends PerTilePerCycleParser<BclData>{
return SUPPORTED_TYPES;
}
-
@Override
public BclData next() {
final BclData bclData = super.next();
- final byte [][] bases = bclData.bases;
- final byte [][] qualities = bclData.qualities;
+ final byte[][] bases = bclData.getBases();
+ final byte[][] qualities = bclData.getQualities();
//first run EAMSS
if (this.applyEamssFilter) {
- for(int i = 0; i < bases.length; i++) {
+ for (int i = 0; i < bases.length; i++) {
runEamssForReadInPlace(bases[i], qualities[i]);
}
}
@@ -140,14 +106,14 @@ class BclParser extends PerTilePerCycleParser<BclData>{
* EAMSS is an Illumina Developed Algorithm for detecting reads whose quality has deteriorated towards
* their end and revising the quality to the masking quality (2) if this is the case. This algorithm
* works as follows (with one exception):
- *
+ * <p/>
* Start at the end (high indices, at the right below) of the read and calculate an EAMSS tally at each
* location as follow:
* if(quality[i] < 15) tally += 1
* if(quality[i] >= 15 and < 30) tally = tally
* if(quality[i] >= 30) tally -= 2
- *
- *
+ * <p/>
+ * <p/>
* For each location, keep track of this tally (e.g.)
* Read Starts at <- this end
* Cycle: 1 2 3 4 5 6 7 8 9
@@ -155,138 +121,139 @@ class BclParser extends PerTilePerCycleParser<BclData>{
* Qualities: 32 32 16 15 8 10 32 2 2
* Cycle Score: -2 -2 0 0 1 1 -2 1 1 //The EAMSS Score determined for this cycle alone
* EAMSS TALLY: 0 0 2 2 2 1 0 2 1
- * X - Earliest instance of Max-Score
- *
+ * X - Earliest instance of Max-Score
+ * <p/>
* You must keep track of the maximum EAMSS tally (in this case 2) and the earliest(lowest) cycle at which
* it occurs. If and only if, the max EAMSS tally >= 1 then from there until the end(highest cycle) of the
* read reassign these qualities as 2 (the masking quality). The output qualities would therefore be
* transformed from:
- *
+ * <p/>
* Original Qualities: 32 32 16 15 8 10 32 2 2 to
* Final Qualities: 32 32 2 2 2 2 2 2 2
- * X - Earliest instance of max-tally/end of masking
- *
+ * X - Earliest instance of max-tally/end of masking
+ * <p/>
* IMPORTANT:
* The one exception is: If the max EAMSS Tally is preceded by a long string of G basecalls (10 or more, with a single basecall exception per10 bases)
* then the masking continues to the beginning of that string of G's. E.g.:
- *
+ * <p/>
* Cycle: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
* Bases: C T A C A G A G G G G G G G G C A T
* Qualities: 30 22 26 27 28 30 7 34 20 19 38 15 32 32 10 4 2 5
* Cycle Score: -2 0 0 0 0 -2 1 -2 0 0 -2 0 -2 -2 1 1 1 1
* EAMSS TALLY: -2 -5 -5 -5 -5 -5 -3 -4 -2 -2 -2 0 0 2 4 3 2 1
- * X- Earliest instance of Max-Tally
- *
+ * X- Earliest instance of Max-Tally
+ * <p/>
* Resulting Transformation:
* Bases: C T A C A G A G G G G G G G G C A T
* Original Qualities: 30 22 26 27 28 30 7 34 20 19 38 15 32 32 10 4 2 5
* Final Qualities: 30 22 26 27 28 2 2 2 2 2 2 2 2 2 2 2 2 2
- * X- Earliest instance of Max-Tally
- * X - Start of EAMSS masking due to G-Run
- *
+ * X- Earliest instance of Max-Tally
+ * X - Start of EAMSS masking due to G-Run
+ * <p/>
* To further clarify the exception rule here are a few examples:
* A C G A C G G G G G G G G G G G G G G G G G G G G A C T
- * X - Earliest instance of Max-Tally
- * X - Start of EAMSS masking (with a two base call jump because we have 20 bases in the run already)
- *
+ * X - Earliest instance of Max-Tally
+ * X - Start of EAMSS masking (with a two base call jump because we have 20 bases in the run already)
+ * <p/>
* T T G G A G G G G G G G G G G G G G G G G G G A G A C T
- * X - Earliest instance of Max-Tally
- * X - We can skip this A as well as the earlier A because we have 20 or more bases in the run already
- * X - Start of EAMSS masking (with a two base call jump because we have 20 bases in the run)
- *
+ * X - Earliest instance of Max-Tally
+ * X - We can skip this A as well as the earlier A because we have 20 or more bases in the run already
+ * X - Start of EAMSS masking (with a two base call jump because we have 20 bases in the run)
+ * <p/>
* T T G G G A A G G G G G G G G G G G G G G G G G G T T A T
- * X - Earliest instance of Max-Tally
- * X X - WE can skip these bases because the first A counts as the first skip and as far as the length of the string of G's is
- * concerned, these are both counted like G's
- * X - This A is the 20th base in the string of G's and therefore can be skipped
- * X - Note that the A's previous to the G's are only included because there are G's further on that are within the number
- * of allowable exceptions away (i.e. 2 in this instance), if there were NO G's after the A's you CANNOT count the A's
- * as part of the G strings (even if no exceptions have previously occured) In other words, the end of the string of G's
- * MUST end in a G not an "exception"
- *
+ * X - Earliest instance of Max-Tally
+ * X X - WE can skip these bases because the first A counts as the first skip and as far as the length of the string of G's is
+ * concerned, these are both counted like G's
+ * X - This A is the 20th base in the string of G's and therefore can be skipped
+ * X - Note that the A's previous to the G's are only included because there are G's further on that are within the number
+ * of allowable exceptions away (i.e. 2 in this instance), if there were NO G's after the A's you CANNOT count the A's
+ * as part of the G strings (even if no exceptions have previously occured) In other words, the end of the string of G's
+ * MUST end in a G not an "exception"
+ * <p/>
* However, if the max-tally occurs to the right of the run of Gs then this is still part of the string of G's but does count towards
* the number of exceptions allowable
* (e.g.)
* T T G G G G G G G G G G A C G
- * X - Earliest instance of Max-tally
- * The first index CAN be considered as an exception, the above would be masked to
- * the following point:
- * T T G G G G G G G G G G A C G
- * X - End of EAMSS masking due to G-Run
- *
+ * X - Earliest instance of Max-tally
+ * The first index CAN be considered as an exception, the above would be masked to
+ * the following point:
+ * T T G G G G G G G G G G A C G
+ * X - End of EAMSS masking due to G-Run
+ * <p/>
* To sum up the final points, a string of G's CAN START with an exception but CANNOT END in an exception.
*
- *
- * @param bases Bases for a single read in the cluster ( not the entire cluster )
+ * @param bases Bases for a single read in the cluster ( not the entire cluster )
* @param qualities Qualities for a single read in the cluster ( not the entire cluster )
*/
- protected static void runEamssForReadInPlace(final byte [] bases, final byte [] qualities) {
+ protected static void runEamssForReadInPlace(final byte[] bases, final byte[] qualities) {
int eamssTally = 0;
int maxTally = Integer.MIN_VALUE;
int indexOfMax = -1;
- for(int i = bases.length - 1; i >= 0; i--) {
+ for (int i = bases.length - 1; i >= 0; i--) {
final int quality = (0xff & qualities[i]);
- if(quality >= EAMSS_M2_GE_THRESHOLD) {
+ if (quality >= EAMSS_M2_GE_THRESHOLD) {
eamssTally -= 2;
- } else if(quality < EAMSS_S1_LT_THRESHOLD) {
+ } else if (quality < EAMSS_S1_LT_THRESHOLD) {
eamssTally += 1;
}
- if(eamssTally >= maxTally) {
+ if (eamssTally >= maxTally) {
indexOfMax = i;
maxTally = eamssTally;
}
}
- if(maxTally >= 1) {
+ if (maxTally >= 1) {
int numGs = 0;
int exceptions = 0;
- for(int i = indexOfMax; i >= 0; i--) {
- if(bases[i] == 'G') {
+ for (int i = indexOfMax; i >= 0; i--) {
+ if (bases[i] == 'G') {
++numGs;
} else {
- Integer skip = skipBy(i, numGs, exceptions, bases);
- if(skip != null) {
+ final Integer skip = skipBy(i, numGs, exceptions, bases);
+ if (skip != null) {
exceptions += skip;
- numGs += skip;
- i -= (skip-1);
+ numGs += skip;
+ i -= (skip - 1);
} else {
break;
}
}
}
- if(numGs >= 10) {
- indexOfMax = (indexOfMax+1) - numGs;
+ if (numGs >= 10) {
+ indexOfMax = (indexOfMax + 1) - numGs;
}
-
- for(int i = indexOfMax; i < qualities.length; i++) {
+
+ for (int i = indexOfMax; i < qualities.length; i++) {
qualities[i] = MASKING_QUALITY;
}
}
}
- /** Determine whether or not the base at index is part of a skippable section in a run of G's, if so
+ /**
+ * Determine whether or not the base at index is part of a skippable section in a run of G's, if so
* return the number of bases that the section is composed of.
- * @param index Current index, which should be the index of a non-'G' base
- * @param numGs The number of bases in the current string of G's for this read
+ *
+ * @param index Current index, which should be the index of a non-'G' base
+ * @param numGs The number of bases in the current string of G's for this read
* @param prevExceptions The number of exceptions previously detected in this string by this method
- * @param bases The bases of this read
+ * @param bases The bases of this read
* @return If we have not reached our exception limit (1/every 10bases) and a G is within exceptionLimit(numGs/10)
* indices before the current index then return index - (index of next g), else return null Null indicates this is
* NOT a skippable region, if we run into index 0 without finding a g then NULL is also returned
*/
- private static Integer skipBy(int index, int numGs, final int prevExceptions, final byte [] bases) {
+ private static Integer skipBy(final int index, final int numGs, final int prevExceptions, final byte[] bases) {
Integer skip = null;
- for(int backup = 1; backup <= index; backup++) {
+ for (int backup = 1; backup <= index; backup++) {
final int exceptionLimit = Math.max((numGs + backup) / 10, 1);
- if(prevExceptions + backup > exceptionLimit) {
+ if (prevExceptions + backup > exceptionLimit) {
break;
}
- if(bases[index - backup] == 'G') {
+ if (bases[index - backup] == 'G') {
skip = backup;
break;
}
@@ -294,33 +261,35 @@ class BclParser extends PerTilePerCycleParser<BclData>{
return skip;
}
-}
-/** A class that implements the IlluminaData interfaces provided by this parser
- * One BclData object is returned to IlluminaDataProvider per cluster and each
- * first level array in bases and qualities represents a single read in that
- * cluster */
-class BclData implements BaseData, QualityData {
- public final byte [][] bases;
- public final byte [][] qualities;
+ private class BclDataCycleFileParser implements CycleFilesParser<BclData> {
+ final CloseableIterator<BclData> reader;
- public BclData(final int[] outputLengths) {
- bases = new byte[outputLengths.length][];
- qualities = new byte[outputLengths.length][];
+ public BclDataCycleFileParser(final List<File> files) {
+ reader = new BclReader(files, outputMapping.getOutputReadLengths(),
+ bclQualityEvaluationStrategy, false);
+ }
- for(int i = 0; i < outputLengths.length; i++) {
- bases[i] = new byte[outputLengths[i]];
- qualities[i] = new byte[outputLengths[i]];
+ @Override
+ public void close() {
+ reader.close();
}
- }
- @Override
- public byte[][] getBases() {
- return bases;
- }
+ @Override
+ public BclData next() {
+ if (!hasNext()) {
+ throw new NoSuchElementException();
+ }
+ return reader.next();
+ }
- @Override
- public byte[][] getQualities() {
- return qualities;
+ @Override
+ public boolean hasNext() {
+ try {
+ return reader.hasNext();
+ } catch (final NullPointerException npe) {
+ return false;
+ }
+ }
}
}
\ No newline at end of file
diff --git a/src/java/net/sf/picard/illumina/parser/CifParser.java b/src/java/net/sf/picard/illumina/parser/CifParser.java
deleted file mode 100644
index b202d99..0000000
--- a/src/java/net/sf/picard/illumina/parser/CifParser.java
+++ /dev/null
@@ -1,79 +0,0 @@
-/*
- * The MIT License
- *
- * Copyright (c) 2011 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
-package net.sf.picard.illumina.parser;
-
-import net.sf.samtools.util.CollectionUtil;
-
-import java.io.File;
-import java.util.Collections;
-import java.util.Set;
-
-/**
- * CifParser takes a directory, lane, a map of tiles to Cycled file iterators, and a list of desired lengths for the
- * output FourChannelIntensityData and allows iteration over the clusters of all the provided tiles in the given lane.
- *
- * Note: Files passed by CycledIlluminaFileMap are not checked for proper extension (e.g. cif or cnf) so a CifParser
- * can read a map to cnf files and put it in a RawIntensityData, you've been warned!
- *
- * @author jburke at broadinstitute.org
- */
-class CifParser extends IlluminaIntensityParser<RawIntensityData> {
- private static final Set<IlluminaDataType> SupportedTypes = Collections.unmodifiableSet(CollectionUtil.makeSet(IlluminaDataType.RawIntensities));
- /**
- * @param directory BaseCallsDir or analogue directory containing folders like L001/C1.1/s_1_1.cif
- * @param lane The lane being analyzed
- * @param tilesToCycleFiles A map of tile -> CycledFilesIterator for each tile to consider
- * by RawIntensityData
- */
- public CifParser(final File directory, final int lane, final CycleIlluminaFileMap tilesToCycleFiles, final OutputMapping outputMapping) {
- super(directory, lane, tilesToCycleFiles, outputMapping);
- }
-
- /**
- * Populate the RawIntensityData from a short value and input indices for a cycle
- * @param rawIntensityData RawIntensityData to populate
- * @param index And index to the correct FCID and the correct index in that FCID
- * @param channel A,C,G, or T channel to populate
- * @param intensity
- */
- @Override
- protected void addIntensityToIlluminaData(final RawIntensityData rawIntensityData, final OutputMapping.TwoDIndex index, final IntensityChannel channel, final short intensity) {
- rawIntensityData.getRawIntensities()[index.majorIndex].getChannel(channel)[index.minorIndex] = intensity;
- }
-
- @Override
- protected RawIntensityData intensityToIlluminaData(final FourChannelIntensityData[] fcids) {
- return new RawIntensityData() {
- @Override
- public FourChannelIntensityData[] getRawIntensities() {
- return fcids;
- }
- };
- }
-
- @Override
- public Set<IlluminaDataType> supportedTypes() {
- return SupportedTypes;
- }
-}
diff --git a/src/java/net/sf/picard/illumina/parser/CnfParser.java b/src/java/net/sf/picard/illumina/parser/CnfParser.java
deleted file mode 100644
index 3b33359..0000000
--- a/src/java/net/sf/picard/illumina/parser/CnfParser.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * The MIT License
- *
- * Copyright (c) 2011 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
-package net.sf.picard.illumina.parser;
-
-import net.sf.samtools.util.CollectionUtil;
-
-import java.io.File;
-import java.util.Collections;
-import java.util.Set;
-
-/**
- * CnfParser takes a directory, lane, a map of tiles to Cycled file iterators, and a list of desired lengths for the
- * output FourChannelIntensityData and allows iteration over the clusters of all the provided tiles in the given lane.
- *
- * Note: Files passed by CycledIlluminaFileMap are not checked for proper extension (e.g. cif or cnf) so a CnfParser
- * can read a map to cif files and put it in the a NoiseData, you've been warned!
- *
- * @author Jonathan Burke
- */
-class CnfParser extends IlluminaIntensityParser<NoiseData> {
- private static final Set<IlluminaDataType> SupportedTypes = Collections.unmodifiableSet(CollectionUtil.makeSet(IlluminaDataType.Noise));
-
- public CnfParser(final File directory, final int lane, final CycleIlluminaFileMap tilesToCycleFiles, final OutputMapping outputMapping) {
- super(directory, lane, tilesToCycleFiles, outputMapping);
- }
-
- @Override
- protected void addIntensityToIlluminaData(NoiseData illData, final OutputMapping.TwoDIndex index, IntensityChannel channel, short intensity) {
- illData.getNoise()[index.majorIndex].getChannel(channel)[index.minorIndex] = intensity;
- }
-
- @Override
- protected NoiseData intensityToIlluminaData(final FourChannelIntensityData[] fcids) {
- return new NoiseData() {
- @Override
- public FourChannelIntensityData[] getNoise() {
- return fcids;
- }
- };
- }
-
- @Override
- public Set<IlluminaDataType> supportedTypes() {
- return SupportedTypes;
- }
-}
diff --git a/src/java/net/sf/picard/illumina/parser/CycleIlluminaFileMap.java b/src/java/net/sf/picard/illumina/parser/CycleIlluminaFileMap.java
index a3deae7..8fa4c58 100644
--- a/src/java/net/sf/picard/illumina/parser/CycleIlluminaFileMap.java
+++ b/src/java/net/sf/picard/illumina/parser/CycleIlluminaFileMap.java
@@ -24,177 +24,52 @@
package net.sf.picard.illumina.parser;
import net.sf.picard.PicardException;
-import net.sf.samtools.util.StringUtil;
import java.io.File;
-import java.util.*;
+import java.util.List;
+import java.util.Set;
+import java.util.TreeMap;
/**
- * A sorted map of tiles to Iterators, where each iterator traverses the cycle files for the given lane/tile.
+ * For per cycle files. Maps a Cycle -> Tile -> List<File>
+ *
* @author jburke at broadinstitute.org
*/
-class CycleIlluminaFileMap extends TreeMap<Integer, CycleFilesIterator> {
- /** Return a CycleIlluminaFileMap with only the tiles listed and all of the cycles provided, throws an exception if it does not contain any of the tiles listed
+class CycleIlluminaFileMap extends TreeMap<Integer, IlluminaFileMap> {
+ /**
+ * Return a CycleIlluminaFileMap with only the tiles listed and all of the cycles provided.
* Important NOTE: this DOES NOT eliminate cycles from the cycles parameter passed in that are missing in the cyclesFileIterator of any given lane in the CycleIlluminaFileMap
- * */
- public CycleIlluminaFileMap keep(List<Integer> tilesToKeep, final int [] cycles) {
- if(tilesToKeep == null) {
- tilesToKeep = new ArrayList<Integer>(this.keySet());
- }
-
+ */
+ public CycleIlluminaFileMap keep(final List<Integer> tilesToKeep, final Set<Integer> cycles) {
final CycleIlluminaFileMap ciMap = new CycleIlluminaFileMap();
- for(final Integer tile : tilesToKeep) {
- final CycleFilesIterator template = this.get(tile);
- if(template != null) {
- ciMap.put(tile, new CycleFilesIterator(this.get(tile), cycles));
+
+ if (cycles != null) {
+ for (final int cycle : cycles) {
+ final IlluminaFileMap template = this.get(cycle);
+ if (template != null) {
+ ciMap.put(cycle, template.keep(tilesToKeep));
+ }
}
}
+
return ciMap;
}
/**
* Assert that this map has an iterator for all of the expectedTiles and each iterator has expectedCycles number
* of files. Also, assert that each cycle file for a given tile is the same size
- * @param expectedTiles A list of tiles that should be in this map
+ *
+ * @param expectedTiles A list of tiles that should be in this map
* @param expectedCycles The total number of files(cycles) that should be in each CycledFilesIterator
*/
- public void assertValid(final List<Integer> expectedTiles, final int [] expectedCycles) {
- if(size() != expectedTiles.size()) {
- throw new PicardException("Expected CycledIlluminaFileMap to contain " + expectedTiles + " tiles but only " + size() + " were found!");
- }
-
- File curFile = null;
-
- for (final int tile : expectedTiles) {
- get(tile).assertValid(expectedCycles);
- }
- }
-
- /**
- * All files in a CycleFileMap should have a cycle directory (at this point in time). Return the filePath with the cycle
- * in the cycle directory incremented by 1.
- * @param cycleFile The cycleFile for a given tile/cycle
- * @return A cycleFile with the same name but a cycleDir one greater than cycleFile
- */
- public static File incrementCycleCount(final File cycleFile) {
- final File cycleDir = cycleFile.getParentFile();
- final int cycle = Integer.parseInt(cycleDir.getName().substring(1, cycleDir.getName().lastIndexOf(".")));
- return new File(cycleDir.getParentFile(), "C" + cycle + ".1" + File.separator + cycleFile.getName());
- }
-
- public static String remainingCyclesToString(final CycleFilesIterator cfi) {
- String cycles = "";
- if(cfi.hasNext()) {
- cycles += cfi.getNextCycle();
- cfi.next();
+ public void assertValid(final List<Integer> expectedTiles, final int[] expectedCycles) {
+ if (size() != expectedCycles.length) {
+ throw new PicardException("Expected CycledIlluminaFileMap to contain " + expectedCycles.length + " cycles but only " + size() + " were found!");
}
-
- while(cfi.hasNext()) {
- cycles += ", " + cfi.getNextCycle();
- cfi.next();
+ if (this.firstEntry().getValue().size() != expectedTiles.size()) {
+ throw new PicardException("Expected CycledIlluminaFileMap to contain " + expectedTiles.size()
+ + " tiles but only " + this.firstEntry().getValue().size() + " were found!");
}
-
- return cycles;
- }
-}
-
-/**
- * Given a lane directory, lane, tile number, and file extension get provide an iterator over files in the following order
- * <LaneDir>/<nextCycle>.1/s_<lane>_<tile>.<fileExt>
- * In other words iterate through the different cycle directory and find the file for the current cycle with the
- * given file extension while lane/tile stay the same. Stop if the next file does not exist.
- */
- class CycleFilesIterator implements Iterator<File>, Iterable<File> {
- protected final File parentDir;
- protected final int lane;
- private final int tile;
- protected final String fileExt;
- protected final int [] cycles;
- protected int nextCycleIndex;
-
- public CycleFilesIterator(final File laneDir, final int lane, final int tile, final int [] cycles, final String fileExt) {
- this.parentDir = laneDir;
- this.lane = lane;
- this.tile = tile;
- this.fileExt = fileExt;
- this.cycles = cycles;
- this.nextCycleIndex = 0;
}
- CycleFilesIterator(final CycleFilesIterator template, final int [] cycles) {
- this(template.parentDir, template.lane, template.tile, (cycles != null) ? cycles : template.cycles, template.fileExt);
- }
-
- public void reset() {
- this.nextCycleIndex = 0;
- }
-
- @Override
- public boolean hasNext() {
- return nextCycleIndex < cycles.length;
- }
-
- @Override
- public File next() {
- if (!hasNext()) {
- throw new NoSuchElementException(summarizeIterator());
- }
-
- final File curFile = getCurrentFile();
-
- nextCycleIndex++;
- return curFile;
- }
-
- /** Allow for overriding */
- protected File getCurrentFile() {
- return getFileForCycle(cycles[nextCycleIndex]);
- }
-
- /** Allow for overriding */
- protected File getFileForCycle(final int cycle) {
- final File cycleDir = new File(parentDir, "C" + cycle + ".1");
- return new File(cycleDir, "s_" + lane + "_" + tile + fileExt);
- }
-
- public int getNextCycle() {
- return cycles[nextCycleIndex];
- }
-
- private String summarizeIterator() {
- String cyclesSummary = "";
- if(cycles.length > 0) {
- cyclesSummary = String.valueOf(cycles[0]);
- for(int i = 1; i < cycles.length; i++) {
- cyclesSummary += ", " + String.valueOf(cycles[i]);
- }
- }
-
- return " Parent dir (" + parentDir.getAbsolutePath() + ")" +
- " Lane (" + lane + ") Tile (" + tile + ") FileExt(" + fileExt + ")" +
- " CycleIndex (" + nextCycleIndex + ")" + "Cycles(" + cyclesSummary + ")";
- }
-
- @Override
- public void remove() {
- throw new UnsupportedOperationException("Remove is not supported by " + CycleFilesIterator.class.getName());
- }
-
- @Override
- public Iterator<File> iterator() {
- return this;
- }
-
- public void assertValid(final int[] expectedCycles) {
- if (!Arrays.equals(cycles, expectedCycles)) {
- // TODO: Make more informative if necessary
- throw new PicardException(summarizeIterator() + " does not have expected cycles");
- }
- for (final int cycle : expectedCycles) {
- final File file = getFileForCycle(cycle);
- if (!file.exists()) {
- throw new PicardException(file.getAbsolutePath() + " does not exist for " + summarizeIterator());
- }
- }
- }
}
diff --git a/src/java/net/sf/picard/illumina/parser/IlluminaDataProvider.java b/src/java/net/sf/picard/illumina/parser/IlluminaDataProvider.java
index 29d63ff..837cfcc 100644
--- a/src/java/net/sf/picard/illumina/parser/IlluminaDataProvider.java
+++ b/src/java/net/sf/picard/illumina/parser/IlluminaDataProvider.java
@@ -27,7 +27,10 @@ package net.sf.picard.illumina.parser;
import net.sf.picard.PicardException;
import java.io.File;
-import java.util.*;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.NoSuchElementException;
+import java.util.Set;
/**
* Parse various formats and versions of Illumina Basecall files, and use them the to populate
@@ -36,23 +39,24 @@ import java.util.*;
*
* @author jburke at broadinstitute.org
*/
-public class IlluminaDataProvider implements Iterator<ClusterData>, Iterable<ClusterData>{
+public class IlluminaDataProvider implements Iterator<ClusterData>, Iterable<ClusterData> {
/** contains QSeqs, bcls, or other Illumina file types that will be parsed by this class */
private final File basecallDirectory; //These two are for error reporting only
private final int lane;
/** A list of parsers (already initialized) that should output data in a format consistent with readStructure */
- private final IlluminaParser [] parsers;
+ private final IlluminaParser[] parsers;
/**
* for each parser in this.parsers there is an array of IlluminaDataTypes that specifies what datatypes that parser is providing in
* this particular run. A parser may be able to provide data types which may not be listed here because client code may not
- * have specified these data types*/
- private final IlluminaDataType [][] dataTypes;
+ * have specified these data types
+ */
+ private final IlluminaDataType[][] dataTypes;
- /** Calculated once, outputReadTypes describes the type of read data for each ReadData that will be found in ouput ClusterData objects */
- private final ReadType [] outputReadTypes;
+ /** Calculated once, outputReadTypes describes the type of read data for each ReadData that will be found in output ClusterData objects */
+ private final ReadType[] outputReadTypes;
/** Number of reads in each ClusterData */
private final int numReads;
@@ -60,8 +64,9 @@ public class IlluminaDataProvider implements Iterator<ClusterData>, Iterable<Clu
/**
* Create an IlluminaDataProvider given a map of parsersToDataTypes for particular file formats. Compute once the miscellaneous data for the
* run that will be passed to each ClusterData.
+ *
* @param basecallDirectory For error reporting only.
- * @param lane For error reporting only.
+ * @param lane For error reporting only.
*/
IlluminaDataProvider(final OutputMapping outputMapping,
final Map<IlluminaParser, Set<IlluminaDataType>> parsersToDataTypes,
@@ -71,14 +76,14 @@ public class IlluminaDataProvider implements Iterator<ClusterData>, Iterable<Clu
numReads = outputMapping.numOutputReads();
final int numParsers = parsersToDataTypes.size();
- if(numParsers == 0) {
+ if (numParsers == 0) {
throw new PicardException("There were 0 parsers passed to IlluminaDataProvider!");
}
int i = 0;
parsers = new IlluminaParser[numParsers];
dataTypes = new IlluminaDataType[numParsers][];
- for(final Map.Entry<IlluminaParser, Set<IlluminaDataType>> pToD : parsersToDataTypes.entrySet()) {
+ for (final Map.Entry<IlluminaParser, Set<IlluminaDataType>> pToD : parsersToDataTypes.entrySet()) {
parsers[i] = pToD.getKey();
final Set<IlluminaDataType> dts = pToD.getValue();
dataTypes[i] = new IlluminaDataType[dts.size()];
@@ -87,7 +92,7 @@ public class IlluminaDataProvider implements Iterator<ClusterData>, Iterable<Clu
this.outputReadTypes = new ReadType[numReads];
i = 0;
- for(final ReadDescriptor rd : outputMapping.getOutputDescriptors()) {
+ for (final ReadDescriptor rd : outputMapping.getOutputDescriptors()) {
outputReadTypes[i++] = rd.type;
}
}
@@ -97,9 +102,9 @@ public class IlluminaDataProvider implements Iterator<ClusterData>, Iterable<Clu
*/
public boolean hasNext() {
final boolean more = parsers[0].hasNext();
- if(!more) {
- for(int i = 1; i < parsers.length; i++) {
- if(parsers[i].hasNext()) {
+ if (!more) {
+ for (int i = 1; i < parsers.length; i++) {
+ if (parsers[i].hasNext()) {
throw new PicardException("Unequal length Illumina files in " + basecallDirectory + ", lane " + lane + ". Failing parser: " + parsers[i].getClass().getName());
}
}
@@ -124,10 +129,10 @@ public class IlluminaDataProvider implements Iterator<ClusterData>, Iterable<Clu
//boundary the last cluster in the previous tile will have the wrong tile number
cluster.setTile(parsers[0].getTileOfNextCluster());
- for(int i = 0; i < parsers.length; i++) {
+ for (int i = 0; i < parsers.length; i++) {
final IlluminaData ilData = parsers[i].next();
- for(final IlluminaDataType ilDataType : dataTypes[i]) {
- switch(ilDataType) {
+ for (final IlluminaDataType ilDataType : dataTypes[i]) {
+ switch (ilDataType) {
case Position:
addData(cluster, (PositionalData) ilData);
break;
@@ -148,14 +153,6 @@ public class IlluminaDataProvider implements Iterator<ClusterData>, Iterable<Clu
addReadData(cluster, numReads, (QualityData) ilData);
break;
- case RawIntensities:
- addReadData(cluster, numReads, (RawIntensityData) ilData);
- break;
-
- case Noise:
- addReadData(cluster, numReads, (NoiseData) ilData);
- break;
-
default:
throw new PicardException("Unknown data type " + ilDataType + " requested by IlluminaDataProviderFactory");
}
@@ -173,7 +170,7 @@ public class IlluminaDataProvider implements Iterator<ClusterData>, Iterable<Clu
clusterData.setY(posData.getYCoordinate());
}
- private void addData(final ClusterData clusterData, final PfData pfData) {
+ private void addData(final ClusterData clusterData, final PfData pfData) {
clusterData.setPf(pfData.isPf());
}
@@ -182,29 +179,29 @@ public class IlluminaDataProvider implements Iterator<ClusterData>, Iterable<Clu
}
private void addReadData(final ClusterData clusterData, final int numReads, final BaseData baseData) {
- final byte [][] bases = baseData.getBases();
- for(int i = 0; i < numReads; i++) {
+ final byte[][] bases = baseData.getBases();
+ for (int i = 0; i < numReads; i++) {
clusterData.getRead(i).setBases(bases[i]);
}
}
private void addReadData(final ClusterData clusterData, final int numReads, final QualityData qualityData) {
- final byte [][] qualities = qualityData.getQualities();
- for(int i = 0; i < numReads; i++) {
+ final byte[][] qualities = qualityData.getQualities();
+ for (int i = 0; i < numReads; i++) {
clusterData.getRead(i).setQualities(qualities[i]);
}
}
private void addReadData(final ClusterData clusterData, final int numReads, final RawIntensityData rawIntensityData) {
final FourChannelIntensityData[] fcids = rawIntensityData.getRawIntensities();
- for(int i = 0; i < numReads; i++) {
+ for (int i = 0; i < numReads; i++) {
clusterData.getRead(i).setRawIntensities(fcids[i]);
}
}
private void addReadData(final ClusterData clusterData, final int numReads, final NoiseData noiseData) {
final FourChannelIntensityData[] fcids = noiseData.getNoise();
- for(int i = 0; i < numReads; i++) {
+ for (int i = 0; i < numReads; i++) {
clusterData.getRead(i).setNoise(fcids[i]);
}
}
@@ -215,7 +212,7 @@ public class IlluminaDataProvider implements Iterator<ClusterData>, Iterable<Clu
/** Jump so that the next record returned will be from the specified tile. */
public void seekToTile(final int oneBasedTileNumber) {
- for (final IlluminaParser parser: parsers) {
+ for (final IlluminaParser parser : parsers) {
parser.seekToTile(oneBasedTileNumber);
}
}
@@ -224,4 +221,10 @@ public class IlluminaDataProvider implements Iterator<ClusterData>, Iterable<Clu
public Iterator<ClusterData> iterator() {
return this;
}
+
+ public void close() {
+ for (final IlluminaParser parser : parsers) {
+ parser.close();
+ }
+ }
}
diff --git a/src/java/net/sf/picard/illumina/parser/IlluminaDataProviderFactory.java b/src/java/net/sf/picard/illumina/parser/IlluminaDataProviderFactory.java
index 4d3d3cf..10c2b22 100644
--- a/src/java/net/sf/picard/illumina/parser/IlluminaDataProviderFactory.java
+++ b/src/java/net/sf/picard/illumina/parser/IlluminaDataProviderFactory.java
@@ -24,23 +24,32 @@
package net.sf.picard.illumina.parser;
-import java.io.File;
-import java.util.*;
-
import net.sf.picard.PicardException;
+import net.sf.picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat;
import net.sf.picard.illumina.parser.readers.BclQualityEvaluationStrategy;
import net.sf.picard.util.Log;
-import net.sf.picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat;
import net.sf.samtools.util.StringUtil;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
import static net.sf.samtools.util.CollectionUtil.makeList;
import static net.sf.samtools.util.CollectionUtil.makeSet;
/**
* IlluminaDataProviderFactory accepts options for parsing Illumina data files for a lane and creates an
* IlluminaDataProvider, an iterator over the ClusterData for that lane, which utilizes these options.
- *
- *
+ * <p/>
+ * <p/>
* Note: Since we tend to use IlluminaDataProviderFactory in multithreaded environments (e.g. we call makeDataProvider
* in a different thread per tile in IlluminaBasecallsToSam). I've made it essentially immutable. makeDataProvider/getTiles
* are now idempotent (well as far as IlluminaDataProviderFactory is concerned, many file handles and other things are
@@ -53,38 +62,35 @@ import static net.sf.samtools.util.CollectionUtil.makeSet;
public class IlluminaDataProviderFactory {
private static final Log log = Log.getInstance(IlluminaDataProviderFactory.class);
- /** A map of data types to a list of file formats in the order in which we prefer those file types (E.g. we would rather parse Bcls before QSeqs, Locs files before Clocs files ...)
+ /**
+ * A map of data types to a list of file formats in the order in which we prefer those file types (E.g. we would rather parse Bcls before QSeqs, Locs files before Clocs files ...)
* We try to prefer data types that will be the fastest to parse/smallest in memory
* NOTE: In the code below, if Qseq is chosen to provide for ANY data type then it is used for ALL its data types (since we'll have to parse the entire line for each Qseq anyways)
- * */
+ */
private static final Map<IlluminaDataType, List<SupportedIlluminaFormat>> DATA_TYPE_TO_PREFERRED_FORMATS = new HashMap<IlluminaDataType, List<SupportedIlluminaFormat>>();
+
static {
/** For types found in Qseq, we prefer the NON-Qseq file formats first. However, if we end up using Qseqs then we use Qseqs for EVERY type it provides,
* see determineFormats
*/
- DATA_TYPE_TO_PREFERRED_FORMATS.put(IlluminaDataType.BaseCalls, makeList(
- SupportedIlluminaFormat.MultiTileBcl, SupportedIlluminaFormat.Bcl, SupportedIlluminaFormat.Qseq));
+ DATA_TYPE_TO_PREFERRED_FORMATS.put(IlluminaDataType.BaseCalls, makeList(
+ SupportedIlluminaFormat.MultiTileBcl, SupportedIlluminaFormat.Bcl));
DATA_TYPE_TO_PREFERRED_FORMATS.put(IlluminaDataType.QualityScores, makeList(
- SupportedIlluminaFormat.MultiTileBcl, SupportedIlluminaFormat.Bcl, SupportedIlluminaFormat.Qseq));
- DATA_TYPE_TO_PREFERRED_FORMATS.put(IlluminaDataType.PF, makeList(
- SupportedIlluminaFormat.MultiTileFilter, SupportedIlluminaFormat.Filter, SupportedIlluminaFormat.Qseq));
- DATA_TYPE_TO_PREFERRED_FORMATS.put(IlluminaDataType.Position, makeList(
- SupportedIlluminaFormat.MultiTileLocs, SupportedIlluminaFormat.Locs, SupportedIlluminaFormat.Clocs,
- SupportedIlluminaFormat.Pos, SupportedIlluminaFormat.Qseq));
-
- DATA_TYPE_TO_PREFERRED_FORMATS.put(IlluminaDataType.Barcodes, makeList(SupportedIlluminaFormat.Barcode));
- DATA_TYPE_TO_PREFERRED_FORMATS.put(IlluminaDataType.RawIntensities, makeList(SupportedIlluminaFormat.Cif));
- DATA_TYPE_TO_PREFERRED_FORMATS.put(IlluminaDataType.Noise, makeList(SupportedIlluminaFormat.Cnf));
+ SupportedIlluminaFormat.MultiTileBcl, SupportedIlluminaFormat.Bcl));
+ DATA_TYPE_TO_PREFERRED_FORMATS.put(IlluminaDataType.PF, makeList(
+ SupportedIlluminaFormat.MultiTileFilter, SupportedIlluminaFormat.Filter));
+ DATA_TYPE_TO_PREFERRED_FORMATS.put(IlluminaDataType.Position, makeList(
+ SupportedIlluminaFormat.MultiTileLocs, SupportedIlluminaFormat.Locs, SupportedIlluminaFormat.Clocs,
+ SupportedIlluminaFormat.Pos));
+
+ DATA_TYPE_TO_PREFERRED_FORMATS.put(IlluminaDataType.Barcodes, makeList(SupportedIlluminaFormat.Barcode));
}
// The following properties must be specified by caller.
- /** basecallDirectory holds QSeqs or bcls **/
+ /** basecallDirectory holds QSeqs or bcls * */
private final File basecallDirectory;
private final int lane;
- //rawIntensity directory is assumed to be the parent of basecallDirectory
- private final File intensitiesDirectory;
-
/**
* Whether or not to apply EAMSS filtering if parsing BCLs for the bases and quality scores.
*/
@@ -102,7 +108,7 @@ public class IlluminaDataProviderFactory {
private final List<Integer> availableTiles;
private final OutputMapping outputMapping;
- private final BclQualityEvaluationStrategy bclQualityEvaluationStrategy;
+ private final BclQualityEvaluationStrategy bclQualityEvaluationStrategy;
/**
* Create factory with the specified options, one that favors using QSeqs over all other files
@@ -112,13 +118,12 @@ public class IlluminaDataProviderFactory {
* @param readStructure The read structure to which output clusters will conform. When not using QSeqs, EAMSS masking(see BclParser) is run on individual reads as found in the readStructure, if
* the readStructure specified does not match the readStructure implied by the sequencer's output than the quality scores output may differ than what would be found
* in a run's QSeq files
- * @param dataTypesArg Which data types to read
+ * @param dataTypesArg Which data types to read
*/
public IlluminaDataProviderFactory(final File basecallDirectory, final int lane, final ReadStructure readStructure,
final BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
final IlluminaDataType... dataTypesArg) {
- this.basecallDirectory = basecallDirectory;
- this.intensitiesDirectory = basecallDirectory.getParentFile();
+ this.basecallDirectory = basecallDirectory;
this.bclQualityEvaluationStrategy = bclQualityEvaluationStrategy;
this.lane = lane;
@@ -141,22 +146,24 @@ public class IlluminaDataProviderFactory {
//find if we have any IlluminaDataType with NO available file formats and, if any exist, throw an exception
final Set<IlluminaDataType> unmatchedDataTypes = findUnmatchedTypes(dataTypes, formatToDataTypes);
- if(unmatchedDataTypes.size() > 0) {
+ if (unmatchedDataTypes.size() > 0) {
throw new PicardException("Could not find a format with available files for the following data types: " + StringUtil.join(", ", new ArrayList<IlluminaDataType>(unmatchedDataTypes)));
}
log.debug("The following file formats will be used by IlluminaDataProvider: " + StringUtil.join("," + formatToDataTypes.keySet()));
availableTiles = fileUtil.getActualTiles(new ArrayList<SupportedIlluminaFormat>(formatToDataTypes.keySet()));
- if(availableTiles.isEmpty()) {
+ if (availableTiles.isEmpty()) {
throw new PicardException("No available tiles were found, make sure that " + basecallDirectory.getAbsolutePath() + " has a lane " + lane);
}
- outputMapping = new OutputMapping(readStructure);
+ outputMapping = new OutputMapping(readStructure);
}
- /** Sometimes (in the case of skipped reads) the logical read structure of the output cluster data is different from the input
+ /**
+ * Sometimes (in the case of skipped reads) the logical read structure of the output cluster data is different from the input
* readStructure
+ *
* @return The ReadStructure describing the output cluster data
*/
public ReadStructure getOutputReadStructure() {
@@ -185,22 +192,23 @@ public class IlluminaDataProviderFactory {
public IlluminaDataProvider makeDataProvider() {
return makeDataProvider(null);
}
+
/**
* Call this method to create a ClusterData iterator over the specified tiles.
*
* @return An iterator for reading the Illumina basecall output for the lane specified in the constructor.
*/
public IlluminaDataProvider makeDataProvider(List<Integer> requestedTiles) {
- if(requestedTiles == null ) {
+ if (requestedTiles == null) {
requestedTiles = availableTiles;
} else {
- if(requestedTiles.size() == 0) {
+ if (requestedTiles.size() == 0) {
throw new PicardException("Zero length tile list supplied to makeDataProvider, you must specify at least 1 tile OR pass NULL to use all available tiles");
}
}
final Map<IlluminaParser, Set<IlluminaDataType>> parsersToDataType = new HashMap<IlluminaParser, Set<IlluminaDataType>>();
- for(final Map.Entry<SupportedIlluminaFormat, Set<IlluminaDataType>> fmToDt : formatToDataTypes.entrySet()) {
+ for (final Map.Entry<SupportedIlluminaFormat, Set<IlluminaDataType>> fmToDt : formatToDataTypes.entrySet()) {
parsersToDataType.put(makeParser(fmToDt.getKey(), requestedTiles), fmToDt.getValue());
}
@@ -211,13 +219,14 @@ public class IlluminaDataProviderFactory {
/**
* Given a set of formats to data types they provide, find any requested data types that do not have a format associated with them and return them
- * @param requestedDataTypes Data types that need to be provided
+ *
+ * @param requestedDataTypes Data types that need to be provided
* @param formatToMatchedTypes A map of file formats to data types that will support them
* @return The data types that go unsupported by the formats found in formatToMatchedTypes
*/
public static Set<IlluminaDataType> findUnmatchedTypes(final Set<IlluminaDataType> requestedDataTypes, final Map<SupportedIlluminaFormat, Set<IlluminaDataType>> formatToMatchedTypes) {
final Set<IlluminaDataType> copiedTypes = new HashSet<IlluminaDataType>(requestedDataTypes);
- for(final Set<IlluminaDataType> matchedTypes : formatToMatchedTypes.values()) {
+ for (final Set<IlluminaDataType> matchedTypes : formatToMatchedTypes.values()) {
copiedTypes.removeAll(matchedTypes);
}
@@ -227,9 +236,10 @@ public class IlluminaDataProviderFactory {
/**
* For all requestedDataTypes return a map of file format to set of provided data types that covers as many requestedDataTypes as possible and
* chooses the most preferred available formats possible
+ *
* @param requestedDataTypes Data types to be provided
- * @param fileUtil A file util for the lane/directory we wish to provide data for
- * @return A Map<Supported file format, Set of data types file format provides>
+ * @param fileUtil A file util for the lane/directory we wish to provide data for
+ * @return A Map<Supported file format, Set of data types file format provides>
*/
public static Map<SupportedIlluminaFormat, Set<IlluminaDataType>> determineFormats(final Set<IlluminaDataType> requestedDataTypes, final IlluminaFileUtil fileUtil) {
//For predictable ordering and uniqueness only, put the requestedDataTypes into a treeSet
@@ -237,32 +247,18 @@ public class IlluminaDataProviderFactory {
final Map<SupportedIlluminaFormat, Set<IlluminaDataType>> fileTypeToDataTypes = new HashMap<SupportedIlluminaFormat, Set<IlluminaDataType>>();
final Map<IlluminaDataType, SupportedIlluminaFormat> dataTypeToFormat = new HashMap<IlluminaDataType, SupportedIlluminaFormat>();
- boolean useQSeq = false;
- for(final IlluminaDataType ts : toSupport) {
+ for (final IlluminaDataType ts : toSupport) {
final SupportedIlluminaFormat preferredFormat = findPreferredAvailableFormat(ts, fileUtil);
- if(preferredFormat != null) {
- useQSeq |= preferredFormat == SupportedIlluminaFormat.Qseq;
+ if (preferredFormat != null) {
dataTypeToFormat.put(ts, preferredFormat);
}
}
- //If no NON-qseq files exist for a file type put it in requiringQSeqs
- if(useQSeq) {
- //Since QSeqs contain the data we want, if we MUST parse QSeqs for at least one data type then use QSeqs for every
- //data type we can (since we prefer to parse only one file if possible)
- final Set<IlluminaDataType> qseqProvidedTypes = new HashSet<IlluminaDataType>(QseqParser.SUPPORTED_TYPES);
- qseqProvidedTypes.retainAll(toSupport);
- toSupport.removeAll(qseqProvidedTypes);
-
- fileTypeToDataTypes.put(SupportedIlluminaFormat.Qseq, qseqProvidedTypes);
- }
-
- //If there are any types not covered by QSeqs (or QSeqs aren't required/available) then find parsers for all remaining data types
- for(final IlluminaDataType dt : toSupport) {
+ for (final IlluminaDataType dt : toSupport) {
final SupportedIlluminaFormat format = dataTypeToFormat.get(dt);
- if(format != null) {
- if(fileTypeToDataTypes.containsKey(format)) {
+ if (format != null) {
+ if (fileTypeToDataTypes.containsKey(format)) {
fileTypeToDataTypes.get(format).add(dt);
} else {
fileTypeToDataTypes.put(dataTypeToFormat.get(dt), makeSet(dt));
@@ -275,7 +271,8 @@ public class IlluminaDataProviderFactory {
/**
* Given a data type find the most preferred file format that also has files available
- * @param dt Type of desired data
+ *
+ * @param dt Type of desired data
* @param fileUtil Util for the lane/directory in which we will find data
* @return The file format that is "most preferred" (i.e. fastest to parse/smallest in memory)
*/
@@ -285,23 +282,23 @@ public class IlluminaDataProviderFactory {
/**
* Given a data type find the most preferred file format even if files are not available
- * @param dt Type of desired data
+ *
+ * @param dt Type of desired data
* @param fileUtil Util for the lane/directory in which we will find data
* @return The file format that is "most preferred" (i.e. fastest to parse/smallest in memory)
*/
- public static SupportedIlluminaFormat findPreferredFormat(final IlluminaDataType dt, final IlluminaFileUtil fileUtil){
+ public static SupportedIlluminaFormat findPreferredFormat(final IlluminaDataType dt, final IlluminaFileUtil fileUtil) {
return findPreferredFormat(dt, fileUtil, false);
}
private static SupportedIlluminaFormat findPreferredFormat(final IlluminaDataType dt, final IlluminaFileUtil fileUtil,
- final boolean checkAvailable){
+ final boolean checkAvailable) {
final List<SupportedIlluminaFormat> preferredFormats = DATA_TYPE_TO_PREFERRED_FORMATS.get(dt);
SupportedIlluminaFormat format = null;
- for(int i = 0; i < preferredFormats.size() && format == null; i++) {
- if(checkAvailable && fileUtil.getUtil(preferredFormats.get(i)).filesAvailable()) {
+ for (int i = 0; i < preferredFormats.size() && format == null; i++) {
+ if (checkAvailable && fileUtil.getUtil(preferredFormats.get(i)).filesAvailable()) {
format = preferredFormats.get(i);
- }
- else if(!checkAvailable){
+ } else if (!checkAvailable) {
format = preferredFormats.get(i);
}
}
@@ -312,7 +309,8 @@ public class IlluminaDataProviderFactory {
/**
* There are multiple parsers for the same IlluminaDataType (e.g. BCLParser and QSeqParser). Instantiate an instance of the preferred parser for
* the given data type with the information available and return it.
- * @param format The type of data we want to parse
+ *
+ * @param format The type of data we want to parse
* @param requestedTiles The requestedTiles over which we will be parsing data
* @return A parser that will parse dataType data over the given requestedTiles and cycles and output it in groupings of the sizes specified in outputLengths
*/
@@ -320,58 +318,43 @@ public class IlluminaDataProviderFactory {
final IlluminaParser parser;
switch (format) {
case Barcode:
- parser = new BarcodeParser(fileUtil.barcode().getFiles(requestedTiles));
+ parser = new BarcodeParser(((PerTileFileUtil)fileUtil.getUtil(SupportedIlluminaFormat.Barcode)).getFiles(requestedTiles));
break;
case Bcl: {
- final CycleIlluminaFileMap bclFileMap = fileUtil.bcl().getFiles(requestedTiles, outputMapping.getOutputCycles());
+ final CycleIlluminaFileMap bclFileMap = ((PerTilePerCycleFileUtil)fileUtil.getUtil(SupportedIlluminaFormat.Bcl))
+ .getFiles(requestedTiles, outputMapping.getOutputCycles());
bclFileMap.assertValid(requestedTiles, outputMapping.getOutputCycles());
parser = new BclParser(basecallDirectory, lane, bclFileMap, outputMapping, this.applyEamssFiltering, bclQualityEvaluationStrategy);
break;
}
- case Cif:
- final CycleIlluminaFileMap cifFileMap = fileUtil.cif().getFiles(requestedTiles, outputMapping.getOutputCycles());
- cifFileMap.assertValid(requestedTiles, outputMapping.getOutputCycles());
- parser = new CifParser(intensitiesDirectory, lane, cifFileMap, outputMapping);
- break;
-
- case Cnf:
- final CycleIlluminaFileMap cnfFileMap = fileUtil.cnf().getFiles(requestedTiles, outputMapping.getOutputCycles());
- cnfFileMap.assertValid(requestedTiles, outputMapping.getOutputCycles());
- parser = new CnfParser(intensitiesDirectory, lane, cnfFileMap, outputMapping);
- break;
-
case Filter:
- final IlluminaFileMap filterFileMap = fileUtil.filter().getFiles(requestedTiles);
+ final IlluminaFileMap filterFileMap = ((PerTileFileUtil)fileUtil.getUtil(SupportedIlluminaFormat.Filter)).getFiles(requestedTiles);
parser = new FilterParser(filterFileMap);
break;
case Locs:
case Clocs:
case Pos:
- final IlluminaFileUtil.PerTileFileUtil fu = (IlluminaFileUtil.PerTileFileUtil) fileUtil.getUtil(format);
+ final PerTileFileUtil fu = (PerTileFileUtil) fileUtil.getUtil(format);
parser = new PosParser(fu.getFiles(requestedTiles), format);
break;
- case Qseq:
- final List<IlluminaFileMap> readTileMap = fileUtil.qseq().getFiles(requestedTiles);
- parser = new QseqParser(lane, readTileMap, outputMapping);
- break;
-
case MultiTileFilter:
- parser = fileUtil.multiTileFilter().makeParser(requestedTiles);
+ parser = ((MultiTileFilterFileUtil)fileUtil.getUtil(SupportedIlluminaFormat.MultiTileFilter)).makeParser(requestedTiles);
break;
case MultiTileLocs:
- parser = fileUtil.multiTileLocs().makeParser(requestedTiles);
+ parser = ((MultiTileLocsFileUtil)fileUtil.getUtil(SupportedIlluminaFormat.MultiTileLocs)).makeParser(requestedTiles);
break;
case MultiTileBcl: {
- final CycleIlluminaFileMap bclFileMap = fileUtil.multiTileBcl().getFiles(requestedTiles, outputMapping.getOutputCycles());
+ final MultiTileBclFileUtil util = (MultiTileBclFileUtil) fileUtil.getUtil(SupportedIlluminaFormat.MultiTileBcl);
+ final CycleIlluminaFileMap bclFileMap = util.getFiles(requestedTiles, outputMapping.getOutputCycles());
bclFileMap.assertValid(requestedTiles, outputMapping.getOutputCycles());
parser = new MultiTileBclParser(basecallDirectory, lane, bclFileMap, outputMapping,
- this.applyEamssFiltering, bclQualityEvaluationStrategy, fileUtil.multiTileBcl().tileIndex);
+ this.applyEamssFiltering, bclQualityEvaluationStrategy, util.tileIndex);
break;
}
diff --git a/src/java/net/sf/picard/illumina/parser/IlluminaDataType.java b/src/java/net/sf/picard/illumina/parser/IlluminaDataType.java
index 342635b..558971b 100644
--- a/src/java/net/sf/picard/illumina/parser/IlluminaDataType.java
+++ b/src/java/net/sf/picard/illumina/parser/IlluminaDataType.java
@@ -31,5 +31,5 @@ package net.sf.picard.illumina.parser;
* @author jburke at broadinstitute.org
*/
public enum IlluminaDataType {
- Position, BaseCalls, QualityScores, RawIntensities, Noise, PF, Barcodes;
+ Position, BaseCalls, QualityScores, PF, Barcodes
}
diff --git a/src/java/net/sf/picard/illumina/parser/IlluminaFileMap.java b/src/java/net/sf/picard/illumina/parser/IlluminaFileMap.java
index 90e9d35..c6550a6 100644
--- a/src/java/net/sf/picard/illumina/parser/IlluminaFileMap.java
+++ b/src/java/net/sf/picard/illumina/parser/IlluminaFileMap.java
@@ -29,34 +29,21 @@ import java.io.File;
import java.util.*;
/**
- * For "non-cycle" files (e.g. qseqs and other files that have multiple cycles per file). Maps a Tile -> File
+ * For "non-cycle" files (files that have multiple cycles per file). Maps a Tile -> File
* @author jburke at broadinstitute.org
*/
class IlluminaFileMap extends TreeMap<Integer, File> {
- public IlluminaFileMap() {
- }
-
- //For testing purposes
- public IlluminaFileMap(final List<Integer> tiles, final List<File> files) {
- if(tiles.size() != files.size()) {
- throw new PicardException("Tiles and Files were not of the same length: Tiles(" + tiles.size() + ") Files(" + files.size() + ") ");
- }
-
- for(int i = 0; i < tiles.size(); i++) {
- put(tiles.get(i), files.get(i));
- }
- }
/** Return a file map that includes only the tiles listed */
- public IlluminaFileMap keep(final List<Integer> toInclude) {
- final IlluminaFileMap fm = new IlluminaFileMap();
- for(final Integer tile : toInclude) {
+ public IlluminaFileMap keep(final List<Integer> tilesToKeep) {
+ final IlluminaFileMap fileMap = new IlluminaFileMap();
+ for(final Integer tile : tilesToKeep) {
final File file = this.get(tile);
if(file != null) {
- fm.put(tile, file);
+ fileMap.put(tile, file);
}
}
- return fm;
+ return fileMap;
}
/**
@@ -65,7 +52,7 @@ class IlluminaFileMap extends TreeMap<Integer, File> {
* @param startingTile The first File in the returned list will correspond to this tile
* @return A List of files for all tiles >= startingTile that are contained in this FileMap
*/
- public List<File> getFilesStartingAt(int startingTile) {
+ public List<File> getFilesStartingAt(final int startingTile) {
return new ArrayList<File>(this.tailMap(startingTile).values());
}
}
diff --git a/src/java/net/sf/picard/illumina/parser/IlluminaFileUtil.java b/src/java/net/sf/picard/illumina/parser/IlluminaFileUtil.java
index 3be24a0..e1ff17f 100644
--- a/src/java/net/sf/picard/illumina/parser/IlluminaFileUtil.java
+++ b/src/java/net/sf/picard/illumina/parser/IlluminaFileUtil.java
@@ -25,39 +25,22 @@ package net.sf.picard.illumina.parser;
import net.sf.picard.PicardException;
import net.sf.picard.illumina.parser.fakers.BarcodeFileFaker;
-import net.sf.picard.illumina.parser.fakers.BciFileFaker;
import net.sf.picard.illumina.parser.fakers.BclFileFaker;
-import net.sf.picard.illumina.parser.fakers.CifFileFaker;
import net.sf.picard.illumina.parser.fakers.ClocsFileFaker;
-import net.sf.picard.illumina.parser.fakers.CnfFileFaker;
-import net.sf.picard.illumina.parser.fakers.FileFaker;
import net.sf.picard.illumina.parser.fakers.FilterFileFaker;
import net.sf.picard.illumina.parser.fakers.LocsFileFaker;
-import net.sf.picard.illumina.parser.fakers.MultiTileBclFileFaker;
-import net.sf.picard.illumina.parser.fakers.MultiTileLocsFileFaker;
import net.sf.picard.illumina.parser.fakers.PosFileFaker;
-import net.sf.picard.illumina.parser.fakers.QSeqFileFaker;
import net.sf.picard.illumina.parser.readers.TileMetricsOutReader;
import net.sf.picard.io.IoUtil;
import net.sf.samtools.util.CloserUtil;
-import net.sf.samtools.util.StringUtil;
import java.io.File;
-import java.io.IOException;
import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
import java.util.HashMap;
-import java.util.HashSet;
import java.util.Iterator;
-import java.util.LinkedList;
import java.util.List;
import java.util.Map;
-import java.util.Set;
-import java.util.SortedMap;
-import java.util.TreeMap;
import java.util.TreeSet;
-import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
@@ -71,12 +54,10 @@ import java.util.regex.Pattern;
* @author jburke at broadinstitute.org
*/
public class IlluminaFileUtil {
+ public static final Pattern CYCLE_SUBDIRECTORY_PATTERN = Pattern.compile("^C(\\d+)\\.1$");
public enum SupportedIlluminaFormat {
- Qseq,
Bcl,
- Cif,
- Cnf,
Locs,
Clocs,
Pos,
@@ -87,81 +68,27 @@ public class IlluminaFileUtil {
MultiTileBcl
}
+ private final File basecallLaneDir;
private final File intensityLaneDir;
private final File basecallDir;
+ private final File intensityDir;
private final int lane;
-
- /**
- * A regex string matching only qseq files
- */
- private final QSeqIlluminaFileUtil qseq;
- private final PerTilePerCycleFileUtil bcl;
- private final PerTilePerCycleFileUtil cif;
- private final PerTilePerCycleFileUtil cnf;
- private final PerTileFileUtil pos;
- private final PerTileFileUtil locs;
- private final PerTileFileUtil clocs;
- private final PerTileFileUtil filter;
- private final PerTileFileUtil barcode;
- private final MultiTileFilterFileUtil multiTileFilter;
- private final MultiTileLocsFileUtil multiTileLocs;
- private final MultiTileBclFileUtil multiTileBcl;
private final File tileMetricsOut;
- private final Map<SupportedIlluminaFormat, ParameterizedFileUtil> utils;
-
+ private final Map<SupportedIlluminaFormat, ParameterizedFileUtil> utils = new HashMap<SupportedIlluminaFormat, ParameterizedFileUtil>();
public IlluminaFileUtil(final File basecallDir, final int lane) {
+ this.lane = lane;
this.basecallDir = basecallDir;
- final File intensityDir = basecallDir.getParentFile();
+ this.intensityDir = basecallDir.getParentFile();
final File dataDir = intensityDir.getParentFile();
- final File interopDir = new File(dataDir.getParentFile(), "InterOp");
- this.lane = lane;
-
- final File basecallLaneDir = new File(basecallDir, longLaneStr(lane));
+ this.basecallLaneDir = new File(basecallDir, longLaneStr(lane));
this.intensityLaneDir = new File(intensityDir, longLaneStr(lane));
-
- utils = new HashMap<SupportedIlluminaFormat, ParameterizedFileUtil>();
-
- qseq = new QSeqIlluminaFileUtil();
- utils.put(SupportedIlluminaFormat.Qseq, qseq);
-
- bcl = new PerTilePerCycleFileUtil(inferBclExtension(basecallLaneDir), basecallLaneDir, new BclFileFaker());
- utils.put(SupportedIlluminaFormat.Bcl, bcl);
-
- cif = new PerTilePerCycleFileUtil(".cif", new CifFileFaker());
- utils.put(SupportedIlluminaFormat.Cif, cif);
-
- cnf = new PerTilePerCycleFileUtil(".cnf", new CnfFileFaker());
- utils.put(SupportedIlluminaFormat.Cnf, cnf);
-
- locs = new PerTileFileUtil(".locs", false, new LocsFileFaker());
- utils.put(SupportedIlluminaFormat.Locs, locs);
-
- clocs = new PerTileFileUtil(".clocs", false, new ClocsFileFaker());
- utils.put(SupportedIlluminaFormat.Clocs, clocs);
-
- pos = new PerTileFileUtil("_pos.txt", false, intensityDir, new PosFileFaker());
- utils.put(SupportedIlluminaFormat.Pos, pos);
-
- filter = new PerTileFileUtil(".filter", true, basecallLaneDir, new FilterFileFaker());
- utils.put(SupportedIlluminaFormat.Filter, filter);
-
- barcode = new PerTileFileUtil("_barcode.txt", true, basecallDir, new BarcodeFileFaker());
- utils.put(SupportedIlluminaFormat.Barcode, barcode);
-
- multiTileFilter = new MultiTileFilterFileUtil(basecallLaneDir);
- utils.put(SupportedIlluminaFormat.MultiTileFilter, multiTileFilter);
-
- multiTileLocs = new MultiTileLocsFileUtil(new File(intensityDir, basecallLaneDir.getName()), basecallLaneDir);
- utils.put(SupportedIlluminaFormat.MultiTileLocs, multiTileLocs);
-
- multiTileBcl = new MultiTileBclFileUtil(basecallLaneDir);
- utils.put(SupportedIlluminaFormat.MultiTileBcl, multiTileBcl);
-
+ final File interopDir = new File(dataDir.getParentFile(), "InterOp");
tileMetricsOut = new File(interopDir, "TileMetricsOut.bin");
}
+
/**
* Return the lane we're inspecting
*/
@@ -173,7 +100,59 @@ public class IlluminaFileUtil {
* Given a file type, get the Parameterized File Util object associated with it
*/
public ParameterizedFileUtil getUtil(final SupportedIlluminaFormat format) {
- return utils.get(format);
+ ParameterizedFileUtil parameterizedFileUtil = utils.get(format);
+ if (parameterizedFileUtil == null) {
+ switch (format) {
+ case Bcl:
+ final ParameterizedFileUtil bclFileUtil = new PerTilePerCycleFileUtil(".bcl", basecallLaneDir, new BclFileFaker(), lane);
+ final ParameterizedFileUtil gzBclFileUtil = new PerTilePerCycleFileUtil(".bcl.gz", basecallLaneDir, new BclFileFaker(), lane);
+ if (bclFileUtil.filesAvailable() && !gzBclFileUtil.filesAvailable()) {
+ parameterizedFileUtil = bclFileUtil;
+ } else if (!bclFileUtil.filesAvailable() && gzBclFileUtil.filesAvailable()) {
+ parameterizedFileUtil = gzBclFileUtil;
+ } else if (!bclFileUtil.filesAvailable() && !gzBclFileUtil.filesAvailable()) {
+ parameterizedFileUtil = bclFileUtil;
+ } else {
+ throw new PicardException(
+ "Not all BCL files in " + basecallLaneDir.getAbsolutePath() + " have the same extension!");
+ }
+ utils.put(SupportedIlluminaFormat.Bcl, parameterizedFileUtil);
+ break;
+ case Locs:
+ parameterizedFileUtil = new PerTileFileUtil(".locs", intensityLaneDir, new LocsFileFaker(), lane);
+ utils.put(SupportedIlluminaFormat.Locs, parameterizedFileUtil);
+ break;
+ case Clocs:
+ parameterizedFileUtil = new PerTileFileUtil(".clocs", intensityLaneDir, new ClocsFileFaker(), lane);
+ utils.put(SupportedIlluminaFormat.Clocs, parameterizedFileUtil);
+ break;
+ case Pos:
+ parameterizedFileUtil = new PerTileFileUtil("_pos.txt", intensityDir, new PosFileFaker(), lane);
+ utils.put(SupportedIlluminaFormat.Pos, parameterizedFileUtil);
+ break;
+ case Filter:
+ parameterizedFileUtil = new PerTileFileUtil(".filter", basecallLaneDir, new FilterFileFaker(), lane);
+ utils.put(SupportedIlluminaFormat.Filter, parameterizedFileUtil);
+ break;
+ case Barcode:
+ parameterizedFileUtil = new PerTileFileUtil("_barcode.txt", basecallDir, new BarcodeFileFaker(), lane);
+ utils.put(SupportedIlluminaFormat.Barcode, parameterizedFileUtil);
+ break;
+ case MultiTileFilter:
+ parameterizedFileUtil = new MultiTileFilterFileUtil(basecallLaneDir, lane);
+ utils.put(SupportedIlluminaFormat.MultiTileFilter, parameterizedFileUtil);
+ break;
+ case MultiTileLocs:
+ parameterizedFileUtil = new MultiTileLocsFileUtil(new File(intensityDir, basecallLaneDir.getName()), basecallLaneDir, lane);
+ utils.put(SupportedIlluminaFormat.MultiTileLocs, parameterizedFileUtil);
+ break;
+ case MultiTileBcl:
+ parameterizedFileUtil = new MultiTileBclFileUtil(basecallLaneDir, lane);
+ utils.put(SupportedIlluminaFormat.MultiTileBcl, parameterizedFileUtil);
+ break;
+ }
+ }
+ return parameterizedFileUtil;
}
/**
@@ -213,9 +192,9 @@ public class IlluminaFileUtil {
"0 Formats were specified. You need to specify at least SupportedIlluminaFormat to use getTiles");
}
- final List<Integer> tiles = utils.get(formats.get(0)).getTiles();
- for (int i = 0; i < formats.size(); i++) {
- final List<Integer> fmTiles = utils.get(formats.get(i)).getTiles();
+ final List<Integer> tiles = getUtil(formats.get(0)).getTiles();
+ for (int i = 1; i < formats.size(); i++) {
+ final List<Integer> fmTiles = getUtil(formats.get(i)).getTiles();
if (tiles.size() != fmTiles.size() || !tiles.containsAll(fmTiles)) {
throw new PicardException(
"Formats do not have the same number of tiles! " + summarizeTileCounts(formats));
@@ -225,1116 +204,17 @@ public class IlluminaFileUtil {
return tiles;
}
- public QSeqIlluminaFileUtil qseq() {
- return qseq;
- }
-
- public PerTilePerCycleFileUtil bcl() {
- return bcl;
- }
-
- public PerTilePerCycleFileUtil cif() {
- return cif;
- }
-
- public PerTilePerCycleFileUtil cnf() {
- return cnf;
- }
-
- public PerTileFileUtil locs() {
- return locs;
- }
-
- public PerTileFileUtil clocs() {
- return clocs;
- }
-
- public PerTileFileUtil pos() {
- return pos;
- }
-
- public PerTileFileUtil filter() {
- return filter;
- }
-
- public PerTileFileUtil barcode() {
- return barcode;
- }
-
- public MultiTileFilterFileUtil multiTileFilter() {
- return multiTileFilter;
- }
-
- public MultiTileLocsFileUtil multiTileLocs() {
- return multiTileLocs;
- }
-
- public MultiTileBclFileUtil multiTileBcl() {
- return multiTileBcl;
- }
-
public File tileMetricsOut() {
return tileMetricsOut;
}
- public static final String UNPARAMETERIZED_PER_TILE_PATTERN = "s_(\\d+)_(\\d{1,5})";
- public static final String UNPARAMETERIZED_QSEQ_PATTERN = "s_(\\d+)_(\\d)_(\\d{4})_qseq\\.txt(\\.gz|\\.bz2)?";
- private static final Pattern CYCLE_SUBDIRECTORY_PATTERN = Pattern.compile("^C(\\d+)\\.1$");
-
- public static String makeParameterizedLaneAndTileRegex(final int lane) {
- if (lane < 0) {
- throw new PicardException("Lane (" + lane + ") cannot be negative");
- }
- return "s_" + lane + "_(\\d{1,5})";
- }
-
- public static String makeParameterizedQseqRegex(final int lane) {
- if (lane < 0) {
- throw new PicardException("Lane (" + lane + ") cannot be negative");
- }
- return "s_" + lane + "_(\\d)_(\\d{4})_qseq\\.txt(\\.gz|\\.bz2)?";
- }
-
- /**
- * An object providing utilities for locating Illumina files of specific types
- */
- public abstract class ParameterizedFileUtil {
- /**
- * The file extension for this class, file extension does not have the standard meaning
- * in this instance. It means, all the characters that come after the identifying portion of
- * the file (after lane, tile, and end that is). So _qseq.txt and .filter are both file extensions
- */
- public final String extension;
-
- /**
- * A pattern that will match files of this type for this lane
- */
- public final Pattern pattern;
-
- /**
- * A pattern that will match files of this type for this lane
- */
- public final Pattern unparameterizedPattern;
-
- /**
- * If you think of the file system as a tree, this is the deepest directory(node) on the tree that
- * still contains all of the files for this given type (e.g. If we're talking about BCLs the directory
- * structure is:
- * <p/>
- * BaseCall Dir
- * |
- * L001
- * | | |
- * C1.1 C2.1 ... Cn.1
- * | | |
- * bcl Files ... bclFiles
- * <p/>
- * L001 is the base because it contains every BCL file in the run (though those files are nested in
- * other folders).
- */
- protected final File base;
-
- protected final FileFaker faker;
-
- public ParameterizedFileUtil(final String unparameterizedPattern, final String patternStr,
- final String extension, final File base,
- final FileFaker faker) {
- this.pattern = Pattern.compile(escapePeriods(patternStr));
- this.unparameterizedPattern = Pattern.compile(escapePeriods(unparameterizedPattern));
- this.extension = extension;
- this.base = base;
- this.faker = faker;
- }
-
- /**
- * The period separator is expected in the file extension, since some do not start with it
- */
- private String escapePeriods(final String preEscaped) {
- return preEscaped
- .replaceAll("\\.", "\\."); //In the first one the \\ is inside a regex in the second it's NOT
- }
-
- /**
- * Determine whether or not files are available
- *
- * @return return true if files are found matching this types pattern, false otherwise
- */
- public abstract boolean filesAvailable();
-
- /**
- * Illumina file names contain at least lane and tile information and sometimes end info. Return all
- * available lane tile and end information.
- *
- * @param fileName Filename to analyze for data
- *
- * @return A LaneTileEnd object with discovered values or null if that value is not available in the given file name
- */
- public abstract LaneTileEnd fileToLaneTileEnd(final String fileName);
-
- /**
- * Return a list of all tiles available for this file format and run
- *
- * @return A List of tile integers
- */
- public abstract List<Integer> getTiles();
-
-
- /**
- * Given the expected tiles/expected cycles for this file type, return a list of error messages describing any
- * missing/or malformed files
- *
- * @param expectedTiles An ordered list of tile numbers
- * @param expectedCycles An ordered list of cycle numbers that may contain gaps
- *
- * @return A list of error messages for this format
- */
- public abstract List<String> verify(List<Integer> expectedTiles, int[] expectedCycles);
-
- /**
- * Given the expected tiles/expected cycles for this file type create a set of fake files such that the
- * verification criteria are met.
- *
- * @param expectedTiles An ordered list of tile numbers
- * @param cycles An ordered list of cycle numbers that may contain gaps
- * @param format The format of the files that are to be faked
- *
- * @return A list of error messages for this format
- */
- public abstract List<String> fakeFiles(List<Integer> expectedTiles, int[] cycles,
- SupportedIlluminaFormat format);
- }
-
- /**
- * Represents file types that have one file per tile
- */
- class PerTileFileUtil extends ParameterizedFileUtil {
- protected final boolean txtBased;
- protected final boolean padTile;
- protected final IlluminaFileMap fileMap;
- protected final List<Integer> tiles;
-
- public PerTileFileUtil(final String fileNameEndPattern, final boolean padTile, final File base,
- final FileFaker fileFaker) {
- super(makeLTRegex(processTxtExtension(fileNameEndPattern)),
- makeLTRegex(processTxtExtension(fileNameEndPattern), lane), fileNameEndPattern, base,
- fileFaker);
- this.txtBased = fileNameEndPattern.endsWith(".txt");
- this.padTile = padTile;
- this.fileMap = getTiledFiles(base, pattern, this);
-
- if (fileMap.size() > 0) {
- this.tiles = Collections.unmodifiableList(new ArrayList<Integer>(this.fileMap.keySet()));
- } else {
- this.tiles = new ArrayList<Integer>();
- }
- }
-
- public PerTileFileUtil(final String fileNameEndPattern, final boolean padTile, final FileFaker fileFaker) {
- this(fileNameEndPattern, padTile, intensityLaneDir, fileFaker);
- }
-
- @Override
- public boolean filesAvailable() {
- return !fileMap.isEmpty();
- }
-
- /**
- * Returns only lane and tile information as PerTileFt's do not have End information.
- *
- * @param fileName Filename to analyze for data
- *
- * @return A LaneTileEnd object with the discovered Lane and Tile information and a null end field.
- */
- public LaneTileEnd fileToLaneTileEnd(final String fileName) {
- return laneAndTileFromFirstTwoMatches(fileName, unparameterizedPattern);
- }
-
- public IlluminaFileMap getFiles() {
- return fileMap;
- }
-
- public IlluminaFileMap getFiles(final List<Integer> tiles) {
- return fileMap.keep(tiles);
- }
-
- public List<Integer> getTiles() {
- return tiles;
- }
-
- @Override
- public List<String> verify(final List<Integer> expectedTiles, final int[] expectedCycles) {
- final List<String> failures = new LinkedList<String>();
-
- if (!base.exists()) {
- failures.add("Base directory(" + base.getAbsolutePath() + ") does not exist!");
- } else {
- for (final Integer tile : expectedTiles) {
- if (!tiles.contains(tile)) {
- failures.add("Missing tile " + tile + " for file type " + extension + ".");
- } else if (fileMap.get(tile).length() == 0) {
- failures.add("Tile " + tile + " is empty for file type " + extension + ".");
- }
- }
- }
-
- return failures;
- }
-
- @Override
- public List<String> fakeFiles(final List<Integer> expectedTiles, final int[] cycles,
- final SupportedIlluminaFormat format) {
- final List<String> failures = new LinkedList<String>();
- if (!base.exists()) {
- failures.add("Base directory(" + base.getAbsolutePath() + ") does not exist!");
- } else {
- for (final Integer tile : expectedTiles) {
- if (!tiles.contains(tile) || fileMap.get(tile).length() == 0) {
- //create a new file of this type
- try {
- faker.fakeFile(base, tile, lane, extension);
- } catch (final IOException e) {
- failures.add(String.format("Could not create fake file %s: %s", fileMap.get(tile),
- e.getMessage()));
- }
-
- }
- }
- }
- return failures;
- }
- }
-
- /**
- * A base class for file types that occur 1 for each tile/cycle.
- */
- class PerTilePerCycleFileUtil extends ParameterizedFileUtil {
- private final CycleIlluminaFileMap cycleFileMap;
- private final List<Integer> tiles;
- private int[] detectedCycles;
-
- public PerTilePerCycleFileUtil(final String fileNameEndPattern, final File base, final FileFaker fileFaker) {
- super(makeLTRegex(fileNameEndPattern), makeLTRegex(fileNameEndPattern, lane), fileNameEndPattern, base,
- fileFaker);
- this.cycleFileMap = getPerTilePerCycleFiles(); //sideEffect, assigned to numCycles
-
- if (cycleFileMap.size() > 0) {
- this.tiles = Collections.unmodifiableList(new ArrayList<Integer>(this.cycleFileMap.keySet()));
- } else {
- this.tiles = new ArrayList<Integer>();
- }
- }
-
- public PerTilePerCycleFileUtil(final String fileNameEndPattern, final FileFaker fileFaker) {
- this(fileNameEndPattern, intensityLaneDir, fileFaker);
- }
-
- /**
- * Returns only lane and tile information as PerTilePerCycleFt's do not have End information.
- *
- * @param fileName Filename to analyze for data
- *
- * @return A LaneTileEnd object with the discovered Lane and Tile information and a null end field.
- */
- public LaneTileEnd fileToLaneTileEnd(final String fileName) {
- return laneAndTileFromFirstTwoMatches(fileName, unparameterizedPattern);
- }
-
- /**
- * Given a cycle directory, return a list of tiles in that directory. If expectedTiles equals null
- * return all files discovered otherwise filter by expectedTiles.
- *
- * @param cycleDir The file object of the cycle directory we are searching
- *
- * @return A list of tile integers describing the tiles available in a cycle directory
- */
- private List<Integer> getTilesInCycleDir(final File cycleDir) {
- final File[] files = IoUtil.getFilesMatchingRegexp(cycleDir, pattern);
- final List<Integer> tiles = new ArrayList<Integer>();
- for (final File file : files) {
- if (file.length() > 0) {
- tiles.add(fileToLaneTileEnd(file.getName()).tile);
- }
- }
-
- return tiles;
- }
-
- /**
- * For the given tiles, populate a CycleIlluminaFileMap that contains all these tiles and will iterate through
- * all the files for these tiles in expectedBase
- * Side Effect: Assigns numCycles
- *
- * @return A CycleIlluminaFileMap with the listed (or all) tiles for at least expectedCycles number of cycles(or total available
- * cycles if expectedCycles is null)
- */
- private CycleIlluminaFileMap getPerTilePerCycleFiles() {
- final CycleIlluminaFileMap cycledMap = new CycleIlluminaFileMap();
-
- final File laneDir = base;
- final File[] tempCycleDirs;
- tempCycleDirs = IoUtil.getFilesMatchingRegexp(laneDir, CYCLE_SUBDIRECTORY_PATTERN);
- if (tempCycleDirs == null || tempCycleDirs.length == 0) {
- return cycledMap;
- }
-
- int lowestCycle = Integer.MAX_VALUE;
- int lowestCycleDirIndex = 0;
- final int[] cycles = new int[tempCycleDirs.length];
- for (int i = 0; i < tempCycleDirs.length; ++i) {
- cycles[i] = getCycleFromDir(tempCycleDirs[i]);
- if (cycles[i] < lowestCycle) {
- lowestCycle = cycles[i];
- lowestCycleDirIndex = i;
- }
- }
-
- final File firstCycleDir = tempCycleDirs[lowestCycleDirIndex];
-
- Arrays.sort(cycles);
- detectedCycles = cycles;
-
- final List<Integer> tiles = getTilesInCycleDir(firstCycleDir);
- for (final int tile : tiles) {
- cycledMap.put(tile, new CycleFilesIterator(laneDir, lane, tile, cycles,
- extension)); //Gonna have a problem here if we ever get a (.txt.gz for these types of files)
- }
-
- return cycledMap;
- }
-
- public CycleIlluminaFileMap getFiles() {
- return cycleFileMap;
- }
-
- public CycleIlluminaFileMap getFiles(final List<Integer> tiles) {
- return cycleFileMap.keep(tiles, null);
- }
-
- /**
- * Returns a cycleIlluminaFileMap with all available tiles but limited to the cycles passed in. Any cycles that are missing
- * cycle files or directories will be removed from the cycle list that is kept.
- *
- * @param cycles Cycles that should be present in the output CycleIlluminaFileMap
- *
- * @return A CycleIlluminaFileMap with all available tiles but at most the cycles passed in by the cycles parameter
- */
- public CycleIlluminaFileMap getFiles(final int[] cycles) {
- //Remove any cycles that were discovered to be NON-EXISTENT when this util was instantiated
- final int[] filteredCycles = removeNonExistentCycles(cycles);
- return cycleFileMap.keep(null, filteredCycles);
- }
-
- /**
- * Returns a cycleIlluminaFileMap that contains only the tiles and cycles specified (and fewer if the orginal CycleIlluminaFileMap, created
- * on util instantiation, doesn't contain any of these tiles/cycles).
- *
- * @param cycles Cycles that should be present in the output CycleIlluminaFileMap
- *
- * @return A CycleIlluminaFileMap with at most the tiles/cycles listed in the parameters
- */
- public CycleIlluminaFileMap getFiles(final List<Integer> tiles, final int[] cycles) {
- //Remove any cycles that were discovered to be NON-EXISTENT when this util was instantiated
- final int[] filteredCycles = removeNonExistentCycles(cycles);
- return cycleFileMap.keep(tiles, filteredCycles);
- }
-
- private int[] removeNonExistentCycles(final int[] cycles) {
- final TreeSet<Integer> detectedCyclesSet = new TreeSet<Integer>();
- for (final Integer cycle : detectedCycles) {
- detectedCyclesSet.add(cycle);
- }
-
- final TreeSet<Integer> inputCyclesSet = new TreeSet<Integer>();
- for (final Integer inputCycle : cycles) {
- inputCyclesSet.add(inputCycle);
- }
-
- //This also sorts outputCycles
- final int[] outputCycles;
- inputCyclesSet.retainAll(detectedCyclesSet);
- outputCycles = new int[inputCyclesSet.size()];
- int i = 0;
- for (final Integer element : inputCyclesSet) {
- outputCycles[i++] = element;
- }
-
- return outputCycles;
- }
-
- public int[] getDetectedCycles() {
- return detectedCycles;
- }
-
- /**
- * Discover all files of this type in expectedBase that match pattern and construct a list of tiles
- * available based on these files. The same number of tiles is expected in each cycle dir.
- *
- * @return A list of tile integers for all tiles available
- */
- public List<Integer> getTiles() {
- return tiles;
- }
-
- public boolean filesAvailable() {
- return !cycleFileMap.isEmpty();
- }
-
- @Override
- public List<String> verify(final List<Integer> expectedTiles, final int[] expectedCycles) {
- final List<String> failures = new LinkedList<String>();
-
- if (!base.exists()) {
- failures.add("Base directory(" + base.getAbsolutePath() + ") does not exist!");
- } else {
- final CycleIlluminaFileMap cfm = getFiles(expectedTiles, expectedCycles);
-
- final Set<Integer> detectedCycleSet = new HashSet<Integer>();
- for (final Integer cycle : detectedCycles) {
- detectedCycleSet.add(cycle);
- }
-
- final Set<Integer> missingCycleSet = new TreeSet<Integer>();
- for (final Integer cycle : expectedCycles) {
- missingCycleSet.add(cycle);
- }
-
- missingCycleSet.removeAll(detectedCycleSet);
-
- for (final Integer tile : expectedTiles) {
- final CycleFilesIterator cfIterator = cfm.get(tile);
- if (cfIterator == null) {
- failures.add("File type " + extension + " is missing tile " + tile);
- } else if (!cfIterator.hasNext()) {
- failures.add("File type " + extension + " has 0 cycle files for tile " + tile);
- } else {
- int expectedCycleIndex = 0;
- Long cycleSize = null;
-
- while (cfIterator.hasNext() && expectedCycleIndex < expectedCycles.length) {
- final int currentCycle = expectedCycles[expectedCycleIndex];
-
- if (cfIterator.getNextCycle() == currentCycle) {
- final File cycleFile = cfIterator.next();
-
- if (!missingCycleSet.contains(currentCycle)) {
- if (!cycleFile.exists()) {
- failures.add("Missing file(" + cycleFile.getAbsolutePath() + ")");
- } else if (cycleFile.length() == 0) {
- failures.add("0 Length tile file(" + cycleFile.getAbsolutePath() + ")");
- } else if (cycleSize == null) {
- cycleSize = cycleFile.length();
- } else if (!extension.equals(".bcl.gz") && cycleSize != cycleFile.length()) {
- // TODO: The gzip bcl files might not be the same length despite having the same content,
- // for now we're punting on this but this should be looked into at some point
- failures.add("File type " + extension
- + " has cycles files of different length. Current cycle ("
- + currentCycle + ") " +
- "Length of first non-empty file (" + cycleSize
- + ") length of current cycle (" + cycleFile.length() + ")"
- + " File(" + cycleFile.getAbsolutePath() + ")");
- }
- } else {
- cfIterator.reset();
- throw new PicardException(
- "Malformed CycleIlluminaFileMap! CycleIlluminaFileMap has cycle "
- + currentCycle
- + " even though the directory does not exist! CycleFileIterator("
- + CycleIlluminaFileMap.remainingCyclesToString(cfIterator) + ")");
- }
- } else if (!missingCycleSet.contains(currentCycle)) {
- cfIterator.reset();
- throw new PicardException(
- "Malformed CycleIlluminaFileMap! Tile " + tile + "CycleFileIterator("
- + CycleIlluminaFileMap.remainingCyclesToString(cfIterator) + ")");
- }
-
- expectedCycleIndex += 1;
- }
- }
- }
-
- for (final Integer cycle : missingCycleSet) {
- failures.add("Missing cycle directory " + cycle + " in directory " + base.getAbsolutePath()
- + " for file type " + extension);
- }
- }
-
- return failures;
- }
-
- @Override
- public List<String> fakeFiles(final List<Integer> expectedTiles, final int[] expectedCycles,
- final SupportedIlluminaFormat format) {
- final List<String> failures = new LinkedList<String>();
-
- if (!base.exists()) {
- base.mkdirs();
- }
-
- final Set<Integer> detectedCycleSet = new HashSet<Integer>();
-
- if (detectedCycles == null) {
- detectedCycles = new int[0];
- }
-
- for (final Integer cycle : detectedCycles) {
- detectedCycleSet.add(cycle);
- }
-
- final Set<Integer> missingCycleSet = new TreeSet<Integer>();
- for (final Integer cycle : expectedCycles) {
- missingCycleSet.add(cycle);
- }
-
- missingCycleSet.removeAll(detectedCycleSet);
- for (final Integer cycle : missingCycleSet) {
- final File cycleDirectory = new File(base, "C" + cycle + ".1");
- if (cycleDirectory.mkdirs()) {
- detectedCycleSet.add(cycle);
- }
- }
-
- final CycleIlluminaFileMap cfm = getPerTilePerCycleFiles();
-
- for (final Integer tile : expectedTiles) {
- final CycleFilesIterator cfIterator = cfm.get(tile);
- if (cfIterator == null) {
- for (final Integer cycle : missingCycleSet) {
- final File cycleDirectory = new File(base, "C" + cycle + ".1");
- try {
- faker.fakeFile(cycleDirectory, tile, lane, extension);
- } catch (final IOException e) {
- failures.add(String.format("Could not create fake file %s: %s", tile + extension,
- e.getMessage()));
- }
- }
- } else if (!cfIterator.hasNext()) {
- failures.add("File type " + extension + " has 0 cycle files for tile " + tile);
- } else {
- int expectedCycleIndex = 0;
- Long cycleSize = null;
- while (cfIterator.hasNext() && expectedCycleIndex < expectedCycles.length) {
- final int currentCycle = expectedCycles[expectedCycleIndex];
-
- if (cfIterator.getNextCycle() == currentCycle) {
- final File cycleFile = cfIterator.next();
-
- if (cycleSize == null) {
- cycleSize = cycleFile.length();
- }
-
- if (!cycleFile.exists() || cycleFile.length() == 0) {
- try {
- faker.fakeFile(cycleFile, cycleSize.intValue());
- } catch (final IOException e) {
- failures.add("Could not create fake file: " + cycleFile);
- }
- }
- }
- expectedCycleIndex += 1;
- }
- }
- }
-
- for (final Integer cycle : missingCycleSet) {
- failures.add("Missing cycle directory " + cycle + " in directory " + base.getAbsolutePath()
- + " for file type " + extension);
- }
- return failures;
- }
- }
-
- /**
- * QSeq files are really tiled and ended so define it's own nested format since no other file types
- * are structured the same.
- */
- class QSeqIlluminaFileUtil extends ParameterizedFileUtil {
- private final List<Integer> tiles;
- private final List<IlluminaFileMap> readFileMaps;
-
- public QSeqIlluminaFileUtil() {
- super(UNPARAMETERIZED_QSEQ_PATTERN, makeParameterizedQseqRegex(lane), "_qseq.txt", basecallDir,
- new QSeqFileFaker());
- readFileMaps = getFiles();
-
- if (readFileMaps.size() > 0) {
- tiles = Collections.unmodifiableList(new ArrayList<Integer>(readFileMaps.get(0).keySet()));
- } else {
- tiles = new ArrayList<Integer>();
- }
- }
-
- /**
- * Make a qSeq regex string with the lane and end already filled in
- */
- private String makeLaneAndEndSpecificRegex(final int lane, final int end) {
- return "^s_" + lane + "_" + end + "_\\d{4}_qseq\\.txt(\\.gz|\\.bz2)?$";
- }
-
- /**
- * Return the number of ends found in the basecallDir
- *
- * @return The highest end number found among the files in the basecallDir
- */
- public int numberOfEnds() {
- return readFileMaps.size();
- }
-
- /**
- * Given a file name return it's Lane, Tile, and End information
- *
- * @param fileName The name of a file to analyze
- *
- * @return The lane, tile, and end of the file with the given name
- */
- @Override
- public LaneTileEnd fileToLaneTileEnd(final String fileName) {
- final Matcher matcher = unparameterizedPattern.matcher(fileName);
- if (!matcher.matches()) {
- return null;
- }
- return new LaneTileEnd(Integer.parseInt(matcher.group(1)), Integer.parseInt(matcher.group(3)),
- Integer.parseInt(matcher.group(2)));
- }
-
- /**
- * For each tile in tiles with the given end find the corresponding QSeq file. Place that qseq file in an IlluminaFileMap
- * and after all tiles are processed, return that fileMap;
- *
- * @param end A single end integer
- *
- * @return A map of tiles->Files where each file is represents the given tile and end
- */
- private IlluminaFileMap getFiles(final int end) {
- final String regex = makeLaneAndEndSpecificRegex(lane, end);
- return getTiledFiles(basecallDir, Pattern.compile(regex), this);
- }
-
- /**
- * Return a list of illumina file map, where index 0 contains files for end 1, index 1 contains files for end 2, etc...
- *
- * @return An list of illuminaFileMaps with containing all files for all ends for each given tile
- */
- public List<IlluminaFileMap> getFiles() {
- final List<IlluminaFileMap> readTileMap = new ArrayList<IlluminaFileMap>();
-
- boolean emptyMap = false;
- for (int i = 1; !emptyMap; i++) {
- final IlluminaFileMap fm = getFiles(i);
- if (fm.isEmpty()) {
- emptyMap = true;
- } else {
- readTileMap.add(fm);
- }
- }
- return readTileMap;
- }
-
- public List<IlluminaFileMap> getFiles(final List<Integer> tiles) {
- final List<IlluminaFileMap> filteredMaps = new ArrayList<IlluminaFileMap>();
-
- for (final IlluminaFileMap fm : readFileMaps) {
- filteredMaps.add(fm.keep(tiles));
- }
-
- return filteredMaps;
- }
-
- public List<Integer> getTiles() {
- return tiles;
- }
-
- @Override
- public List<String> verify(final List<Integer> expectedTiles, final int[] expectedCycles) {
- final List<String> failures = new LinkedList<String>();
-
- if (!this.base.exists()) {
- failures.add("Base directory( " + this.base.getAbsolutePath() + ") does not exist!");
- } else {
- final List<IlluminaFileMap> fileMapPerRead = getFiles(expectedTiles);
- final int[] qseqReadLengths = new int[numberOfEnds()];
- int lastCycle = 0;
- for (int i = 0; i < qseqReadLengths.length; i++) {
- final File currentReadForTile = fileMapPerRead.get(i).get(expectedTiles.get(0));
- qseqReadLengths[i] = QseqReadParser.getReadLength(currentReadForTile);
- lastCycle += qseqReadLengths[i];
- }
-
- final Range cycleRange = new Range(1, lastCycle);
- for (final int expectedCycle : expectedCycles) {
- if (expectedCycle < cycleRange.start || expectedCycle > cycleRange.end) {
- failures.add("Expected cycle(" + expectedCycle
- + ") is not within the range provided by available qseqs. " +
- "Min Available Cycle(" + cycleRange.start + ") Max Available Cycle("
- + cycleRange.end + ") Length of Qseqs( " + StringUtil.join(", ", qseqReadLengths));
- }
- }
-
- //ensure that those same ends exist for each expectedTile
- for (int i = 1; i < expectedTiles.size(); i++) {
- final Integer tile = expectedTiles.get(i);
- for (int j = 0; j < qseqReadLengths.length; j++) {
- final File currentReadForTile = fileMapPerRead.get(j).get(tile);
- if (currentReadForTile == null || !currentReadForTile.exists()) {
- failures.add("Missing file " + "s_" + lane + "_" + (j + 1) + "_" + longTileStr(tile)
- + "_qseq.txt");
- }
- }
- }
- }
-
- return failures;
- }
-
- @Override
- public List<String> fakeFiles(final List<Integer> expectedTiles, final int[] expectedCycles,
- final SupportedIlluminaFormat format) {
- final List<String> failures = new LinkedList<String>();
-
- if (!this.base.exists()) {
- failures.add("Base directory( " + this.base.getAbsolutePath() + ") does not exist!");
- } else {
- final List<IlluminaFileMap> fileMapPerRead = getFiles(expectedTiles);
- final int[] qseqReadLengths = new int[numberOfEnds()];
- int lastCycle = 0;
- for (int i = 0; i < qseqReadLengths.length; i++) {
- final File currentReadForTile = fileMapPerRead.get(i).get(expectedTiles.get(0));
- qseqReadLengths[i] = QseqReadParser.getReadLength(currentReadForTile);
- lastCycle += qseqReadLengths[i];
- }
-
- final Range cycleRange = new Range(1, lastCycle);
- for (final int expectedCycle : expectedCycles) {
- if (expectedCycle < cycleRange.start || expectedCycle > cycleRange.end) {
- failures.add("Expected cycle(" + expectedCycle
- + ") is not within the range provided by available qseqs. " +
- "Min Available Cycle(" + cycleRange.start + ") Max Available Cycle("
- + cycleRange.end + ") Length of Qseqs( " + StringUtil.join(", ", qseqReadLengths));
- }
- }
-
- //ensure that those same ends exist for each expectedTile
- for (int i = 1; i < expectedTiles.size(); i++) {
- final Integer tile = expectedTiles.get(i);
- for (int j = 0; j < qseqReadLengths.length; j++) {
- final File currentReadForTile = fileMapPerRead.get(j).get(tile);
- if (currentReadForTile == null || !currentReadForTile.exists()) {
- failures.add("Missing file " + "s_" + lane + "_" + (j + 1) + "_" + longTileStr(tile)
- + "_qseq.txt");
- }
- }
- }
- }
-
- return failures;
- }
-
- public boolean filesAvailable() {
- return !tiles.isEmpty();
- }
- }
-
- /**
- * For file types for which there is one file per lane, with fixed record size, and all the tiles in it,
- * so the s_<lane>.bci file can be used to figure out where each tile starts and ends.
- */
- abstract class MultiTileFileUtil<OUTPUT_RECORD extends IlluminaData> extends ParameterizedFileUtil {
- protected final File bci;
- protected TileIndex tileIndex;
- protected File dataFile;
-
- MultiTileFileUtil(final String extension, final File base, final File bciDir, final FileFaker fileFaker) {
- super(makeLaneRegex(extension), makeLaneRegex(extension, lane), extension, base, fileFaker);
- bci = new File(bciDir, "s_" + lane + ".bci");
- if (bci.exists()) {
- tileIndex = new TileIndex(bci);
- } else {
- tileIndex = null;
- }
- final File[] filesMatchingRegexp = IoUtil.getFilesMatchingRegexp(base, pattern);
- if (filesMatchingRegexp == null || filesMatchingRegexp.length == 0) {
- dataFile = null;
- } else if (filesMatchingRegexp.length == 1) {
- dataFile = filesMatchingRegexp[0];
- } else {
- throw new PicardException("More than one filter file found in " + base.getAbsolutePath());
- }
- }
-
- @Override
- public boolean filesAvailable() {
- return tileIndex != null && dataFile != null && dataFile.exists();
- }
-
- @Override
- public LaneTileEnd fileToLaneTileEnd(final String fileName) {
- throw new UnsupportedOperationException();
- }
-
- @Override
- public List<Integer> getTiles() {
- if (tileIndex == null) {
- return Collections.EMPTY_LIST;
- }
- return tileIndex.getTiles();
- }
-
- /**
- * expectedCycles are not checked in this implementation.
- */
- @Override
- public List<String> verify(final List<Integer> expectedTiles, final int[] expectedCycles) {
- if (tileIndex == null) {
- return Collections.singletonList("Tile index(" + bci.getAbsolutePath() + ") does not exist!");
- }
- return tileIndex.verify(expectedTiles);
- }
-
- @Override
- public List<String> fakeFiles(final List<Integer> expectedTiles, final int[] expectedCycles,
- final SupportedIlluminaFormat format) {
- //we need to fake a bci file for the tile index
- final BciFileFaker bciFileFaker = new BciFileFaker();
- try {
- bciFileFaker.fakeBciFile(bci, expectedTiles);
- tileIndex = new TileIndex(bci);
- faker.fakeFile(base, expectedTiles, lane, extension);
- final File[] filesMatchingRegexp = IoUtil.getFilesMatchingRegexp(base, pattern);
- if (filesMatchingRegexp == null || filesMatchingRegexp.length == 0) {
- dataFile = null;
- } else if (filesMatchingRegexp.length == 1) {
- dataFile = filesMatchingRegexp[0];
- } else {
- throw new PicardException("More than one filter file found in " + base.getAbsolutePath());
- }
- } catch (final IOException e) {
- return Collections.singletonList("Could not create tile index file: " + bci.getAbsolutePath());
- }
- return tileIndex.verify(expectedTiles);
- }
-
- abstract IlluminaParser<OUTPUT_RECORD> makeParser(List<Integer> requestedTiles);
- }
-
- class MultiTileFilterFileUtil extends MultiTileFileUtil<PfData> {
-
- /**
- * @param basecallLaneDir location of .filter file and also .bci file
- */
- MultiTileFilterFileUtil(final File basecallLaneDir) {
- super(".filter", basecallLaneDir, basecallLaneDir, new FilterFileFaker());
- }
-
- @Override
- IlluminaParser<PfData> makeParser(final List<Integer> requestedTiles) {
- return new MultiTileFilterParser(tileIndex, requestedTiles, dataFile);
- }
- }
-
- class MultiTileLocsFileUtil extends MultiTileFileUtil<PositionalData> {
-
- MultiTileLocsFileUtil(final File basecallLaneDir, final File bciDir) {
- super(".locs", basecallLaneDir, bciDir, new MultiTileLocsFileFaker());
- }
-
- @Override
- IlluminaParser<PositionalData> makeParser(final List<Integer> requestedTiles) {
- return new MultiTileLocsParser(tileIndex, requestedTiles, dataFile, lane);
- }
- }
-
- /**
- * NextSeq-style bcl's have all tiles for a cycle in a single file.
- */
- class MultiTileBclFileUtil extends ParameterizedFileUtil {
- final File basecallLaneDir;
- final File bci;
- final TileIndex tileIndex;
- final SortedMap<Integer, File> cycleFileMap = new TreeMap<Integer, File>();
-
- MultiTileBclFileUtil(final File basecallLaneDir) {
- // Since these file names do not contain lane number, first two args to ctor are the same.
- super("^(\\d{4}).bcl.bgzf$", "^(\\d{4}).bcl.bgzf$", ".bcl.bgzf", basecallLaneDir,
- new MultiTileBclFileFaker());
- this.basecallLaneDir = basecallLaneDir;
- bci = new File(basecallLaneDir, "s_" + lane + ".bci");
- // Do this once rather than when deciding if these files exist and again later.
- final File[] cycleFiles = IoUtil.getFilesMatchingRegexp(base, pattern);
- if (cycleFiles != null) {
- for (final File file : cycleFiles) {
- final String fileName = file.getName();
- final String cycleNum = fileName.substring(0, fileName.indexOf('.'));
- cycleFileMap.put(Integer.valueOf(cycleNum), file);
- }
- }
- if (bci.exists()) {
- tileIndex = new TileIndex(bci);
- } else {
- tileIndex = null;
- }
-
- }
-
- public CycleIlluminaFileMap getFiles(final List<Integer> tiles, final int[] cycles) {
- // Filter input list of cycles according to which actually exist
- final ArrayList<Integer> goodCycleList = new ArrayList<Integer>(cycles.length);
- for (final int cycle : cycles) {
- if (cycleFileMap.containsKey(cycle)) {
- goodCycleList.add(cycle);
- }
- }
- // Ensure cycles are sorted.
- Collections.sort(goodCycleList);
- final int[] goodCycles = new int[goodCycleList.size()];
- for (int i = 0; i < goodCycles.length; ++i) {
- goodCycles[i] = goodCycleList.get(i);
- }
-
- // Create the map.
- final CycleIlluminaFileMap cycledMap = new CycleIlluminaFileMap();
- if (goodCycles.length > 0) {
- for (final int tile : tiles) {
- cycledMap.put(tile,
- new MultiTileBclCycleFilesIterator(basecallLaneDir, lane, tile, goodCycles, extension));
- }
- }
- return cycledMap;
- }
-
- @Override
- public boolean filesAvailable() {
- return bci.exists() && cycleFileMap.size() > 0;
- }
-
- @Override
- public LaneTileEnd fileToLaneTileEnd(final String fileName) {
- throw new UnsupportedOperationException();
- }
-
-
- @Override
- public List<Integer> getTiles() {
- if (tileIndex == null) {
- return Collections.EMPTY_LIST;
- }
- return tileIndex.getTiles();
- }
-
- @Override
- public List<String> verify(final List<Integer> expectedTiles, final int[] expectedCycles) {
- if (tileIndex == null) {
- return Collections.singletonList("Tile index(" + bci.getAbsolutePath() + ") does not exist!");
- }
- final List<String> ret = tileIndex.verify(expectedTiles);
- for (final int expectedCycle : expectedCycles) {
- if (!cycleFileMap.containsKey(expectedCycle)) {
- ret.add(expectedCycle + ".bcl.bgzf not found in " + base);
- }
- }
- return ret;
- }
-
- @Override
- public List<String> fakeFiles(final List<Integer> expectedTiles, final int[] expectedCycles,
- final SupportedIlluminaFormat format) {
- if (tileIndex == null) {
- return Collections.singletonList("Tile index(" + bci.getAbsolutePath() + ") does not exist!");
- }
- final List<String> ret = tileIndex.verify(expectedTiles);
- for (final int expectedCycle : expectedCycles) {
- if (!cycleFileMap.containsKey(expectedCycle)) {
- ret.add(expectedCycle + ".bcl.bgzf not found in " + base);
- }
- }
- return ret;
- }
- }
-
- /**
- * A support class for return lane tile and end information for a given file
- */
- static class LaneTileEnd {
- public final Integer lane;
- public final Integer tile;
- public final Integer end;
-
- public LaneTileEnd(final Integer lane, final Integer tile, final Integer end) {
- this.lane = lane;
- this.tile = tile;
- this.end = end;
- }
-
- public LaneTileEnd(final Integer lane, final Integer tile) {
- this(lane, tile, null);
- }
- }
-
- /**
- * Return a regex string for finding Lane and Tile given a file extension pattern
- */
- public static String makeLTRegex(final String fileNameEndPattern) {
- return "^" + UNPARAMETERIZED_PER_TILE_PATTERN + fileNameEndPattern + "$";
- }
-
- /**
- * Return a regex string for finding Lane and Tile given a file extension pattern
- */
- private static String makeLTRegex(final String fileNameEndPattern, final int lane) {
- return "^" + makeParameterizedLaneAndTileRegex(lane) + fileNameEndPattern + "$";
- }
-
- private static String makeLaneRegex(final String fileNameEndPattern) {
- return "^s_(\\d+)" + fileNameEndPattern + "$";
- }
-
- private static String makeLaneRegex(final String fileNameEndPattern, final int lane) {
- return "^s_" + lane + fileNameEndPattern + "$";
- }
-
- private static int getCycleFromDir(final File tempCycleDir) {
- final char[] name = tempCycleDir.getName().toCharArray();
- if (name[0] != 'C') {
- throw new PicardException("Invalid cycle directory name " + tempCycleDir.getName());
- }
-
- String intStr = "";
- boolean periodFound = false;
- for (int i = 1; i < name.length && !periodFound; i++) {
- if (name[i] == '.') {
- periodFound = true;
- } else if (name[i] == '1' || name[i] == '2' || name[i] == '3' ||
- name[i] == '4' || name[i] == '5' || name[i] == '6' ||
- name[i] == '7' || name[i] == '8' || name[i] == '9' ||
- name[i] == '0') {
- intStr += name[i];
- } else {
- throw new PicardException("Invalid cycle directory name " + tempCycleDir.getAbsolutePath());
- }
- }
-
- return Integer.parseInt(intStr);
- }
-
- /**
- * Given a pattern and file name return a LaneTileEnd with the first two matches to the pattern returned
- * as the lane and tile respectively
- */
- private static LaneTileEnd laneAndTileFromFirstTwoMatches(final String fileName, final Pattern pattern) {
- final Matcher matcher = pattern.matcher(fileName);
- if (!matcher.matches()) {
- return null;
- }
- return new LaneTileEnd(Integer.parseInt(matcher.group(1)), Integer.parseInt(matcher.group(2)));
- }
-
- /**
+ /*
* Return a string representing the Lane in the format "L00<lane>"
*
* @param lane The lane to transform
- *
* @return A long string representation of the name
*/
- private static String longLaneStr(final int lane) {
+ public static String longLaneStr(final int lane) {
String lstr = String.valueOf(lane);
final int zerosToAdd = 3 - lstr.length();
@@ -1344,54 +224,6 @@ public class IlluminaFileUtil {
return "L" + lstr;
}
- /**
- * Return a string representing the Lane in the format "000<tile>"
- *
- * @param tile The tile to transform
- *
- * @return A long string representation of the name
- */
- private static String longTileStr(final int tile) {
- String tstr = String.valueOf(tile);
- final int zerosToAdd = 4 - tstr.length();
-
- for (int i = 0; i < zerosToAdd; i++) {
- tstr = "0" + tstr;
- }
- return tstr;
- }
-
- /**
- * Return all files that match pattern of the given file type in the given base directory
- */
- private static IlluminaFileMap getTiledFiles(final File baseDirectory, final Pattern pattern,
- final ParameterizedFileUtil ift) {
- final IlluminaFileMap fileMap = new IlluminaFileMap();
- if (baseDirectory.exists()) {
- IoUtil.assertDirectoryIsReadable(baseDirectory);
- final File[] files = IoUtil.getFilesMatchingRegexp(baseDirectory, pattern);
- for (final File file : files) {
- if (file.length() > 0) {
- final LaneTileEnd lt = ift.fileToLaneTileEnd(file.getName());
- fileMap.put(lt.tile, file);
- }
- }
- }
-
- return fileMap;
- }
-
- /**
- * For filename patterns that end with .txt tack on the option .gz extension
- */
- private static String processTxtExtension(final String fileNameEndPattern) {
- if (fileNameEndPattern.endsWith(".txt")) {
- return fileNameEndPattern + "(\\.gz|\\.bz2)?";
- } else {
- return fileNameEndPattern;
- }
- }
-
private String liToStr(final List<Integer> intList) {
if (intList.size() == 0) {
@@ -1408,12 +240,12 @@ public class IlluminaFileUtil {
private String summarizeTileCounts(final List<SupportedIlluminaFormat> formats) {
String summary;
- ParameterizedFileUtil pfu = utils.get(formats.get(0));
+ ParameterizedFileUtil pfu = getUtil(formats.get(0));
List<Integer> tiles = pfu.getTiles();
summary = pfu.extension + "(" + liToStr(tiles) + ")";
for (final SupportedIlluminaFormat format : formats) {
- pfu = utils.get(format);
+ pfu = getUtil(format);
tiles = pfu.getTiles();
summary += ", " + pfu.extension + "(" + liToStr(tiles) + ")";
@@ -1421,43 +253,4 @@ public class IlluminaFileUtil {
return summary;
}
-
- /**
- * We want to be able to predetermine if the BCL files are gzipped or not and we also want to verify
- * that all of the files are the same. Look through all of the cycle dirs in this lane and grab all
- * BCL (gzipped or not) files in the tree. Determine the exension and then verify that they're all the same.
- * <p/>
- * If there are no BCL files, return the standard extension (i.e. ".bcl") to conserve backwards compatibility
- */
- private String inferBclExtension(final File laneDir) {
- final Pattern bclExtensionPattern = Pattern.compile(".*.bcl(\\.gz)?$");
- final String bclGzipExtension = ".bcl.gz";
- String bclExtension = ".bcl";
-
- final File[] cycleDirs = IoUtil.getFilesMatchingRegexp(laneDir, CYCLE_SUBDIRECTORY_PATTERN);
- final List<File> allBclFiles = new ArrayList<File>();
- if (cycleDirs != null && cycleDirs.length > 0) {
- // Get all of the BCL files in the various cycle dirs
- for (final File cycleDir : cycleDirs) {
- allBclFiles.addAll(Arrays.asList(IoUtil.getFilesMatchingRegexp(cycleDir, bclExtensionPattern)));
- }
-
- if (allBclFiles.size() > 0) {
- // Define the extension to be the one the first file has. After that, verify that all files have the
- // same extension
- if (allBclFiles.get(0).getPath().endsWith(bclGzipExtension)) {
- bclExtension = bclGzipExtension;
- }
-
- for (final File bclFile : allBclFiles) {
- if (!bclFile.getPath().endsWith(bclExtension)) {
- throw new PicardException(
- "Not all BCL files in " + laneDir.getAbsolutePath() + " have the same extension!");
- }
- }
- }
- }
-
- return bclExtension;
- }
}
diff --git a/src/java/net/sf/picard/illumina/parser/IlluminaIntensityParser.java b/src/java/net/sf/picard/illumina/parser/IlluminaIntensityParser.java
deleted file mode 100644
index 72cc846..0000000
--- a/src/java/net/sf/picard/illumina/parser/IlluminaIntensityParser.java
+++ /dev/null
@@ -1,132 +0,0 @@
-package net.sf.picard.illumina.parser;
-
-import net.sf.picard.PicardException;
-
-import java.io.File;
-import java.util.List;
-import java.util.Map;
-
-/**
- * Common parent class to CnfParser and CifParser. Creates the relevant CycleFileParser to read Intensity files and
- * partially implements the makeData used to create either the RawIntensityData or NoiseData object that will be
- * returned in IlluminaCycledFileSetParser.next().
- *
- * @author jburke at broadinstitute.org
- */
-abstract class IlluminaIntensityParser<T extends IlluminaData> extends PerTilePerCycleParser<T> {
- public IlluminaIntensityParser(final File directory, final int lane, final CycleIlluminaFileMap tilesToCycleFiles, final OutputMapping outputMapping) {
- super(directory, lane, tilesToCycleFiles, outputMapping);
- this.initialize();
- }
-
- /**
- * Add the intensity for one cycle to the illData object at index for the given channel.
- * @param illData The IlluminaDataObject created in the makeData method for this cluster
- * @param index Where in the FCID arrays where intensity should be placed
- * @param channel A,C,G, or T
- * @param intensity The value read by the CycleFileParser for this cycle
- */
- protected abstract void addIntensityToIlluminaData(final T illData, final OutputMapping.TwoDIndex index, final IntensityChannel channel, final short intensity);
-
- /**
- * Both CnfParser and CifParser produces an array of FCIDs, implement this method to convert them into the relevant IlluminaData subclass(RawIntensityData or NoiseData)
- * @param fcids The intensity data that should be returned by the IlluminaData subclass
- * @return Fcids wrapped by an IlluminaData class of type T
- */
- protected abstract T intensityToIlluminaData(final FourChannelIntensityData[] fcids);
-
- /**
- * Make an IlluminaData object of type T with FCIDs of the given lengths.
- * @param outputLengths The expected lengths of the output data
- * @return IlluminaData object of Type T
- */
- @Override
- protected T makeData(final int[] outputLengths) {
- final FourChannelIntensityData [] fcids = new FourChannelIntensityData[outputLengths.length];
- for(int i = 0; i < outputLengths.length; i++) {
- fcids[i] = new FourChannelIntensityData(outputLengths[i]);
- }
-
- return intensityToIlluminaData(fcids);
- }
-
- /**
- * Return an IntensityFileParser for the given file/cycle
- * @param file The file to parse
- * @param cycle The cycle that file represents
- * @return CycleFileParser
- */
- @Override
- protected CycleFileParser<T> makeCycleFileParser(final File file, final int cycle, final int tileNumber) {
- return new IntensityFileParser(file, cycle);
- }
-
- @Override
- public void verifyData(final List<Integer> tiles, final int [] cycles) {
- //Verify we have the correct number of cycles and for each cycle we have the correct number of tiles
- super.verifyData(tiles, cycles);
-
- Long fileSize;
- Integer numClusters;
- Integer elementSize = null;
-
- for(final Map.Entry<Integer, CycleFilesIterator> tileToFiles : tilesToCycleFiles.entrySet()) {
- fileSize = null;
- numClusters = null;
-
- for(final File intensityFile : tileToFiles.getValue()) {
- final ClusterIntensityFileReader.ClusterIntensityFileHeader header = ClusterIntensityFileReader.readHeaders(intensityFile); //catches a number of file structure errors
- if(fileSize == null) {
- fileSize = intensityFile.length();
- numClusters = header.numClusters;
- elementSize = header.elementSize;
- } else {
- if(fileSize != intensityFile.length()) {
- throw new PicardException("Intensity cycle files for tile(" + tileToFiles.getValue() + ") were not of the same size, offending file(" + intensityFile.getAbsolutePath() + ")");
- }
-
- if(numClusters != header.numClusters) {
- throw new PicardException("Intensity cycle files for tile(" + tileToFiles.getValue() + ") did not have the same number of clusters(" + intensityFile.getAbsolutePath() + ")");
- }
-
- if(elementSize != header.elementSize) {
- throw new PicardException("Intensity cycle files for tile(" + tileToFiles.getValue() + ") did not have the same element sizes(" + intensityFile.getAbsolutePath() + ")");
- }
-
- if(header.numCycles != 1) {
- throw new PicardException("Intensity cycle file for tile(" + tileToFiles.getValue() + ") had more than one cycle per file num cycles found(" + header.numCycles + ")");
- }
- }
- }
- }
- }
-
- protected class IntensityFileParser implements CycleFileParser<T>{
- private final ClusterIntensityFileReader reader;
- private final int cycle;
- private int cluster;
- private final OutputMapping.TwoDIndex index;
-
- public IntensityFileParser(final File file, final int cycle) {
- reader = new ClusterIntensityFileReader(file);
- cluster = 0;
- index = outputMapping.getOutputIndexForCycle(cycle);
- this.cycle = cycle;
- }
-
- public void close() {
- }
-
- public void next(final T ild) {
- for(final IntensityChannel channel : IntensityChannel.values()) {
- addIntensityToIlluminaData(ild, index, channel, reader.getValue(cluster, channel, cycle));
- }
- ++cluster;
- }
-
- public boolean hasNext() {
- return cluster < reader.getNumClusters();
- }
- }
-}
-
diff --git a/src/java/net/sf/picard/illumina/parser/IlluminaParser.java b/src/java/net/sf/picard/illumina/parser/IlluminaParser.java
index 5e59030..5a1e101 100644
--- a/src/java/net/sf/picard/illumina/parser/IlluminaParser.java
+++ b/src/java/net/sf/picard/illumina/parser/IlluminaParser.java
@@ -45,25 +45,31 @@ interface IlluminaParser<DATA_TYPE extends IlluminaData> extends Iterator<DATA_T
/**
* Is there a DATA_TYPE object for another cluster remaining.
+ *
* @return TRUE if there is a DATA_TYPE object for the next cluster that can be provided by
* next
*/
boolean hasNext();
- /** Get the tile for the NEXT DATA_TYPE object that will be returned by this parser. This should
- * be called BEFORE next if you want the tile for the value returned by next */
+ /**
+ * Get the tile for the NEXT DATA_TYPE object that will be returned by this parser. This should
+ * be called BEFORE next if you want the tile for the value returned by next
+ */
public int getTileOfNextCluster();
/**
* Given the expected tiles and cycles for this run, make sure this parser can provide data for
- * all tiles/cycles or throw's an exception if it's missing any required data or data structures
+ * all tiles/cycles or throws an exception if it's missing any required data or data structures
* it relies on do not disagree with the provided tiles/cycles
- * @param tiles The number of tiles in the current run
+ *
+ * @param tiles The number of tiles in the current run
* @param cycles The number of cycles in the current run
*/
- void verifyData(final List<Integer> tiles, final int [] cycles);
+ void verifyData(final List<Integer> tiles, final int[] cycles);
/** The DataTypes that this parser can provide */
Set<IlluminaDataType> supportedTypes();
+ void close();
+
}
diff --git a/src/java/net/sf/picard/illumina/parser/MultiTileBclCycleFilesIterator.java b/src/java/net/sf/picard/illumina/parser/MultiTileBclCycleFilesIterator.java
deleted file mode 100644
index 15403a0..0000000
--- a/src/java/net/sf/picard/illumina/parser/MultiTileBclCycleFilesIterator.java
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * The MIT License
- *
- * Copyright (c) 2014 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
-package net.sf.picard.illumina.parser;
-
-import java.io.File;
-
-/**
- * Overrides standard file naming scheme for multi-tile BCL files.
- */
-public class MultiTileBclCycleFilesIterator extends CycleFilesIterator {
- public MultiTileBclCycleFilesIterator(File laneDir, int lane, int tile, int[] cycles, String fileExt) {
- super(laneDir, lane, tile, cycles, fileExt);
- }
-
- @Override
- protected File getFileForCycle(final int cycle) {
- return new File(parentDir, String.format("%04d%s", cycle, fileExt));
- }
-}
diff --git a/src/java/net/sf/picard/illumina/parser/MultiTileBclFileUtil.java b/src/java/net/sf/picard/illumina/parser/MultiTileBclFileUtil.java
new file mode 100644
index 0000000..26410d2
--- /dev/null
+++ b/src/java/net/sf/picard/illumina/parser/MultiTileBclFileUtil.java
@@ -0,0 +1,115 @@
+package net.sf.picard.illumina.parser;
+
+import net.sf.picard.illumina.parser.fakers.MultiTileBclFileFaker;
+import net.sf.picard.io.IoUtil;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+/**
+ * NextSeq-style bcl's have all tiles for a cycle in a single file.
+ */
+public class MultiTileBclFileUtil extends ParameterizedFileUtil {
+ final File basecallLaneDir;
+ final File bci;
+ final TileIndex tileIndex;
+ final CycleIlluminaFileMap cycleFileMap = new CycleIlluminaFileMap();
+
+ MultiTileBclFileUtil(final File basecallLaneDir, final int lane) {
+ // Since these file names do not contain lane number, first two args to ctor are the same.
+ super("^(\\d{4}).bcl.bgzf$", ".bcl.bgzf", basecallLaneDir,
+ new MultiTileBclFileFaker(), lane);
+ this.basecallLaneDir = basecallLaneDir;
+ bci = new File(basecallLaneDir, "s_" + lane + ".bci");
+ // Do this once rather than when deciding if these files exist and again later.
+ final File[] cycleFiles = IoUtil.getFilesMatchingRegexp(base, matchPattern);
+ if (bci.exists()) {
+ tileIndex = new TileIndex(bci);
+ if (cycleFiles != null) {
+ for (final File file : cycleFiles) {
+ final String fileName = file.getName();
+ final String cycleNum = fileName.substring(0, fileName.indexOf('.'));
+ final IlluminaFileMap fileMap = new IlluminaFileMap();
+ for(final Integer tile : tileIndex.getTiles()) {
+ fileMap.put(tile, file);
+ }
+ cycleFileMap.put(Integer.valueOf(cycleNum), fileMap);
+ }
+ }
+ } else {
+ tileIndex = null;
+ }
+
+ }
+
+ public CycleIlluminaFileMap getFiles(final List<Integer> tiles, final int[] cycles) {
+ // Filter input list of cycles according to which actually exist
+ final ArrayList<Integer> goodCycleList = new ArrayList<Integer>(cycles.length);
+ for (final int cycle : cycles) {
+ if (cycleFileMap.containsKey(cycle)) {
+ goodCycleList.add(cycle);
+ }
+ }
+ // Ensure cycles are sorted.
+ Collections.sort(goodCycleList);
+ final int[] goodCycles = new int[goodCycleList.size()];
+ for (int i = 0; i < goodCycles.length; ++i) {
+ goodCycles[i] = goodCycleList.get(i);
+ }
+
+ // Create the map.
+ final CycleIlluminaFileMap cycledMap = new CycleIlluminaFileMap();
+ if (goodCycles.length > 0) {
+ for(final int cycle : goodCycles) {
+ final IlluminaFileMap fileMap = cycleFileMap.get(cycle).keep(tiles);
+ cycledMap.put(cycle, fileMap);
+ }
+ }
+ return cycledMap;
+ }
+
+ @Override
+ public boolean filesAvailable() {
+ return bci.exists() && cycleFileMap.size() > 0;
+ }
+
+ @Override
+ public List<Integer> getTiles() {
+ if (tileIndex == null) {
+ return Collections.emptyList();
+ }
+ return tileIndex.getTiles();
+ }
+
+ @Override
+ public List<String> verify(final List<Integer> expectedTiles, final int[] expectedCycles) {
+ if (tileIndex == null) {
+ return Collections.singletonList("Tile index(" + bci.getAbsolutePath() + ") does not exist!");
+ }
+ final List<String> ret = tileIndex.verify(expectedTiles);
+ for (final int expectedCycle : expectedCycles) {
+ if (!cycleFileMap.containsKey(expectedCycle)) {
+ ret.add(expectedCycle + ".bcl.bgzf not found in " + base);
+ }
+ }
+ return ret;
+ }
+
+ @Override
+ public List<String> fakeFiles(final List<Integer> expectedTiles, final int[] expectedCycles,
+ final IlluminaFileUtil.SupportedIlluminaFormat format) {
+ if (tileIndex == null) {
+ return Collections.singletonList("Tile index(" + bci.getAbsolutePath() + ") does not exist!");
+ }
+ final List<String> ret = tileIndex.verify(expectedTiles);
+ for (final int expectedCycle : expectedCycles) {
+ if (!cycleFileMap.containsKey(expectedCycle)) {
+ ret.add(expectedCycle + ".bcl.bgzf not found in " + base);
+ }
+ }
+ return ret;
+ }
+}
+
diff --git a/src/java/net/sf/picard/illumina/parser/MultiTileBclParser.java b/src/java/net/sf/picard/illumina/parser/MultiTileBclParser.java
index fd2fd93..c11edd8 100644
--- a/src/java/net/sf/picard/illumina/parser/MultiTileBclParser.java
+++ b/src/java/net/sf/picard/illumina/parser/MultiTileBclParser.java
@@ -23,13 +23,13 @@
*/
package net.sf.picard.illumina.parser;
-import net.sf.picard.PicardException;
import net.sf.picard.illumina.parser.readers.BclIndexReader;
import net.sf.picard.illumina.parser.readers.BclQualityEvaluationStrategy;
import net.sf.picard.illumina.parser.readers.BclReader;
import net.sf.samtools.util.CloseableIterator;
import java.io.File;
+import java.util.List;
import java.util.NoSuchElementException;
/**
@@ -38,57 +38,67 @@ import java.util.NoSuchElementException;
*/
public class MultiTileBclParser extends BclParser {
private final TileIndex tileIndex;
+ private MultiTileBclDataCycleFileParser cycleFileParser = null;
public MultiTileBclParser(final File directory, final int lane, final CycleIlluminaFileMap tilesToCycleFiles,
final OutputMapping outputMapping, final boolean applyEamssFilter,
final BclQualityEvaluationStrategy bclQualityEvaluationStrategy,
final TileIndex tileIndex) {
super(directory, lane, tilesToCycleFiles, outputMapping, applyEamssFilter, bclQualityEvaluationStrategy);
this.tileIndex = tileIndex;
- super.initialize();
+ this.initialize();
}
- /**
- * Defer initialization until after this class is fully constructed. This is necessary because superclass
- * ctor calls makeReader, which is overridden below, and the override requires that this.tileIndex is initialized,
- * and that doesn't happen until after superclass has been constructed.
- */
@Override
- protected void initialize() {
+ public void initialize(){
+ if(tileIndex != null){
+ seekToTile(currentTile);
+ }
}
- @Override
- protected CloseableIterator<BclReader.BclValue> makeReader(final File file, final int cycle, final int tileNumber) {
- final TileIndex.TileIndexRecord tileIndexRecord = tileIndex.findTile(tileNumber);
-
- final BclIndexReader bclIndexReader = new BclIndexReader(file);
- if (tileIndex.getNumTiles() != bclIndexReader.getNumTiles()) {
- throw new PicardException(String.format("%s.getNumTiles(%d) != %s.getNumTiles(%d)",
- tileIndex.getFile().getAbsolutePath(), tileIndex.getNumTiles(), bclIndexReader.getBciFile().getAbsolutePath(), bclIndexReader.getNumTiles()));
+ private CountLimitedIterator makeReader(final List<File> files) {
+ if(tileIndex != null) {
+ final BclReader bclReader = BclReader.makeSeekable(files, bclQualityEvaluationStrategy, outputMapping.getOutputReadLengths());
+ final int numClustersInTile = bclReader.seek(files, tileIndex, currentTile);
+ return new CountLimitedIterator(bclReader, numClustersInTile);
}
+ else{
+ return null;
+ }
+ }
- final BclReader bclReader = BclReader.makeSeekable(file, bclQualityEvaluationStrategy);
- bclReader.seek(bclIndexReader.get(tileIndexRecord.zeroBasedTileNumber));
-
- return new CountLimitedIterator(bclReader, tileIndexRecord.numClustersInTile);
+ @Override
+ protected CycleFilesParser<BclData> makeCycleFileParser(final List<File> files) {
+ if (cycleFileParser == null) {
+ cycleFileParser = new MultiTileBclDataCycleFileParser(files, currentTile);
+ } else {
+ final int numClustersInTile = cycleFileParser.getReader().seek(files, tileIndex, currentTile);
+ cycleFileParser.setCurrentTile(currentTile);
+ cycleFileParser.resetClusterLimit(numClustersInTile);
+ }
+ return cycleFileParser;
}
/**
* An iterator wrapper that stops when it has return a pre-determined number of records even if the underlying
* iterator still had more records.
*/
- static class CountLimitedIterator implements CloseableIterator<BclReader.BclValue> {
- private final CloseableIterator<BclReader.BclValue> underlyingIterator;
- private final int recordLimit;
+ static class CountLimitedIterator implements CloseableIterator<BclData> {
+ public BclReader getUnderlyingIterator() {
+ return underlyingIterator;
+ }
+
+ private final BclReader underlyingIterator;
+ private int recordLimit;
private int numRecordsRead = 0;
- CountLimitedIterator(final CloseableIterator<BclReader.BclValue> underlyingIterator, final int recordLimit) {
+ CountLimitedIterator(final BclReader underlyingIterator, final int recordLimit) {
this.underlyingIterator = underlyingIterator;
this.recordLimit = recordLimit;
}
@Override
public void close() {
- underlyingIterator.close();
+ //underlyingIterator.close();
}
@Override
@@ -97,7 +107,7 @@ public class MultiTileBclParser extends BclParser {
}
@Override
- public BclReader.BclValue next() {
+ public BclData next() {
if (!hasNext()) throw new NoSuchElementException();
++numRecordsRead;
return underlyingIterator.next();
@@ -108,4 +118,54 @@ public class MultiTileBclParser extends BclParser {
throw new UnsupportedOperationException();
}
}
+
+
+ private class MultiTileBclDataCycleFileParser implements CycleFilesParser<BclData> {
+ final CountLimitedIterator reader;
+ int currentTile;
+
+ public MultiTileBclDataCycleFileParser(final List<File> files, final int currentTile) {
+ this.currentTile = currentTile;
+ reader = makeReader(files);
+ }
+
+ @Override
+ public void close() {
+ reader.close();
+ }
+
+ @Override
+ public BclData next() {
+ if (!hasNext()) {
+ throw new NoSuchElementException();
+ }
+ return reader.next();
+ }
+
+ @Override
+ public boolean hasNext() {
+ try {
+ return reader.hasNext();
+ } catch (final NullPointerException npe) {
+ return false;
+ }
+ }
+
+ public int getCurrentTile(){
+ return currentTile;
+ }
+
+ public BclReader getReader() {
+ return reader.getUnderlyingIterator();
+ }
+
+ public void resetClusterLimit(final int numClustersInTile) {
+ reader.recordLimit = numClustersInTile;
+ reader.numRecordsRead = 0;
+ }
+
+ public void setCurrentTile(final int currentTile) {
+ this.currentTile = currentTile;
+ }
+ }
}
diff --git a/src/java/net/sf/picard/illumina/parser/MultiTileFileUtil.java b/src/java/net/sf/picard/illumina/parser/MultiTileFileUtil.java
new file mode 100644
index 0000000..044eac0
--- /dev/null
+++ b/src/java/net/sf/picard/illumina/parser/MultiTileFileUtil.java
@@ -0,0 +1,120 @@
+package net.sf.picard.illumina.parser;
+
+import net.sf.picard.PicardException;
+import net.sf.picard.illumina.parser.fakers.BciFileFaker;
+import net.sf.picard.illumina.parser.fakers.FileFaker;
+import net.sf.picard.illumina.parser.fakers.FilterFileFaker;
+import net.sf.picard.illumina.parser.fakers.MultiTileLocsFileFaker;
+import net.sf.picard.io.IoUtil;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Collections;
+import java.util.List;
+
+/**
+ * For file types for which there is one file per lane, with fixed record size, and all the tiles in it,
+ * so the s_<lane>.bci file can be used to figure out where each tile starts and ends.
+ */
+public abstract class MultiTileFileUtil<OUTPUT_RECORD extends IlluminaData> extends ParameterizedFileUtil {
+ protected final File bci;
+ protected TileIndex tileIndex;
+ protected File dataFile;
+
+ MultiTileFileUtil(final String extension, final File base, final File bciDir, final FileFaker fileFaker,
+ final int lane) {
+ super(false, extension, base, fileFaker, lane);
+ bci = new File(bciDir, "s_" + lane + ".bci");
+ if (bci.exists()) {
+ tileIndex = new TileIndex(bci);
+ } else {
+ tileIndex = null;
+ }
+ final File[] filesMatchingRegexp = IoUtil.getFilesMatchingRegexp(base, matchPattern);
+ if (filesMatchingRegexp == null || filesMatchingRegexp.length == 0) {
+ dataFile = null;
+ } else if (filesMatchingRegexp.length == 1) {
+ dataFile = filesMatchingRegexp[0];
+ } else {
+ throw new PicardException("More than one filter file found in " + base.getAbsolutePath());
+ }
+ }
+
+ @Override
+ public boolean filesAvailable() {
+ return tileIndex != null && dataFile != null && dataFile.exists();
+ }
+
+ @Override
+ public List<Integer> getTiles() {
+ if (tileIndex == null) {
+ return Collections.emptyList();
+ }
+ return tileIndex.getTiles();
+ }
+
+ /**
+ * expectedCycles are not checked in this implementation.
+ */
+ @Override
+ public List<String> verify(final List<Integer> expectedTiles, final int[] expectedCycles) {
+ if (tileIndex == null) {
+ return Collections.singletonList("Tile index(" + bci.getAbsolutePath() + ") does not exist!");
+ }
+ return tileIndex.verify(expectedTiles);
+ }
+
+ @Override
+ public List<String> fakeFiles(final List<Integer> expectedTiles, final int[] expectedCycles,
+ final IlluminaFileUtil.SupportedIlluminaFormat format) {
+ //we need to fake a bci file for the tile index
+ final BciFileFaker bciFileFaker = new BciFileFaker();
+ try {
+ bciFileFaker.fakeBciFile(bci, expectedTiles);
+ tileIndex = new TileIndex(bci);
+ faker.fakeFile(base, expectedTiles, lane, extension);
+ final File[] filesMatchingRegexp = IoUtil.getFilesMatchingRegexp(base, matchPattern);
+ if (filesMatchingRegexp == null || filesMatchingRegexp.length == 0) {
+ dataFile = null;
+ } else if (filesMatchingRegexp.length == 1) {
+ dataFile = filesMatchingRegexp[0];
+ } else {
+ throw new PicardException("More than one filter file found in " + base.getAbsolutePath());
+ }
+ } catch (final IOException e) {
+ return Collections.singletonList("Could not create tile index file: " + bci.getAbsolutePath());
+ }
+ return tileIndex.verify(expectedTiles);
+ }
+
+ abstract IlluminaParser<OUTPUT_RECORD> makeParser(List<Integer> requestedTiles);
+
+}
+
+class MultiTileFilterFileUtil extends MultiTileFileUtil<PfData> {
+
+ /**
+ * @param basecallLaneDir location of .filter file and also .bci file
+ */
+ MultiTileFilterFileUtil(final File basecallLaneDir, final int lane) {
+ super(".filter", basecallLaneDir, basecallLaneDir, new FilterFileFaker(), lane);
+ }
+
+ @Override
+ IlluminaParser<PfData> makeParser(final List<Integer> requestedTiles) {
+ return new MultiTileFilterParser(tileIndex, requestedTiles, dataFile);
+ }
+}
+
+class MultiTileLocsFileUtil extends MultiTileFileUtil<PositionalData> {
+
+ MultiTileLocsFileUtil(final File basecallLaneDir, final File bciDir, final int lane) {
+ super(".locs", basecallLaneDir, bciDir, new MultiTileLocsFileFaker(), lane);
+ }
+
+ @Override
+ IlluminaParser<PositionalData> makeParser(final List<Integer> requestedTiles) {
+ return new MultiTileLocsParser(tileIndex, requestedTiles, dataFile, lane);
+ }
+}
+
diff --git a/src/java/net/sf/picard/illumina/parser/MultiTileFilterParser.java b/src/java/net/sf/picard/illumina/parser/MultiTileFilterParser.java
index 3927fc5..74453ae 100644
--- a/src/java/net/sf/picard/illumina/parser/MultiTileFilterParser.java
+++ b/src/java/net/sf/picard/illumina/parser/MultiTileFilterParser.java
@@ -35,6 +35,7 @@ import java.util.List;
*/
public class MultiTileFilterParser extends MultiTileParser<PfData> {
private final FilterFileReader reader;
+
public MultiTileFilterParser(final TileIndex tileIndex, final List<Integer> requestedTiles, final File filterFile) {
super(tileIndex, requestedTiles, Collections.singleton(IlluminaDataType.PF));
reader = new FilterFileReader(filterFile);
@@ -55,4 +56,9 @@ public class MultiTileFilterParser extends MultiTileParser<PfData> {
void skipRecords(final int numToSkip) {
reader.skipRecords(numToSkip);
}
+
+ @Override
+ public void close() {
+ //no-op
+ }
}
diff --git a/src/java/net/sf/picard/illumina/parser/MultiTileLocsParser.java b/src/java/net/sf/picard/illumina/parser/MultiTileLocsParser.java
index ac05fe8..fb20eae 100644
--- a/src/java/net/sf/picard/illumina/parser/MultiTileLocsParser.java
+++ b/src/java/net/sf/picard/illumina/parser/MultiTileLocsParser.java
@@ -74,4 +74,9 @@ public class MultiTileLocsParser extends MultiTileParser<PositionalData> {
void skipRecords(final int numToSkip) {
reader.skipRecords(numToSkip);
}
+
+ @Override
+ public void close() {
+ reader.close();
+ }
}
diff --git a/src/java/net/sf/picard/illumina/parser/ParameterizedFileUtil.java b/src/java/net/sf/picard/illumina/parser/ParameterizedFileUtil.java
new file mode 100644
index 0000000..53fd2a3
--- /dev/null
+++ b/src/java/net/sf/picard/illumina/parser/ParameterizedFileUtil.java
@@ -0,0 +1,174 @@
+package net.sf.picard.illumina.parser;
+
+import net.sf.picard.PicardException;
+import net.sf.picard.illumina.parser.fakers.FileFaker;
+import net.sf.picard.io.IoUtil;
+
+import java.io.File;
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+public abstract class ParameterizedFileUtil {
+ public static final String PER_TILE_PATTERN_STRING = "s_(\\d+)_(\\d{1,5})";
+ /**
+ * The file extension for this class, file extension does not have the standard meaning
+ * in this instance. It means, all the characters that come after the identifying portion of
+ * the file (after lane, tile, and end that is). So _qseq.txt and .filter are both file extensions
+ */
+ protected final String extension;
+
+ /**
+ * A pattern that will match files of this type for this lane
+ */
+ protected Pattern matchPattern;
+
+ protected final int lane;
+ protected List<Integer> tiles;
+ /**
+ * If you think of the file system as a tree, this is the deepest directory(node) on the tree that
+ * still contains all of the files for this given type (e.g. If we're talking about BCLs the directory
+ * structure is:
+ * <p/>
+ * BaseCall Dir
+ * |
+ * L001
+ * | | |
+ * C1.1 C2.1 ... Cn.1
+ * | | |
+ * bcl Files ... bclFiles
+ * <p/>
+ * L001 is the base because it contains every BCL file in the run (though those files are nested in
+ * other folders).
+ */
+ protected final File base;
+ protected final FileFaker faker;
+
+ public ParameterizedFileUtil(final boolean laneTileRegex, final String extension, final File base,
+ final FileFaker faker, final int lane) {
+ this(extension, base, faker, lane);
+ if (laneTileRegex) {
+ matchPattern = Pattern.compile(escapePeriods(makeLaneTileRegex(processTxtExtension(extension), lane)));
+ } else {
+ matchPattern = Pattern.compile(escapePeriods(makeLaneRegex(extension, lane)));
+ }
+ }
+
+ public ParameterizedFileUtil(final String pattern, final String extension, final File base, final FileFaker faker,
+ final int lane) {
+ this(extension, base, faker, lane);
+ this.matchPattern = Pattern.compile(pattern);
+ }
+
+ private ParameterizedFileUtil(final String extension, final File base, final FileFaker faker,
+ final int lane) {
+ this.faker = faker;
+ this.extension = extension;
+ this.base = base;
+ this.lane = lane;
+ }
+
+ /**
+ * Determine whether or not files are available
+ *
+ * @return return true if files are found matching this types pattern, false otherwise
+ */
+ public abstract boolean filesAvailable();
+
+ /**
+ * Return a list of all tiles available for this file format and run
+ *
+ * @return A List of tile integers
+ */
+ public List<Integer> getTiles() {
+ return tiles;
+ }
+
+ /**
+ * Given the expected tiles/expected cycles for this file type, return a list of error messages describing any
+ * missing/or malformed files
+ *
+ * @param expectedTiles An ordered list of tile numbers
+ * @param expectedCycles An ordered list of cycle numbers that may contain gaps
+ * @return A list of error messages for this format
+ */
+ public abstract List<String> verify(List<Integer> expectedTiles, int[] expectedCycles);
+
+ /**
+ * Given the expected tiles/expected cycles for this file type create a set of fake files such that the
+ * verification criteria are met.
+ *
+ * @param expectedTiles An ordered list of tile numbers
+ * @param cycles An ordered list of cycle numbers that may contain gaps
+ * @param format The format of the files that are to be faked
+ * @return A list of error messages for this format
+ */
+ public abstract List<String> fakeFiles(List<Integer> expectedTiles, int[] cycles,
+ IlluminaFileUtil.SupportedIlluminaFormat format);
+
+ /**
+ * Returns only lane and tile information as PerTileFt's do not have End information.
+ *
+ * @param fileName Filename to analyze for data
+ * @return A LaneTile object with the discovered Lane and Tile information and a null end field.
+ */
+ protected Integer fileToTile(final String fileName) {
+ final Matcher matcher = matchPattern.matcher(fileName);
+ if (!matcher.matches()) {
+ return null;
+ }
+ return Integer.parseInt(matcher.group(1));
+ }
+
+ /**
+ * Return a regex string for finding Lane and Tile given a file extension pattern
+ */
+ public static String makeLaneTileRegex(final String fileNameEndPattern, final int lane) {
+ if (lane < 0) {
+ throw new PicardException("Lane (" + lane + ") cannot be negative");
+ }
+ return "^" + "s_" + lane + "_(\\d{1,5})" + fileNameEndPattern + "$";
+ }
+
+ private String makeLaneRegex(final String fileNameEndPattern, final int lane) {
+ return "^s_" + lane + fileNameEndPattern + "$";
+ }
+
+ /**
+ * The period separator is expected in the file extension, since some do not start with it
+ */
+ private String escapePeriods(final String preEscaped) {
+ return preEscaped
+ .replaceAll("\\.", "\\."); //In the first one the \\ is inside a regex in the second it's NOT
+ }
+
+ /**
+ * For filename patterns that end with .txt tack on the option .gz extension
+ */
+ private String processTxtExtension(final String fileNameEndPattern) {
+ if (fileNameEndPattern.endsWith(".txt")) {
+ return fileNameEndPattern + "(\\.gz|\\.bz2)?";
+ } else {
+ return fileNameEndPattern;
+ }
+ }
+
+ /**
+ * Return all files that match pattern of the given file type in the given base directory
+ */
+ protected IlluminaFileMap getTiledFiles(final File baseDirectory, final Pattern pattern) {
+ final IlluminaFileMap fileMap = new IlluminaFileMap();
+ if (baseDirectory.exists()) {
+ IoUtil.assertDirectoryIsReadable(baseDirectory);
+ final File[] files = IoUtil.getFilesMatchingRegexp(baseDirectory, pattern);
+ for (final File file : files) {
+ if (file.length() > 0) {
+ fileMap.put(fileToTile(file.getName()), file);
+ }
+ }
+ }
+
+ return fileMap;
+ }
+
+}
diff --git a/src/java/net/sf/picard/illumina/parser/PerTileCycleParser.java b/src/java/net/sf/picard/illumina/parser/PerTileCycleParser.java
new file mode 100644
index 0000000..afb09cd
--- /dev/null
+++ b/src/java/net/sf/picard/illumina/parser/PerTileCycleParser.java
@@ -0,0 +1,203 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2011 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+package net.sf.picard.illumina.parser;
+
+import net.sf.picard.PicardException;
+import org.broadinstitute.variant.variantcontext.writer.BCF2FieldWriter;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.NoSuchElementException;
+import java.util.Set;
+import java.util.TreeSet;
+
+/**
+ * PerTilePerCycleParser is an abstract IlluminaParser that maintains a list of file parsers for the current tile (1 for each cycle)
+ * and coordinates the construction/population of an IlluminaData object on a cycle by cycle basis.
+ *
+ * @param <ILLUMINA_DATA>
+ */
+abstract class PerTileCycleParser<ILLUMINA_DATA extends IlluminaData> implements IlluminaParser<ILLUMINA_DATA> {
+
+ /** Location of illumina output files to be parsed. Typically this is Data/Intensities/L00<lane> */
+ private final File laneDirectory;
+
+ /** The lane to iterate over */
+ private final int lane;
+
+ /** A parser for the current tile */
+ private CycleFilesParser<ILLUMINA_DATA> cycleFilesParser;
+
+ final OutputMapping outputMapping;
+
+ /** The current tile number */
+ protected int currentTile;
+
+ /** Map of Cycle -> Tile -> List<File> */
+ private final CycleIlluminaFileMap cyclesToTileFiles;
+
+ private final TreeSet<Integer> tileOrder;
+
+ /**
+ * Construct a per tile parser
+ *
+ * @param directory The directory containing the lane we are analyzing (i.e. the parent of the L00<lane> directory)
+ * @param lane The lane that is being iterated over
+ * @param cyclesToTileFiles A map of tile to CycleFilesIterators whose iterators contain only the cycles we want to output
+ * @param outputMapping Data structure containing information on how we should output data
+ */
+ PerTileCycleParser(final File directory, final int lane, final CycleIlluminaFileMap cyclesToTileFiles, final OutputMapping outputMapping) {
+ this.tileOrder = getTileOrder(cyclesToTileFiles);
+ this.lane = lane;
+ this.laneDirectory = new File(directory, IlluminaFileUtil.longLaneStr(this.lane));
+ this.cyclesToTileFiles = cyclesToTileFiles;
+ this.currentTile = tileOrder.first();
+ this.outputMapping = outputMapping;
+ }
+
+ private TreeSet<Integer> getTileOrder(final CycleIlluminaFileMap cyclesToTileFiles) {
+ final TreeSet<Integer> uniqueTiles = new TreeSet<Integer>();
+
+ for (final IlluminaFileMap fileMap : cyclesToTileFiles.values()) {
+ uniqueTiles.addAll(fileMap.keySet());
+ }
+ return uniqueTiles;
+ }
+
+ /**
+ * For a given cycle, return a CycleFilesParser.
+ *
+ * @param file The file to parse
+ * @return A CycleFilesParser that will populate the correct position in the IlluminaData object with that cycle's data.
+ */
+ protected abstract CycleFilesParser<ILLUMINA_DATA> makeCycleFileParser(final List<File> file);
+
+ public abstract void initialize();
+
+ /**
+ * CycleFileParsers iterate through the clusters of a file and populate an IlluminaData object with a single cycle's
+ * value.
+ *
+ * @param <ILLUMINA_DATA>
+ */
+ protected interface CycleFilesParser<ILLUMINA_DATA> {
+ public void close();
+
+ public ILLUMINA_DATA next();
+
+ public boolean hasNext();
+ }
+
+ /**
+ * Clear the current set of cycleFileParsers and replace them with the ones for the tile indicated by oneBasedTileNumber
+ *
+ * @param tile requested tile
+ */
+ @Override
+ public void seekToTile(final int tile) {
+ currentTile = tile;
+
+ if(cycleFilesParser != null) {
+ cycleFilesParser.close();
+ }
+
+ int totalCycles = 0;
+ final List<File> tileFiles = new ArrayList<File>();
+ for (final Map.Entry<Integer, IlluminaFileMap> entry : cyclesToTileFiles.entrySet()) {
+ tileFiles.add(entry.getValue().get(currentTile));
+ ++totalCycles;
+ }
+ cycleFilesParser = makeCycleFileParser(tileFiles);
+
+ if (totalCycles != outputMapping.getTotalOutputCycles()) {
+ throw new PicardException("Number of cycle OUTPUT files found (" + totalCycles + ") does not equal the number expected (" + outputMapping.getTotalOutputCycles() + ")");
+ }
+ }
+
+ /**
+ * Return the data for the next cluster by:
+ * 1. Advancing tiles if we reached the end of the current tile.
+ * 2. For each cycle, get the appropriate parser and have it populate it's data into the IlluminaData object.
+ *
+ * @return The IlluminaData object for the next cluster
+ */
+ @Override
+ public ILLUMINA_DATA next() { //iterate over clusters
+ if (!hasNext()) {
+ throw new NoSuchElementException("IlluminaData is missing in lane " + lane + " at directory location " + laneDirectory.getAbsolutePath());
+ }
+
+ if (!cycleFilesParser.hasNext()) {
+ seekToTile(tileOrder.higher(currentTile));
+ }
+
+ return cycleFilesParser.next();
+ }
+
+ @Override
+ public boolean hasNext() {
+ return cycleFilesParser.hasNext() || currentTile < tileOrder.last();
+ }
+
+ /**
+ * Returns the tile of the next cluster that will be returned by PerTilePerCycleParser and therefore should be called before
+ * next() if you want to know the tile for the data returned by next()
+ *
+ * @return The tile number of the next ILLUMINA_DATA object to be returned
+ */
+ public int getTileOfNextCluster() {
+ //if the current parser still has more clusters, return the current tile number
+ if (cycleFilesParser.hasNext()) {
+ return currentTile;
+ }
+
+ //if the current parser is EMPTY, return the next tile number
+ if (currentTile < tileOrder.last()) {
+ return tileOrder.higher(currentTile);
+ }
+
+ //If we are at the end of clusters then this method should not be called, throw an exception
+ throw new NoSuchElementException();
+ }
+
+ @Override
+ public void verifyData(List<Integer> tiles, final int[] cycles) {
+ if (tiles == null) {
+ tiles = new ArrayList<Integer>(this.cyclesToTileFiles.keySet());
+ }
+ this.cyclesToTileFiles.assertValid(tiles, cycles);
+ }
+
+ public void remove() {
+ throw new UnsupportedOperationException("Remove is not supported by " + this.getClass().getName());
+ }
+
+ @Override
+ public void close() {
+ cycleFilesParser.close();
+ }
+}
diff --git a/src/java/net/sf/picard/illumina/parser/PerTileFileUtil.java b/src/java/net/sf/picard/illumina/parser/PerTileFileUtil.java
new file mode 100644
index 0000000..87c0b74
--- /dev/null
+++ b/src/java/net/sf/picard/illumina/parser/PerTileFileUtil.java
@@ -0,0 +1,78 @@
+package net.sf.picard.illumina.parser;
+
+import net.sf.picard.illumina.parser.fakers.FileFaker;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.LinkedList;
+import java.util.List;
+
+public class PerTileFileUtil extends ParameterizedFileUtil {
+ private final IlluminaFileMap fileMap;
+
+ public PerTileFileUtil(final String extension, final File base,
+ final FileFaker faker, final int lane) {
+ super(true, extension, base, faker, lane);
+ this.fileMap = getTiledFiles(base, matchPattern);
+ if (fileMap.size() > 0) {
+ this.tiles = Collections.unmodifiableList(new ArrayList<Integer>(this.fileMap.keySet()));
+ } else {
+ this.tiles = new ArrayList<Integer>();
+ }
+ }
+
+ @Override
+ public boolean filesAvailable() {
+ return !fileMap.isEmpty();
+ }
+
+ public IlluminaFileMap getFiles() {
+ return fileMap;
+ }
+
+ public IlluminaFileMap getFiles(final List<Integer> tiles) {
+ return fileMap.keep(tiles);
+ }
+
+ @Override
+ public List<String> verify(final List<Integer> expectedTiles, final int[] expectedCycles) {
+ final List<String> failures = new LinkedList<String>();
+
+ if (!base.exists()) {
+ failures.add("Base directory(" + base.getAbsolutePath() + ") does not exist!");
+ } else {
+ if (!tiles.containsAll(expectedTiles)) {
+ final List<Integer> missing = new ArrayList<Integer>(expectedTiles);
+ missing.removeAll(tiles);
+ failures.add("Missing tile " + missing + " for file type " + extension + ".");
+ }
+ }
+ return failures;
+ }
+
+ @Override
+ public List<String> fakeFiles(final List<Integer> expectedTiles, final int[] cycles,
+ final IlluminaFileUtil.SupportedIlluminaFormat format) {
+ final List<String> failures = new LinkedList<String>();
+ if (!base.exists()) {
+ failures.add("Base directory(" + base.getAbsolutePath() + ") does not exist!");
+ } else {
+ for (final Integer tile : expectedTiles) {
+ if (!tiles.contains(tile) || fileMap.get(tile).length() == 0) {
+ //create a new file of this type
+ try {
+ faker.fakeFile(base, tile, lane, extension);
+ } catch (final IOException e) {
+ failures.add(String.format("Could not create fake file %s: %s", fileMap.get(tile),
+ e.getMessage()));
+ }
+
+ }
+ }
+ }
+ return failures;
+ }
+
+}
diff --git a/src/java/net/sf/picard/illumina/parser/PerTilePerCycleFileUtil.java b/src/java/net/sf/picard/illumina/parser/PerTilePerCycleFileUtil.java
new file mode 100644
index 0000000..8565773
--- /dev/null
+++ b/src/java/net/sf/picard/illumina/parser/PerTilePerCycleFileUtil.java
@@ -0,0 +1,268 @@
+package net.sf.picard.illumina.parser;
+
+import net.sf.picard.PicardException;
+import net.sf.picard.illumina.parser.fakers.FileFaker;
+import net.sf.picard.illumina.parser.readers.BclReader;
+import net.sf.picard.io.IoUtil;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Set;
+import java.util.TreeSet;
+import java.util.regex.Matcher;
+import java.util.Map;
+import java.util.HashMap;
+
+public class PerTilePerCycleFileUtil extends ParameterizedFileUtil {
+
+ private final CycleIlluminaFileMap cycleFileMap;
+ private final Set<Integer> detectedCycles = new TreeSet<Integer>();
+
+ public PerTilePerCycleFileUtil(final String extension,
+ final File base, final FileFaker faker, final int lane) {
+ super(true, extension, base, faker, lane);
+ //sideEffect, assigned to numCycles
+ this.cycleFileMap = getPerTilePerCycleFiles();
+ }
+
+ /**
+ * For the given tiles, populate a CycleIlluminaFileMap that contains all these tiles and will iterate through
+ * all the files for these tiles in expectedBase
+ * Side Effect: Assigns numCycles
+ *
+ * @return A CycleIlluminaFileMap with the listed (or all) tiles for at least expectedCycles number of cycles(or total available
+ * cycles if expectedCycles is null)
+ */
+ protected CycleIlluminaFileMap getPerTilePerCycleFiles() {
+ final CycleIlluminaFileMap cycledMap = new CycleIlluminaFileMap();
+
+ final File laneDir = base;
+ final File[] tempCycleDirs;
+ tempCycleDirs = IoUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN);
+ if (tempCycleDirs == null || tempCycleDirs.length == 0) {
+ return cycledMap;
+ }
+
+ for (final File tempCycleDir : tempCycleDirs) {
+ detectedCycles.add(getCycleFromDir(tempCycleDir));
+ }
+
+ final Set<Integer> uniqueTiles = new HashSet<Integer>();
+
+ for (final File cycleDir : tempCycleDirs) {
+ final IlluminaFileMap fileMap = getTiledFiles(cycleDir, matchPattern);
+ uniqueTiles.addAll(fileMap.keySet());
+ cycledMap.put(getCycleFromDir(cycleDir), fileMap);
+ }
+
+ this.tiles = Collections.unmodifiableList(new ArrayList<Integer>(uniqueTiles));
+ return cycledMap;
+ }
+
+ public CycleIlluminaFileMap getFiles() {
+ return cycleFileMap;
+ }
+
+ public CycleIlluminaFileMap getFiles(final List<Integer> tiles) {
+ return cycleFileMap.keep(tiles, detectedCycles);
+ }
+
+ /**
+ * Returns a cycleIlluminaFileMap with all available tiles but limited to the cycles passed in. Any cycles that are missing
+ * cycle files or directories will be removed from the cycle list that is kept.
+ *
+ * @param cycles Cycles that should be present in the output CycleIlluminaFileMap
+ * @return A CycleIlluminaFileMap with all available tiles but at most the cycles passed in by the cycles parameter
+ */
+ public CycleIlluminaFileMap getFiles(final int[] cycles) {
+ //Remove any cycles that were discovered to be NON-EXISTENT when this util was instantiated
+ final Set<Integer> filteredCycles = removeNonExistentCycles(cycles);
+ return cycleFileMap.keep(tiles, filteredCycles);
+ }
+
+ /**
+ * Returns a cycleIlluminaFileMap that contains only the tiles and cycles specified (and fewer if the original CycleIlluminaFileMap, created
+ * on util instantiation, doesn't contain any of these tiles/cycles).
+ *
+ * @param cycles Cycles that should be present in the output CycleIlluminaFileMap
+ * @return A CycleIlluminaFileMap with at most the tiles/cycles listed in the parameters
+ */
+ public CycleIlluminaFileMap getFiles(final List<Integer> tiles, final int[] cycles) {
+ //Remove any cycles that were discovered to be NON-EXISTENT when this util was instantiated
+ final Set<Integer> filteredCycles = removeNonExistentCycles(cycles);
+ return cycleFileMap.keep(tiles, filteredCycles);
+ }
+
+ private Set<Integer> removeNonExistentCycles(final int[] cycles) {
+
+ final TreeSet<Integer> inputCyclesSet = new TreeSet<Integer>();
+ for (final Integer inputCycle : cycles) {
+ inputCyclesSet.add(inputCycle);
+ }
+
+ inputCyclesSet.retainAll(detectedCycles);
+
+ return inputCyclesSet;
+ }
+
+ public Set<Integer> getDetectedCycles() {
+ return detectedCycles;
+ }
+
+ /**
+ * Discover all files of this type in expectedBase that match pattern and construct a list of tiles
+ * available based on these files. The same number of tiles is expected in each cycle dir.
+ *
+ * @return A list of tile integers for all tiles available
+ */
+ public List<Integer> getTiles() {
+ return tiles;
+ }
+
+ public boolean filesAvailable() {
+ boolean filesAvailable = false;
+ for (final IlluminaFileMap fileMap : cycleFileMap.values()) {
+ if (!fileMap.isEmpty()) {
+ filesAvailable = true;
+ break;
+ }
+ }
+ return filesAvailable;
+ }
+
+ @Override
+ public List<String> verify(final List<Integer> expectedTiles, final int[] expectedCycles) {
+ final List<String> failures = new LinkedList<String>();
+ final Map<Integer, Long> tileToFileLengthMap = new HashMap<Integer, Long>();
+
+ if (!base.exists()) {
+ failures.add("Base directory(" + base.getAbsolutePath() + ") does not exist!");
+ } else {
+ final CycleIlluminaFileMap cfm = getFiles(expectedTiles, expectedCycles);
+ for (final int currentCycle : expectedCycles) {
+ final IlluminaFileMap fileMap = cfm.get(currentCycle);
+ if (fileMap != null) {
+ for (final int tile : expectedTiles) {
+ final File cycleFile = fileMap.get(tile);
+ if (cycleFile != null) {
+ if (tileToFileLengthMap.get(tile) == null) {
+ tileToFileLengthMap.put(tile, cycleFile.length());
+ } else if (!extension.equals(".bcl.gz") && tileToFileLengthMap.get(tile) != cycleFile.length()) {
+
+ // TODO: The gzip bcl files might not be the same length despite having the same content,
+ // for now we're punting on this but this should be looked into at some point
+ failures.add("File type " + extension
+ + " has cycles files of different length. Current cycle ("
+ + currentCycle + ") " +
+ "Length of first non-empty file (" + tileToFileLengthMap.get(tile)
+ + ") length of current cycle (" + cycleFile.length() + ")"
+ + " File(" + cycleFile.getAbsolutePath() + ")");
+ }
+ } else {
+ failures.add("File type " + extension + " is missing a file for cycle " + currentCycle + " and tile " + tile);
+ }
+ }
+ } else {
+ failures.add("Missing file for cycle " + currentCycle + " in directory " + base.getAbsolutePath()
+ + " for file type " + extension);
+ }
+ }
+
+ }
+
+
+ return failures;
+ }
+
+ @Override
+ public List<String> fakeFiles(final List<Integer> expectedTiles, final int[] expectedCycles,
+ final IlluminaFileUtil.SupportedIlluminaFormat format) {
+ final List<String> failures = new LinkedList<String>();
+
+ if (!base.exists()) {
+ base.mkdirs();
+ }
+
+ final Set<Integer> missingCycleSet = new TreeSet<Integer>();
+ for (final Integer cycle : expectedCycles) {
+ missingCycleSet.add(cycle);
+ }
+
+ missingCycleSet.removeAll(detectedCycles);
+
+ for (final Integer cycle : missingCycleSet) {
+ final File cycleDirectory = new File(base, "C" + cycle + ".1");
+ if (cycleDirectory.mkdirs()) {
+ detectedCycles.add(cycle);
+ }
+ }
+
+ final CycleIlluminaFileMap cfm = getPerTilePerCycleFiles();
+ Long cycleSize = null;
+ for (final int currentCycle : expectedCycles) {
+ final IlluminaFileMap fileMap = cfm.get(currentCycle);
+
+ if (fileMap == null) {
+ for (final Integer tile : expectedTiles) {
+ final File fileToFake = new File(base + File.separator + getFileForCycle(currentCycle, tile));
+ try {
+ if (cycleSize != null) {
+ faker.fakeFile(fileToFake, cycleSize.intValue());
+ }
+ else{
+ faker.fakeFile(fileToFake, 1);
+ }
+ } catch (final IOException e) {
+ failures.add("Could not create fake file: " + e.getMessage());
+ }
+ }
+ } else {
+ for (final int tile : expectedTiles) {
+ final File cycleFile = fileMap.get(tile);
+ if (cycleFile != null && cycleSize == null) {
+ cycleSize = BclReader.getNumberOfClusters(cycleFile);
+ }
+ try {
+ if (cycleFile == null) {
+ final File fileToFake = new File(base + File.separator + getFileForCycle(currentCycle, tile));
+ if (cycleSize != null) {
+ faker.fakeFile(fileToFake, cycleSize.intValue());
+ } else {
+ faker.fakeFile(fileToFake, 1);
+ }
+ }
+ } catch (final IOException e) {
+ failures.add("Could not create fake file: " + e.getMessage());
+ }
+ }
+ }
+
+ }
+
+ for (final Integer cycle : missingCycleSet) {
+ failures.add("Missing cycle directory " + cycle + " in directory " + base.getAbsolutePath()
+ + " for file type " + extension);
+ }
+ return failures;
+ }
+
+ private String getFileForCycle(final int currentCycle, final int tile) {
+ return "C" + currentCycle + ".1" + File.separator + "s_" + lane + "_" + tile + extension;
+ }
+
+ private static int getCycleFromDir(final File tempCycleDir) {
+ final String fileName = tempCycleDir.getName();
+
+ final Matcher matcher = IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN.matcher(fileName);
+ if (!matcher.matches()) {
+ throw new PicardException("Invalid cycle directory name " + tempCycleDir.getName());
+ }
+
+ return Integer.parseInt(matcher.group(1));
+ }
+}
diff --git a/src/java/net/sf/picard/illumina/parser/PerTilePerCycleParser.java b/src/java/net/sf/picard/illumina/parser/PerTilePerCycleParser.java
deleted file mode 100644
index dd600d7..0000000
--- a/src/java/net/sf/picard/illumina/parser/PerTilePerCycleParser.java
+++ /dev/null
@@ -1,197 +0,0 @@
-/*
- * The MIT License
- *
- * Copyright (c) 2011 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
-package net.sf.picard.illumina.parser;
-
-import net.sf.picard.PicardException;
-import net.sf.samtools.util.CloserUtil;
-
-import java.util.*;
-import java.io.File;
-
-/**
- * PerTilePerCycleParser is an abstract IlluminaParser that maintains a list of file parsers for the current tile (1 for each cycle)
- * and coordinates the construction/population of an IlluminaData object on a cycle by cycle basis.
- * @param <ILLUMINA_DATA>
- */
-abstract class PerTilePerCycleParser<ILLUMINA_DATA extends IlluminaData> implements IlluminaParser<ILLUMINA_DATA> {
-
- /** Location of illumina output files to be parsed. Typically this is Data/Intensities/L00<lane> */
- private final File laneDirectory;
-
- /** The lane to iterate over */
- private final int lane;
-
- /** A set of parsers for the current tile ordered by cycle */
- private final List<CycleFileParser<ILLUMINA_DATA>> cycleFileParsers;
-
- protected final OutputMapping outputMapping;
-
- /** The current tile number */
- private int tileNumber;
-
- /** Map of tiles -> CycledFilesIterator, the CycleFileIterators of this map should contain ONLY cycles to be output */
- protected final CycleIlluminaFileMap tilesToCycleFiles;
-
- /**
- * Construct a per tile parser
- * @param directory The directory containing the lane we are analyzing (i.e. the parent of the L00<lane> directory)
- * @param lane The lane that is being iterated over
- * @param tilesToCycleFiles A map of tile to CycleFilesIterators whose iterators contain only the cycles we want to output
- * @param outputMapping Data structure containing information on how we should output data
- */
- public PerTilePerCycleParser(final File directory, final int lane, final CycleIlluminaFileMap tilesToCycleFiles, final OutputMapping outputMapping) {
- this.lane = lane;
- this.laneDirectory = new File(directory, "L00" + this.lane);
- this.tilesToCycleFiles = tilesToCycleFiles;
- this.tileNumber = tilesToCycleFiles.firstKey();
- this.outputMapping = outputMapping;
-
- cycleFileParsers = new ArrayList<CycleFileParser<ILLUMINA_DATA>>(outputMapping.getTotalOutputCycles());
- }
-
- /** Do initialization work. This bit was excised from the constructor because inheriting classes that called super() could not
- * initialize member variables first. */
- protected void initialize() {
- seekToTile(tilesToCycleFiles.firstKey());
- }
-
- /**
- * Per cluster makeData will make the relevant IlluminaData object with the given outputLengths
- * @param outputLengths The expected lengths of the output data
- * @return An IlluminaData object that has been constructed with default(according to Java construction rules) data
- */
- protected abstract ILLUMINA_DATA makeData(final int [] outputLengths);
-
- /**
- * For a given cycle, return a CycleFileParser.
- * @param file The file to parse
- * @param cycle The cycle that file represents
- * @param tileNumber For files that contain multiple tiles, need to specify tile of interest.
- * @return A CycleFileParser that will populate the correct position in the IlluminaData object with that cycle's data.
- */
- protected abstract CycleFileParser<ILLUMINA_DATA> makeCycleFileParser(final File file, final int cycle, final int tileNumber);
-
- /**
- * CycleFileParsers iterate through the clusters of a file and populate an IlluminaData object with a single cycle's
- * value.
- * @param <ILLUMINA_DATA>
- */
- protected interface CycleFileParser<ILLUMINA_DATA> {
- public void close();
- public void next(final ILLUMINA_DATA ild);
- public boolean hasNext();
- }
-
- /**
- * Clear the current set of cycleFileParsers and replace them with the ones for the tile indicated by oneBasedTileNumber
- * @param oneBasedTileNumber requested tile with indices beginning at 1
- */
- @Override
- public void seekToTile(final int oneBasedTileNumber) {
- tileNumber = oneBasedTileNumber;
- final CycleFilesIterator filesIterator = tilesToCycleFiles.get(tileNumber);
- filesIterator.reset();
-
- CloserUtil.close(cycleFileParsers);
- cycleFileParsers.clear();
-
- int totalCycles = 0;
- while(filesIterator.hasNext()) {
- final int nextCycle = filesIterator.getNextCycle();
- cycleFileParsers.add(makeCycleFileParser(filesIterator.next(), nextCycle, tileNumber));
- ++totalCycles;
- }
-
- if(totalCycles != outputMapping.getTotalOutputCycles()) {
- throw new PicardException("Number of cycle OUTPUT files found (" + totalCycles + ") does not equal the number expected (" + outputMapping.getTotalOutputCycles() +")");
- }
- }
-
- /**
- * Return the data for the next cluster by:
- * 1. Advancing tiles if we reached the end of the current tile.
- * 2. For each cycle, get the appropriate parser and have it populate it's data into the IlluminaData object.
- * @return The IlluminaData object for the next cluster
- */
- @Override
- public ILLUMINA_DATA next() { //iterate over clusters
- if(!hasNext()) {
- throw new NoSuchElementException("IlluminaData is missing in lane " + lane + " at directory location " + laneDirectory.getAbsolutePath());
- }
-
- if(!cycleFileParsers.get(0).hasNext()) {
- seekToTile(tilesToCycleFiles.higherKey(tileNumber));
- }
-
- final ILLUMINA_DATA data = makeData(outputMapping.getOutputReadLengths());
- final int totalOutputCycles = outputMapping.getTotalOutputCycles();
-
- for(int i = 0; i < totalOutputCycles; ++i) {
- cycleFileParsers.get(i).next(data);
- }
-
- return data;
- }
-
- @Override
- public boolean hasNext() {
- if(cycleFileParsers.get(0).hasNext()) {
- return true;
- }
-
- return tileNumber < tilesToCycleFiles.lastKey();
- }
-
- /**
- * Returns the tile of the next cluster that will be returned by PerTilePerCycleParser and therefore should be called before
- * next() if you want to know the tile for the data returned by next()
- * @return The tile number of the next ILLUMINA_DATA object to be returned
- */
- public int getTileOfNextCluster() {
- //if the current parser still has more clusters, return the current tile number
- if(cycleFileParsers.get(0).hasNext()) {
- return tileNumber;
- }
-
- //if the current parser is EMPTY, return the next tile number
- if(tileNumber < tilesToCycleFiles.lastKey()) {
- return tilesToCycleFiles.higherKey(tileNumber);
- }
-
- //If we are at the end of clusters then this method should not be called, throw an exception
- throw new NoSuchElementException();
- }
-
- @Override
- public void verifyData(List<Integer> tiles, final int [] cycles) {
- if(tiles == null) {
- tiles = new ArrayList<Integer>(this.tilesToCycleFiles.keySet());
- }
- this.tilesToCycleFiles.assertValid(tiles, cycles);
- }
-
- public void remove() {
- throw new UnsupportedOperationException("Remove is not supported by " + this.getClass().getName());
- }
-}
diff --git a/src/java/net/sf/picard/illumina/parser/QseqParser.java b/src/java/net/sf/picard/illumina/parser/QseqParser.java
deleted file mode 100644
index e4672f2..0000000
--- a/src/java/net/sf/picard/illumina/parser/QseqParser.java
+++ /dev/null
@@ -1,592 +0,0 @@
-/*
- * The MIT License
- *
- * Copyright (c) 2012 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
-package net.sf.picard.illumina.parser;
-
-import net.sf.picard.util.*;
-import net.sf.picard.PicardException;
-import net.sf.samtools.util.CollectionUtil;
-import net.sf.samtools.util.StringUtil;
-
-import java.io.File;
-import java.util.*;
-import java.util.Map.Entry;
-import static net.sf.picard.illumina.parser.IlluminaDataType.*;
-
-/**
- * QSeqParser takes a List<IlluminaFileMaps>(1 for each "end" in order) and provides an iterator over all clusters in the
- * for all tiles found in the maps. "Clusters" in this sense refers to the chunks delineated by outputLengths. Position, PF, Base, and Quality data
- * is output in chunks specified by these lengths.
- *
- * Each line contains the following fields:
- * lane
- * tile
- * x-coordinate
- * y-coordinate
- * machine
- * run
- * passing filter
- * bases
- * quals
- *
- * Bases, quals and PF are extracted from this file.
- *
- *
- * @author jburke at broadinstitute.org
- */
-
-class QseqParser implements IlluminaParser<QseqReadData> {
- private final int [] outputLengths; //Expected lengths of the bases/qualities arrays in the output QSeqReadData
- private final QseqReadParser[] parsers; //each parser parsers iterates over all tiles for 1 read
- private final List<IlluminaFileMap> tileMapByReadNumber;
- private QseqReadData nextData;
-
- public static final Set<IlluminaDataType> SUPPORTED_TYPES = Collections.unmodifiableSet(CollectionUtil.makeSet(Position, BaseCalls, QualityScores, PF));
-
- public QseqParser(final int lane, final List<IlluminaFileMap> tileMapByReadNumber, final OutputMapping outputMapping) {
- this.outputLengths = outputMapping.getOutputReadLengths();
- this.tileMapByReadNumber = tileMapByReadNumber;
- List<QseqReadParser> parsersList = makeReadParserList(lane, outputMapping);
- parsers = parsersList.toArray(new QseqReadParser[parsersList.size()]);
- retrieveNext();
- }
-
- /**
- * QseqParser delegates the read/write operations of Qseq data providing to individual QseqReadParsers (1 per read that doesn't entirely
- * consist of skips). To do this QseqParser makes a list of QseqReadParsers that each handles all the tile files for ONE specific READ of the run.
- * (E.g. if in lane 1 there are tiles 1,2,3 in the run and reads 1 and 2 then there will be ONE QseqReadParser that handles
- * the tile files s_1_1_0001_qseq.txt, s_1_1_0002_qseq.txt, s_1_1_0003_qseq.txt and ONE QseqReadParser that handles
- * the tile files s_1_2_0001_qseq.txt, s_1_2_0002_qseq.txt, s_1_2_0003_qseq.txt).
- *
- * A QseqReadParser reads the bases/qualities and other info from the qseq file of the current tile being handled
- * and maps them into an QseqReadData object. However, the output bases/quals do not necessarily
- * correspond 1 to 1 with the bases/quals found in the Qseq files. Therefore we create a mapping from
- * input ranges over the bases of a qseq file (RR below) to the location in the output arrays (LO) that the
- * bases in the range RR are to be copied to.
- *
- *
- * Assuming the reads below represent the structure of bases in the set of QSeq files in tileMapByReadNumber and
- * outputLengths = [Read1.length, Read2.length, Read3.length] - The lengths found in qseqs
- * outputRanges = [(3,5),(8,13),(18,20)] - The Indexes(Cycle#-1) of desired output cycles
- *
- * Read 1 Read2 Read 3
- * [B0, B1, B2, B3, B4, B5, B6, B7] [B0, B1, B2, B3] [B0, B1, B2, B3, B4, B5, B6, B7]
- * S S [O0, O1, O2] S S [O0, O1, O2, O3, O4, O5, 06] S S S [O0, O1, O2]
- * OCI 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
- *
- * S = Cycles skipped in the output
- * Ox = cycles to output at array index x of the output array delineated by the []
- * OCI = Index of cycles in the run as a whole (i.e. cycle# - 1)
- *
- * R(x,y) = Range from x to y inclusive
- * T(ar,ele) = 2D array index where, assuming you have an array int [][]arr; you would index arr[ar][ele]
- * For the reads above:
- * RR for Read 1 = [R(2,4),R(7,7)] LO for Read 1 = [T(0,0), T(1,0)]
- * RR for read 2 = [R(0,4)] LO for Read 2 = [T(1,1)]
- * RR for read 3 = [R(0,2), R(5,7)] LO for Read 3 = [T(1,5), T(2,0)]
- *
- * For each cluster, each read does something similar to:
- *
- * for(int i = 0; i < RR.length; i++) {
- * Range R = RR[i]
- * TwoDArrayIndex L = LO[i]
- * System.arrayCopy(qseqData, R.start, R.length, outputArray[L.ar], L.ele)
- * }
- *
- * @param lane The current lane being parsed
- * @param outputMapping Information on what cycles are being output to ClusterData Objects
- * @return A list of QseqReadParsers that do the actual reading of qseq data and populating cluster data objects
- */
- public List<QseqReadParser> makeReadParserList(final int lane, final OutputMapping outputMapping) {
- //Since there is not a one-to-one relationship with ReadDescriptors in the ReadStructure and QSeq reads,
- //we have to inspect all reads for there sizes and exclude those we don't need in the parser itself
- final int [] actualReadLengths = new int[tileMapByReadNumber.size()];
- int availableCycles = 0;
- for(int i = 0; i < actualReadLengths.length; i++) {
- actualReadLengths[i] = QseqReadParser.getReadLength(tileMapByReadNumber.get(i).firstEntry().getValue());
- availableCycles += actualReadLengths[i];
- }
-
- if(availableCycles < outputMapping.getTotalOutputCycles()) {
- throw new PicardException("Expected output cycles (" + outputMapping.getTotalOutputCycles() + ") is greater than the number of cycles in Qseq files (" + availableCycles + ")");
- }
-
- //Parsers required to fill the output cycles specified by OutputMapping
- final List<QseqReadParser> parsersList = new ArrayList<QseqReadParser>(actualReadLengths.length);
-
- //split expected output ranges so that no one output range spans multiple Qseq files but all cycles in outputMapping
- //are still in at least one range
- final List<Range> splitOutputRanges = splitOutputRangesOnQseqBoundaries(actualReadLengths, outputMapping);
-
- //create a list of ranges(1 per read) of input indexes into the base/qual section of the qseq for each outputRages
- final List<List<Range>> inputRangesPerRead = outputRangesToInputRanges(actualReadLengths, splitOutputRanges);
-
- //just a list of the number of input/output range pairs there are for each read
- final List<Integer> outputRangesPerRead = new ArrayList<Integer>(inputRangesPerRead.size());
- for(final List<Range> readRange : inputRangesPerRead) {
- outputRangesPerRead.add(readRange.size());
- }
-
- //convert output ranges from cycle# to output indices, i.e find the exact indices into the 2D output array (on the cluster data object) that signifies
- // the start of that output range
- final List<List<OutputMapping.TwoDIndex>> outputTargets = outputRangesTo2DTargetsPerRead(outputRangesPerRead, splitOutputRanges, outputMapping);
-
- //create a QseqReadParser for each read that has at least one inputRange to outputTarget pair
- for(int i = 0; i < inputRangesPerRead.size(); i++) {
- if(outputRangesPerRead.get(i) > 0) {
- final List<Range> inputRanges = inputRangesPerRead.get(i);
- final List<OutputMapping.TwoDIndex> outputTarget = outputTargets.get(i);
-
- parsersList.add(new QseqReadParser(lane, tileMapByReadNumber.get(i),
- inputRanges.toArray(new Range[inputRanges.size()]),
- outputTarget.toArray(new OutputMapping.TwoDIndex[outputTarget.size()]), outputMapping));
- }
- }
-
- if(parsersList.size() == 0) {
- throw new PicardException("0 Qseq \"ends\" were found to parse!");
- }
-
- return parsersList;
- }
-
- /**
- * Given a list of outputRanges in which NO RANGE SPANS MULTIPLE QSEQ READS, convert these ranges into
- * input indexes for the given reads
- *(E.g.)
- * Read 1 Read 2 Read3
- * QSeq Reads[B0, B1, B2, B3, B4, B5, B6, B7] [B0, B1, B2, B3] [B0, B1, B2, B3, B4, B5, B6, B7]
- * Output Ranges [ Range(1, 4)] [Range(5,7)] [ Range(8,11) ] [R(12,13)] [ Range(15,19) ]
- * ReadRanges = List(
- * List(Range(1, 4), Range(5,7)),
- * List(Range(0, 4)),
- * List(Range(0, 1), Range(3,7))
- * )
- *
- * @param readLengths The length of qseq reads
- * @param outputRanges Ranges of cycle index numbers indicating cycles to output
- * @return A list of Ranges of indices into qseq reads , one per each outputRange segregated by read
- */
- public static List<List<Range>> outputRangesToInputRanges(final int [] readLengths, final List<Range> outputRanges) {
- final List<Range> scratchOutputRanges = new ArrayList<Range>(outputRanges);
- final List<List<Range>> readRanges = new ArrayList<List<Range>>(readLengths.length);
- for(int i = 0; i < readLengths.length; i++) {
- readRanges.add(new LinkedList<Range>());
- }
-
- int currentRead = 0;
- int startingCycle = 0;
- int endCycle = readLengths[startingCycle] - 1;
- List<Range> currentReadList = readRanges.get(currentRead);
-
-
- while(!scratchOutputRanges.isEmpty()) {
- final Range range = scratchOutputRanges.remove(0);
- while(range.start > endCycle) {
- //advance to next read
- currentRead += 1;
- startingCycle = endCycle + 1;
- endCycle = startingCycle + readLengths[currentRead] - 1;
- currentReadList = readRanges.get(currentRead);
- }
-
- final int outRangeEnd;
- if(endCycle < range.end) {
- scratchOutputRanges.add(0, new Range(endCycle + 1, range.end));
- outRangeEnd = endCycle;
- } else{
- outRangeEnd = range.end;
- }
-
- currentReadList.add(new Range(range.start - startingCycle, outRangeEnd - startingCycle));
-
- }
-
- return readRanges;
- }
-
- /**
- * For each outputRange in cycle indices (cycle #s -1), translate the range into a starting "target" in
- * the 2D output array of bases/clusters in the output array
- * @param rangesPerRead An ordered list with one element per read where each element is the number of ranges for the corresponding read
- * @param splitOutputRanges A flat list of output ranges where no single range spans multiple reads
- * @param outputMapping Information on what cycles should be output and how they should be arranged
- * @return An ordered list with one element per read where each element is a list of starting points
- * to copy input ranges to
- */
- public static List<List<OutputMapping.TwoDIndex>> outputRangesTo2DTargetsPerRead(final List<Integer> rangesPerRead, final List<Range> splitOutputRanges, OutputMapping outputMapping) {
- List<List<OutputMapping.TwoDIndex>> outputTargets = new ArrayList<List<OutputMapping.TwoDIndex>>(rangesPerRead.size());
- for(int i = 0; i < rangesPerRead.size(); i++) {
- outputTargets.add(new ArrayList<OutputMapping.TwoDIndex>(rangesPerRead.get(i)));
- }
-
- int count = 0;
- int readIndex = 0;
- int numRangesForRead = rangesPerRead.get(readIndex);
- List<OutputMapping.TwoDIndex> currentReadTargets = outputTargets.get(readIndex);
-
- for(final Range or : splitOutputRanges) {
-
- while(count >= numRangesForRead) {
- count = 0;
- readIndex += 1;
- numRangesForRead = rangesPerRead.get(readIndex);
- currentReadTargets = outputTargets.get(readIndex);
- }
-
- currentReadTargets.add(outputMapping.getOutputIndexForCycle(or.start+1));
- count += 1;
- }
- return outputTargets;
- }
-
- /**
- * Given a List of output cycle ranges with some that may range over multiple qseq read files, return an identical list except all
- * ranges that span multiple qseq read files will be split up and replaced with ranges that span over only 1 qseq file.
- *
- * Read 1 Read 2 Read3
- * QSeq Reads[B0, B1, B2, B3, B4, B5, B6, B7] [B0, B1, B2, B3] [B0, B1, B2, B3, B4, B5, B6, B7]
- * Ranges [ Range(1, 4)] [ Range(5,13) ] [ Range(15,19) ]
- * Output Ranges [ Range(1, 4)] [Range(5,7)] [ Range(8,11) ] [R(12,13)] [ Range(15,19) ]
- * @param qseqReadLengths
- * @param outputMapping
- * @return
- */
- public static List<Range> splitOutputRangesOnQseqBoundaries(int[] qseqReadLengths, OutputMapping outputMapping) {
- List<Range> outputCycleIndexRanges = new LinkedList<Range>(Arrays.asList(outputMapping.getCycleIndexRanges()));
- List<Range> outputRanges = new LinkedList<Range>();
-
- int qseqArray = 0;
- int startCycleIndex = 0;
- while(outputCycleIndexRanges.size() > 0) {
- final Range curRange = outputCycleIndexRanges.remove(0);
- final int endCycleIndex = startCycleIndex + qseqReadLengths[qseqArray] - 1;
- if(curRange.start <= endCycleIndex) {
- if(curRange.end > endCycleIndex) {
- outputRanges.add(new Range(curRange.start, endCycleIndex));
- outputCycleIndexRanges.add(0, new Range(endCycleIndex+1, curRange.end));
- } else {
- outputRanges.add(curRange);
- }
- } else {
- outputCycleIndexRanges.add(0, curRange);
- startCycleIndex = endCycleIndex + 1;
- ++qseqArray;
- }
- }
-
- return outputRanges;
- }
-
- /**
- * Assert that all ends have the same number of tiles and that the tiles for a given end have the same number of bases (checking only the first cluster
- * per file). In the binary formats it will be easier to check the number of clusters etc but for Qseqs any problems with number of clusters will be
- * discovered when we iterate past the end of one of the reads.
- */
- @Override
- public void verifyData(final List<Integer> tiles, final int [] cycles) { //in this case, runConfiguration related information was verified in construction
- Integer numTiles = null;
- int end = 1;
- for(final IlluminaFileMap tilesToFiles : tileMapByReadNumber) {
- if(tiles != null && !tilesToFiles.keySet().containsAll(tiles)) { //now with properly util classes this shouldn't happen but since this is only done once up front, test it anyway
- TreeSet<Integer> missingTiles = new TreeSet<Integer>(tiles);
- missingTiles.removeAll(tilesToFiles.keySet());
- throw new PicardException("IlluminaFileMap for \"end\" number " + end + " is missing tiles: " + StringUtil.join(",", new ArrayList<Integer>(missingTiles)));
- }
-
- if(numTiles == null) { //make sure all ends have the same number of tiles
- numTiles = tilesToFiles.size();
- } else if(numTiles != tilesToFiles.size()) {
- throw new PicardException("Qseq \"end\" files do not have the same number of tiles expected(" + numTiles + ") found(" + tilesToFiles.size() + ") on end (" + end + ")");
- }
-
- //make sure this end has files with the same read lengths
- Integer numBases = null;
- for(final Entry<Integer, File> tileNoToFile : tilesToFiles.entrySet()) {
- final int readLength = QseqReadParser.getReadLength(tileNoToFile.getValue());
- if(numBases == null) {
- numBases = readLength;
- } else if(numBases != readLength) {
- throw new PicardException("Qseq \"end\" (" + end + ") has tiles with different numbers of bases per read. Found on Tile(" + tileNoToFile.getKey() + ") File(" + tileNoToFile.getValue().getAbsolutePath() + ")");
- }
- }
- ++end;
- }
- }
-
- @Override
- public void seekToTile(final int oneBasedTileNumber) {
- for(final QseqReadParser parser : parsers) {
- parser.seekToTile(oneBasedTileNumber);
- }
-
- retrieveNext();
- }
-
- @Override
- public QseqReadData next() {
- if(!hasNext()) {
- throw new NoSuchElementException();
- }
-
- final QseqReadData currentData = nextData;
- retrieveNext();
-
- return currentData;
- }
-
- private void retrieveNext() {
- if(parsers[0].hasNext()) {
- nextData = new QseqReadData(outputLengths);
- for(final QseqReadParser parser : parsers) {
- parser.next(nextData);
- }
- } else {
- nextData = null;
- }
- }
-
- public int getTileOfNextCluster(){
- return nextData.getTile();
- }
-
-
- public void remove() {
- throw new UnsupportedOperationException("Remove is not supported by " + QseqParser.class.getName());
- }
-
- @Override
- public boolean hasNext() {
- return nextData != null;
- }
-
- @Override
- public Set<IlluminaDataType> supportedTypes() {
- return SUPPORTED_TYPES;
- }
-}
-
-/**
- * QSeqReadFilesParser parsers all tiles for 1 particular read (e.g. first of pair, second of pair, barcode).
- */
-class QseqReadParser {
- public static final int MACHINE_COLUMN = 0;
- public static final int RUN__COLUMN = 1;
- public static final int LANE_COLUMN = 2;
- public static final int TILE_COLUMN = 3;
- public static final int X_COLUMN = 4;
- public static final int Y_COLUMN = 5;
- public static final int PF_COLUMN = 10;
- public static final int BASES_COLUMN = 8;
- public static final int QUALS_COLUMN = 9;
-
- private final IlluminaTextIterator textParser; //Parses multiple illumina tabbed delimited files
- private final FormatUtil formatter;
- private final Range[] srcRanges;
- private final OutputMapping.TwoDIndex[] dstStarts;
- private final int [] copyLengths;
- protected final int readLength;
- private static final SolexaQualityConverter qualConverter = SolexaQualityConverter.getSingleton();
-
- public QseqReadParser(final int lane, final IlluminaFileMap tilesToReadFiles, final Range [] srcRanges, final OutputMapping.TwoDIndex[] dstStarts, final OutputMapping outputMapping)
- {
- this.textParser = new IlluminaTextIterator(lane, tilesToReadFiles);
- this.formatter = new FormatUtil();
- this.readLength = QseqReadParser.getReadLength(tilesToReadFiles.firstEntry().getValue());
-
- this.srcRanges = srcRanges;
- this.dstStarts = dstStarts;
-
- copyLengths = new int[srcRanges.length];
- for(int i = 0; i < copyLengths.length; i++) {
- copyLengths[i] = srcRanges[i].length;
- }
- }
-
- public void seekToTile(int oneBasedTileNumber) {
- textParser.seekToTile(oneBasedTileNumber);
- }
-
- public boolean hasNext() {
- return textParser.hasNext();
- }
-
- public void next(final QseqReadData readData) {
- final String [] fields = textParser.next();
-
- final int lane = formatter.parseInt(fields[LANE_COLUMN]);
- textParser.validateLane(lane);
-
- final int tile = formatter.parseInt(fields[TILE_COLUMN]);
- final int x = formatter.parseInt(fields[X_COLUMN]);
- final int y = formatter.parseInt(fields[Y_COLUMN]);
-
- // Currently unused
- //final String machine = fields[MACHINE_COLUMN];
- //final int run = getFormatter().parseInt(fields[RUN__COLUMN]);
- final boolean pf = formatter.parseInt(fields[PF_COLUMN]) == 1;
-
- final String baseString = fields[BASES_COLUMN];
- final String qualString = fields[QUALS_COLUMN];
- if (baseString.length() != qualString.length()) {
- throw new PicardException("Length of bases and quals don't match in " + textParser.getCurrentFilename());
- }
-
- readData.setOrCheckLane(lane);
- readData.setOrCheckTile(tile);
- readData.setOrCheckXCoordinate(x);
- readData.setOrCheckYCoordinate(y);
- readData.setOrCheckPf(pf);
-
- stringToBytes(baseString, srcRanges, dstStarts, readData.getBases());
- stringToQuals(qualString, srcRanges, dstStarts, copyLengths, readData.getQualities());
- }
-
- private static void stringToBytes(final String s, final Range[] sourceRanges, final OutputMapping.TwoDIndex[] destRanges, byte[][] outputBuffers) {
- for(int i = 0; i < sourceRanges.length; i++) {
- s.getBytes(sourceRanges[i].start, sourceRanges[i].end + 1, outputBuffers[destRanges[i].majorIndex], destRanges[i].minorIndex);
- }
- }
-
- private static void stringToQuals(final String s, final Range[] sourceRanges, final OutputMapping.TwoDIndex[] destRanges, final int [] copyLengths, final byte [][] outputBuffers ) {
- stringToBytes(s, sourceRanges, destRanges, outputBuffers);
-
- for(int i = 0; i < destRanges.length; i++) {
- qualConverter.convertSolexa_1_3_QualityCharsToPhredBinary(destRanges[i].minorIndex, copyLengths[i], outputBuffers[destRanges[i].majorIndex]);
- }
- }
-
- public static int getReadLength(final File qseqFile) {
- final BasicInputParser parser = new BasicInputParser(true, qseqFile);
- if (!parser.hasNext()) {
- throw new PicardException("Unexpected empty qseq file: " + qseqFile);
- }
- final String[] fields = parser.next();
- return fields[BASES_COLUMN].length();
- }
-}
-
-
-class QseqReadData implements PositionalData, BaseData, QualityData, PfData {
- private final byte [][] bases;
- private final byte [][] qualities;
- private Boolean pf;
- private Integer xCoord;
- private Integer yCoord;
- private Integer lane;
- private Integer tile;
-
- public QseqReadData(final int [] bufferSizes) {
- bases = new byte[bufferSizes.length][];
- qualities = new byte[bufferSizes.length][];
- for(int i = 0; i < bufferSizes.length; i++) {
- bases[i] = new byte[bufferSizes[i]];
- qualities[i] = new byte[bufferSizes[i]];
- }
-
- pf = null;
- xCoord = null;
- yCoord = null;
- lane = null;
- tile = null;
- }
-
- @Override
- public byte[][] getBases() {
- return bases;
- }
-
- @Override
- public byte[][] getQualities() {
- return qualities;
- }
-
- public void setOrCheckPf(final boolean pf) {
- if(this.pf == null) {
- this.pf = pf;
- } else {
- assertEquals(this.pf, pf, "pf");
- }
- }
-
- @Override
- public boolean isPf() {
- return pf;
- }
-
- @Override
- public int getXCoordinate() {
- return xCoord;
- }
-
- public void setOrCheckXCoordinate(final int xCoord) {
- if(this.xCoord == null) {
- this.xCoord = xCoord;
- } else {
- assertEquals(this.xCoord, xCoord, "xCoord");
- }
- }
-
- @Override
- public int getYCoordinate() {
- return yCoord;
- }
-
- public void setOrCheckYCoordinate(final int yCoord) {
- if(this.yCoord == null) {
- this.yCoord = yCoord;
- } else {
- assertEquals(this.yCoord, yCoord, "yCoord");
- }
- }
-
- public int getLane() {
- return lane;
- }
-
- public void setOrCheckLane(final int lane) {
- if(this.lane == null) {
- this.lane = lane;
- } else {
- assertEquals(this.lane, lane, "lane");
- }
- }
-
- public int getTile() {
- return tile;
- }
-
- public void setOrCheckTile(final int tile) {
- if(this.tile == null) {
- this.tile = tile;
- } else {
- assertEquals(this.tile, tile, "tile");
- }
- }
-
- public <T> void assertEquals(T current, T newValue, String valueName) {
- if(!current.equals(newValue)) {
- throw new PicardException(valueName + " values don't match: original(" + current + ") new(" + newValue + ")");
- }
- }
-}
diff --git a/src/java/net/sf/picard/illumina/parser/TileIndex.java b/src/java/net/sf/picard/illumina/parser/TileIndex.java
index 28b0ffc..57dabb8 100644
--- a/src/java/net/sf/picard/illumina/parser/TileIndex.java
+++ b/src/java/net/sf/picard/illumina/parser/TileIndex.java
@@ -39,7 +39,7 @@ import java.util.*;
* number of clusters in tile: 4-byte int
* Number of records to read is determined by reaching EOF.
*/
-class TileIndex implements Iterable<TileIndex.TileIndexRecord> {
+public class TileIndex implements Iterable<TileIndex.TileIndexRecord> {
private final File tileIndexFile;
private final List<TileIndexRecord> tiles = new ArrayList<TileIndexRecord>();
@@ -126,7 +126,7 @@ class TileIndex implements Iterable<TileIndex.TileIndexRecord> {
throw new NoSuchElementException(String.format("Tile %d not found in %s", tileNumber, tileIndexFile));
}
- static class TileIndexRecord {
+ public static class TileIndexRecord {
/**
* Number of the tile, e.g. 11101. These don't necessarily start at 0, and there may be gaps.
*/
@@ -134,6 +134,14 @@ class TileIndex implements Iterable<TileIndex.TileIndexRecord> {
final int numClustersInTile;
+ public int getNumClustersInTile() {
+ return numClustersInTile;
+ }
+
+ public int getZeroBasedTileNumber() {
+ return zeroBasedTileNumber;
+ }
+
/**
* I.e. the sum of numClustersInTile for all tiles preceding this one.
*/
diff --git a/src/java/net/sf/picard/illumina/parser/fakers/BclFileFaker.java b/src/java/net/sf/picard/illumina/parser/fakers/BclFileFaker.java
index 2ea32d1..527ddf6 100644
--- a/src/java/net/sf/picard/illumina/parser/fakers/BclFileFaker.java
+++ b/src/java/net/sf/picard/illumina/parser/fakers/BclFileFaker.java
@@ -2,17 +2,18 @@ package net.sf.picard.illumina.parser.fakers;
import java.nio.ByteBuffer;
-/**
- * Created by jcarey on 3/13/14.
- */
public class BclFileFaker extends FileFaker {
@Override
public void fakeFile(final ByteBuffer buffer) {
- buffer.putInt(1);
- size -= 4;
+
+ // Write the number of elements to the header. The state variable "size" contains
+ // the number of elements; we've allocated "size" plus the size of the header
+ // (four bytes) to the buffer.
+ buffer.putInt(size);
+
while (size > 0) {
- //fill the file with no calls
+ // Fill the file with no calls
buffer.put((byte) 0);
size--;
}
@@ -24,6 +25,6 @@ public class BclFileFaker extends FileFaker {
}
protected int bufferSize() {
- return size;
+ return size + 4;
}
}
diff --git a/src/java/net/sf/picard/illumina/parser/fakers/CifFileFaker.java b/src/java/net/sf/picard/illumina/parser/fakers/CifFileFaker.java
deleted file mode 100644
index 54f7371..0000000
--- a/src/java/net/sf/picard/illumina/parser/fakers/CifFileFaker.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package net.sf.picard.illumina.parser.fakers;
-
-import java.nio.ByteBuffer;
-
-/**
- * Created by jcarey on 3/13/14.
- */
-public class CifFileFaker extends FileFaker {
-
- @Override
- protected void fakeFile(final ByteBuffer buffer) {
- buffer.putChar('C');
- buffer.putChar('I');
- buffer.putChar('F');
- buffer.put((byte) 1);
- buffer.put((byte) 2);
- buffer.putShort((short) 1);
- buffer.putShort((short) 1);
- buffer.putInt(1);
- }
-
- @Override
- protected boolean addLeadingZeros() {
- return false;
- }
-
- @Override
- protected int bufferSize() {
- return Integer.SIZE + (Character.SIZE * 3) + (Short.SIZE * 2) + 2;
- }
-}
diff --git a/src/java/net/sf/picard/illumina/parser/fakers/CnfFileFaker.java b/src/java/net/sf/picard/illumina/parser/fakers/CnfFileFaker.java
deleted file mode 100644
index a1482be..0000000
--- a/src/java/net/sf/picard/illumina/parser/fakers/CnfFileFaker.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package net.sf.picard.illumina.parser.fakers;
-
-import java.nio.ByteBuffer;
-
-/**
- * Created by jcarey on 3/13/14.
- */
-public class CnfFileFaker extends FileFaker {
-
- @Override
- protected void fakeFile(final ByteBuffer buffer) {
- buffer.putChar('C');
- buffer.putChar('I');
- buffer.putChar('F');
- buffer.put((byte) 1);
- buffer.put((byte) 1);
- buffer.putShort((short) 1);
- buffer.putShort((short) 1);
- buffer.putInt(1);
- }
-
- @Override
- protected boolean addLeadingZeros() {
- return false;
- }
-
- @Override
- protected int bufferSize() {
- return Integer.SIZE + (Character.SIZE * 3) + (Short.SIZE * 2) + 2;
- }
-}
\ No newline at end of file
diff --git a/src/java/net/sf/picard/illumina/parser/fakers/FileFaker.java b/src/java/net/sf/picard/illumina/parser/fakers/FileFaker.java
index 5697a54..77e664d 100644
--- a/src/java/net/sf/picard/illumina/parser/fakers/FileFaker.java
+++ b/src/java/net/sf/picard/illumina/parser/fakers/FileFaker.java
@@ -1,19 +1,20 @@
package net.sf.picard.illumina.parser.fakers;
-import net.sf.samtools.util.CloserUtil;
+import net.sf.picard.illumina.parser.readers.BclReader;
+import net.sf.samtools.util.BlockCompressedOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
+import java.io.OutputStream;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
-import java.nio.channels.FileChannel;
+import java.nio.channels.Channels;
+import java.nio.channels.WritableByteChannel;
import java.util.Collections;
import java.util.List;
+import java.util.zip.GZIPOutputStream;
-/**
- * Created by jcarey on 3/13/14.
- */
public abstract class FileFaker {
int size;
@@ -56,9 +57,14 @@ public abstract class FileFaker {
size = 1;
}
this.size = size;
- final FileOutputStream fileOutputStream = new FileOutputStream(cycleFile);
- final FileChannel channel = fileOutputStream.getChannel();
- final ByteBuffer buffer = ByteBuffer.allocate(size);
+
+ final OutputStream outputStream;
+ if (BclReader.isGzipped(cycleFile)) outputStream = new GZIPOutputStream(new FileOutputStream(cycleFile));
+ else if (BclReader.isBlockGzipped(cycleFile)) outputStream = new BlockCompressedOutputStream(cycleFile);
+ else outputStream = new FileOutputStream(cycleFile);
+
+ final WritableByteChannel channel = Channels.newChannel(outputStream);
+ final ByteBuffer buffer = ByteBuffer.allocate(this.bufferSize());
buffer.order(ByteOrder.LITTLE_ENDIAN);
fakeFile(buffer);
@@ -67,7 +73,7 @@ public abstract class FileFaker {
channel.write(buffer);
- CloserUtil.close(channel);
- CloserUtil.close(fileOutputStream);
+ channel.close();
+ outputStream.close();
}
}
diff --git a/src/java/net/sf/picard/illumina/parser/fakers/QSeqFileFaker.java b/src/java/net/sf/picard/illumina/parser/fakers/QSeqFileFaker.java
deleted file mode 100644
index dc3ba44..0000000
--- a/src/java/net/sf/picard/illumina/parser/fakers/QSeqFileFaker.java
+++ /dev/null
@@ -1,25 +0,0 @@
-package net.sf.picard.illumina.parser.fakers;
-
-import java.nio.ByteBuffer;
-
-/**
- * Created by jcarey on 3/13/14.
- */
-public class QSeqFileFaker extends FileFaker {
- private final String qseqString = "Can not make qseq file";
-
- @Override
- protected void fakeFile(final ByteBuffer buffer) {
- buffer.put(qseqString.getBytes());
- }
-
- @Override
- protected boolean addLeadingZeros() {
- return false;
- }
-
- @Override
- protected int bufferSize() {
- return qseqString.getBytes().length;
- }
-}
\ No newline at end of file
diff --git a/src/java/net/sf/picard/illumina/parser/readers/BclReader.java b/src/java/net/sf/picard/illumina/parser/readers/BclReader.java
index 1c09689..5aaaa15 100644
--- a/src/java/net/sf/picard/illumina/parser/readers/BclReader.java
+++ b/src/java/net/sf/picard/illumina/parser/readers/BclReader.java
@@ -1,262 +1,343 @@
- /*
- * The MIT License
- *
- * Copyright (c) 2012 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
+/*
+* The MIT License
+*
+* Copyright (c) 2012 The Broad Institute
+*
+* Permission is hereby granted, free of charge, to any person obtaining a copy
+* of this software and associated documentation files (the "Software"), to deal
+* in the Software without restriction, including without limitation the rights
+* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the Software is
+* furnished to do so, subject to the following conditions:
+*
+* The above copyright notice and this permission notice shall be included in
+* all copies or substantial portions of the Software.
+*
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+* THE SOFTWARE.
+*/
package net.sf.picard.illumina.parser.readers;
- import net.sf.picard.PicardException;
- import net.sf.picard.util.UnsignedTypeUtil;
- import net.sf.samtools.util.BlockCompressedInputStream;
- import net.sf.samtools.util.CloseableIterator;
- import net.sf.samtools.util.CloserUtil;
- import net.sf.samtools.util.IOUtil;
-
- import java.io.*;
- import java.nio.ByteBuffer;
- import java.nio.ByteOrder;
- import java.util.zip.GZIPInputStream;
+import net.sf.picard.PicardException;
+import net.sf.picard.illumina.parser.BclData;
+import net.sf.picard.illumina.parser.TileIndex;
+import net.sf.picard.util.UnsignedTypeUtil;
+import net.sf.samtools.Defaults;
+import net.sf.samtools.util.BlockCompressedInputStream;
+import net.sf.samtools.util.CloseableIterator;
+import net.sf.samtools.util.CloserUtil;
+import net.sf.samtools.util.IOUtil;
+import net.sf.samtools.util.RuntimeIOException;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
+import java.util.List;
+import java.util.zip.GZIPInputStream;
/**
* BCL Files are base call and quality score binary files containing a (base,quality) pair for successive clusters.
* The file is structured as followed:
- * Bytes 1-4 : unsigned int numClusters
- * Bytes 5-numClusters + 5 : 1 byte base/quality score
- *
- * The base/quality scores are organized as follows (with one exception, SEE BELOW):
- * The right 2 most bits (these are the LEAST significant bits) indicate the base, where
- * A=00(0x00), C=01(0x01), G=10(0x02), and T=11(0x03)
- *
- * The remaining bytes compose the quality score which is an unsigned int.
- *
- * EXCEPTION: If a byte is entirely 0 (e.g. byteRead == 0) then it is a no call, the base
- * becomes '.' and the Quality becomes 2, the default illumina masking value
- *
- * (E.g. if we get a value in binary of 10001011 it gets transformed as follows:
- *
- * Value read: 10001011(0x8B)
- *
- * Quality Base
- *
- * 100010 11
- * 00100010 0x03
- * 0x22 T
- * 34 T
- *
- * So the output base/quality will be a (T/34)
+ * Bytes 1-4 : unsigned int numClusters
+ * Bytes 5-numClusters + 5 : 1 byte base/quality score
+ * <p/>
+ * The base/quality scores are organized as follows (with one exception, SEE BELOW):
+ * The right 2 most bits (these are the LEAST significant bits) indicate the base, where
+ * A=00(0x00), C=01(0x01), G=10(0x02), and T=11(0x03)
+ * <p/>
+ * The remaining bytes compose the quality score which is an unsigned int.
+ * <p/>
+ * EXCEPTION: If a byte is entirely 0 (e.g. byteRead == 0) then it is a no call, the base
+ * becomes '.' and the Quality becomes 2, the default illumina masking value
+ * <p/>
+ * (E.g. if we get a value in binary of 10001011 it gets transformed as follows:
+ * <p/>
+ * Value read: 10001011(0x8B)
+ * <p/>
+ * Quality Base
+ * <p/>
+ * 100010 11
+ * 00100010 0x03
+ * 0x22 T
+ * 34 T
+ * <p/>
+ * So the output base/quality will be a (T/34)
*/
-public class BclReader implements CloseableIterator<BclReader.BclValue> {
- /** The size of the opening header (consisting solely of numClusters*/
+public class BclReader implements CloseableIterator<BclData> {
+ private static final byte BASE_MASK = 0x0003;
private static final int HEADER_SIZE = 4;
-
+ private static final byte[] BASE_LOOKUP = new byte[]{'A', 'C', 'G', 'T'};
+
+ private final InputStream[] streams;
+ private final int[] outputLengths;
+ int[] numClustersPerCycle;
+
private final BclQualityEvaluationStrategy bclQualityEvaluationStrategy;
+ private BclData queue = null;
+
+ public BclReader(final List<File> bclsForOneTile, final int[] outputLengths,
+ final BclQualityEvaluationStrategy bclQualityEvaluationStrategy, final boolean seekable) {
+ try {
+ this.bclQualityEvaluationStrategy = bclQualityEvaluationStrategy;
+ this.outputLengths = outputLengths;
- /** The number of clusters provided in this BCL */
- public final long numClusters;
+ int cycles = 0;
+ for (final int outputLength : outputLengths) {
+ cycles += outputLength;
+ }
+ this.streams = new InputStream[cycles];
+ this.numClustersPerCycle = new int[cycles];
+
+ final ByteBuffer byteBuffer = ByteBuffer.allocate(HEADER_SIZE);
+ byteBuffer.order(ByteOrder.LITTLE_ENDIAN);
+
+ for (int i = 0; i < cycles; ++i) {
+ final File bclFile = bclsForOneTile.get(i);
+ if (bclFile == null) {
+ close();
+ throw new RuntimeIOException(String.format("Could not find BCL file for cycle %d", i));
+ }
+ final String filePath = bclFile.getName();
+ final boolean isGzip = filePath.endsWith(".gz");
+ final boolean isBgzf = filePath.endsWith(".bgzf");
+ final InputStream stream = open(bclFile, seekable, isGzip, isBgzf);
+ final int read = stream.read(byteBuffer.array());
+ if (read != HEADER_SIZE) {
+ close();
+ throw new RuntimeIOException(String.format("BCL %s has invalid header structure.", bclFile.getAbsoluteFile()));
+ }
+ numClustersPerCycle[i] = byteBuffer.getInt();
+ if (!isBgzf && !isGzip) {
+ assertProperFileStructure(bclFile, numClustersPerCycle[i], stream);
+ }
+ this.streams[i] = stream;
+ byteBuffer.clear();
+ }
+ } catch (final IOException ioe) {
+ throw new RuntimeIOException(ioe);
+ }
+ }
- private final InputStream inputStream;
- private final String filePath;
+ public static boolean isGzipped(final File file) {
+ return file.getAbsolutePath().endsWith(".gz");
+ }
- /* This strips off the leading bits in order to compare the read byte against the static values below */
- private final static byte BASE_MASK = 0x0003;
- private final static byte A_VAL = 0x00;
- private final static byte C_VAL = 0x01;
- private final static byte G_VAL = 0x02;
- private final static byte T_VAL = 0x03;
+ public static boolean isBlockGzipped(final File file) {
+ return file.getAbsolutePath().endsWith(".bgzf");
+ }
- /** The index to the next cluster that will be returned by this reader */
- private long nextCluster;
+ public static long getNumberOfClusters(final File file) {
+ InputStream stream = null;
+ try {
+ if (isBlockGzipped(file)) stream = new BlockCompressedInputStream(IOUtil.maybeBufferedSeekableStream(file));
+ else if (isGzipped(file)) stream = new GZIPInputStream(IOUtil.maybeBufferInputStream(new FileInputStream(file)));
+ else stream = IOUtil.maybeBufferInputStream(new FileInputStream(file));
- public class BclValue {
- public final byte base;
- public final byte quality;
+ return getNumberOfClusters(file.getAbsolutePath(), stream);
- public BclValue(final byte base, final byte quality) {
- this.base = base;
- this.quality = quality;
+ } catch (final IOException ioe) {
+ throw new PicardException("Could not open file " + file.getAbsolutePath() + " to get its cluster count: " + ioe.getMessage(), ioe);
+ } finally {
+ CloserUtil.close(stream);
}
}
- public static BclReader make(final File file, final BclQualityEvaluationStrategy bclQualityEvaluationStrategy) {
- return new BclReader(file, bclQualityEvaluationStrategy, false);
+ private static long getNumberOfClusters(final String filePath, final InputStream inputStream) {
+ final byte[] header = new byte[HEADER_SIZE];
+
+ try {
+ final int headerBytesRead = inputStream.read(header);
+ if (headerBytesRead != HEADER_SIZE) {
+ throw new PicardException("Malformed file, expected header of size " + HEADER_SIZE + " but received " + headerBytesRead);
+ }
+ } catch (final IOException ioe) {
+ throw new PicardException("Unable to read header for file (" + filePath + ")", ioe);
+ }
+
+ final ByteBuffer headerBuf = ByteBuffer.wrap(header);
+ headerBuf.order(ByteOrder.LITTLE_ENDIAN);
+ return UnsignedTypeUtil.uIntToLong(headerBuf.getInt());
}
- /**
- * Produces a {@link net.sf.picard.illumina.parser.readers.BclReader} appropriate for when the consumer intends to call
- * {@link net.sf.picard.illumina.parser.readers.BclReader#seek(long)}. If this functionality is not required, call
- * {@link net.sf.picard.illumina.parser.readers.BclReader#make(java.io.File, BclQualityEvaluationStrategy)}.
- */
- public static BclReader makeSeekable(final File file, final BclQualityEvaluationStrategy bclQualityEvaluationStrategy) {
- return new BclReader(file, bclQualityEvaluationStrategy, true);
+
+ public BclReader(final File bclFile, final BclQualityEvaluationStrategy bclQualityEvaluationStrategy, final boolean seekable) {
+ try {
+
+ this.outputLengths = new int[]{1};
+ this.streams = new InputStream[1];
+ this.numClustersPerCycle = new int[]{1};
+ this.bclQualityEvaluationStrategy = bclQualityEvaluationStrategy;
+
+ final ByteBuffer byteBuffer = ByteBuffer.allocate(HEADER_SIZE);
+ final String filePath = bclFile.getName();
+ final boolean isGzip = filePath.endsWith(".gz");
+ final boolean isBgzf = filePath.endsWith(".bgzf");
+ final InputStream stream = open(bclFile, seekable, isGzip, isBgzf);
+ final int read = stream.read(byteBuffer.array());
+
+ if (read != HEADER_SIZE) {
+ throw new RuntimeIOException(String.format("BCL %s has invalid header structure.", bclFile.getAbsoluteFile()));
+ }
+
+ byteBuffer.order(ByteOrder.LITTLE_ENDIAN);
+ this.numClustersPerCycle[0] = byteBuffer.getInt();
+ if (!isBgzf && !isGzip) {
+ assertProperFileStructure(bclFile, this.numClustersPerCycle[0], stream);
+ }
+ this.streams[0] = stream;
+ } catch (final IOException ioe) {
+ throw new PicardException("IOException opening file " + bclFile.getAbsoluteFile(), ioe);
+ }
}
- BclReader(final File file, final BclQualityEvaluationStrategy bclQualityEvaluationStrategy, final boolean requiresSeekability) {
- this.bclQualityEvaluationStrategy = bclQualityEvaluationStrategy;
+ void assertProperFileStructure(final File file, final int numClusters, final InputStream stream) {
+ final long elementsInFile = file.length() - HEADER_SIZE;
+ if (numClusters != elementsInFile) {
+ CloserUtil.close(stream);
+ throw new PicardException("Expected " + numClusters + " in file but found " + elementsInFile);
+ }
+ }
- filePath = file.getAbsolutePath();
- final boolean isGzip = filePath.endsWith(".gz");
- final boolean isBgzf = filePath.endsWith(".bgzf");
+ InputStream open(final File file, final boolean seekable, final boolean isGzip, final boolean isBgzf) throws IOException {
+ final String filePath = file.getAbsolutePath();
try {
// Open up a buffered stream to read from the file and optionally wrap it in a gzip stream
// if necessary
if (isBgzf) {
// Only BlockCompressedInputStreams can seek, and only if they are fed a SeekableStream.
- inputStream = new BlockCompressedInputStream(IOUtil.maybeBufferedSeekableStream(file));
+ return new BlockCompressedInputStream(IOUtil.maybeBufferedSeekableStream(file));
} else if (isGzip) {
- if (requiresSeekability) {
+ if (seekable) {
throw new IllegalArgumentException(
- String.format("Cannot create a seekable reader for gzip bcl: %s.", filePath)
+ String.format("Cannot create a seekable reader for gzip bcl: %s.", filePath)
);
}
- inputStream = new GZIPInputStream(IOUtil.maybeBufferInputStream(new FileInputStream(file)));
+ return (IOUtil.maybeBufferInputStream(new GZIPInputStream(new FileInputStream(file), Defaults.BUFFER_SIZE / 2),
+ Defaults.BUFFER_SIZE / 2));
} else {
- if (requiresSeekability) {
+ if (seekable) {
throw new IllegalArgumentException(
- String.format("Cannot create a seekable reader for provided bcl: %s.", filePath)
+ String.format("Cannot create a seekable reader for provided bcl: %s.", filePath)
);
}
- inputStream = IOUtil.maybeBufferInputStream(new FileInputStream(file));
+ return IOUtil.maybeBufferInputStream(new FileInputStream(file));
}
- } catch (FileNotFoundException fnfe) {
+ } catch (final FileNotFoundException fnfe) {
throw new PicardException("File not found: (" + filePath + ")", fnfe);
- } catch (IOException ioe) {
+ } catch (final IOException ioe) {
throw new PicardException("Error reading file: (" + filePath + ")", ioe);
}
+ }
- // numClusters is used both for the file structure checks and in hasNext()
- numClusters = getNumClusters();
-
- if (file.length() == 0) {
- throw new PicardException("Zero length BCL file detected: " + filePath);
- }
- if (!isGzip && !isBgzf) {
- // The file structure checks rely on the file size (as information is stored as individual bytes) but
- // we can't reliably know the number of uncompressed bytes in the file ahead of time for gzip files. Only
- // run the main check
- assertProperFileStructure(file);
+ public void close() {
+ for (final InputStream stream : this.streams) {
+ CloserUtil.close(stream);
}
-
- nextCluster = 0;
}
- private long getNumClusters() {
- final byte[] header = new byte[HEADER_SIZE];
-
- try {
- final int headerBytesRead = inputStream.read(header);
- if (headerBytesRead != HEADER_SIZE) {
- throw new PicardException("Malformed file, expected header of size " + HEADER_SIZE + " but received " + headerBytesRead);
- }
- } catch (IOException ioe) {
- throw new PicardException("Unable to read header for file (" + filePath + ")", ioe);
+ @Override
+ public boolean hasNext() {
+ if (queue == null) {
+ advance();
}
+ return queue != null;
+ }
- final ByteBuffer headerBuf = ByteBuffer.wrap(header);
- headerBuf.order(ByteOrder.LITTLE_ENDIAN);
- return UnsignedTypeUtil.uIntToLong(headerBuf.getInt());
+ private long getNumClusters() {
+ return numClustersPerCycle[0];
}
protected void assertProperFileStructure(final File file) {
final long elementsInFile = file.length() - HEADER_SIZE;
- if (numClusters != elementsInFile) {
- throw new PicardException("Expected " + numClusters + " in file but found " + elementsInFile);
+ if (numClustersPerCycle[0] != elementsInFile) {
+ throw new PicardException("Expected " + numClustersPerCycle[0] + " in file " + file.getAbsolutePath() + " but found " + elementsInFile);
+
}
}
- public final boolean hasNext() {
- return this.nextCluster < this.numClusters;
+ public BclData next() {
+ if (queue == null) {
+ advance();
+ }
+
+ final BclData data = queue;
+ queue = null;
+ return data;
}
- public BclValue next() {
- // TODO(ish) There are multiple optimizations that could be made here if we find that this becomes a pinch
- // point. For instance base & quality could be moved into BclValue, element & elements could be moved to be
- // class members - all in an attempt to reduce the number of allocations being made.
- final byte base;
- final byte quality;
+ @Override
+ public void remove() {
+ throw new UnsupportedOperationException();
+ }
- final byte element;
- final byte[] elements = new byte[1];
- try {
- if (inputStream.read(elements) != 1) {
- throw new PicardException("Error when reading byte from file (" + filePath + ")");
- }
- } catch (EOFException eofe) {
- throw new PicardException("Attempted to read byte from file but none were available: (" + filePath + ")", eofe);
- }catch (IOException ioe) {
- throw new PicardException("Error when reading byte from file (" + filePath + ")", ioe);
- }
+ void advance() {
+ int totalCycleCount = 0;
+ final BclData data = new BclData(outputLengths);
+ for (int read = 0; read < outputLengths.length; read++) {
+ for (int cycle = 0; cycle < outputLengths[read]; ++cycle) {
+ try {
+ final int readByte = this.streams[totalCycleCount].read();
+ if (readByte == -1) {
+ queue = null;
+ return;
+ }
+
+ if (readByte == 0) {
+ //NO CALL, don't confuse with an A call
+ data.bases[read][cycle] = (byte) '.';
+ data.qualities[read][cycle] = (byte) 2;
+ } else {
+ data.bases[read][cycle] = BASE_LOOKUP[readByte & BASE_MASK];
+ data.qualities[read][cycle] = bclQualityEvaluationStrategy.reviseAndConditionallyLogQuality((byte) (readByte >>> 2));
+ }
+ totalCycleCount++;
+ } catch (final IOException ioe) {
+ throw new RuntimeIOException(ioe);
+ }
- element = elements[0];
- if(element == 0) { //NO CALL, don't confuse with an A call
- base = '.';
- quality = 2;
- } else {
- switch(element & BASE_MASK) {
- case A_VAL:
- base = 'A';
- break;
-
- case C_VAL:
- base = 'C';
- break;
-
- case G_VAL:
- base = 'G';
- break;
-
- case T_VAL:
- base = 'T';
- break;
-
- default:
- throw new PicardException("Impossible case! BCL Base value neither A, C, G, nor T! Value(" + (element & BASE_MASK) + ") + in file(" + filePath + ")");
}
-
- quality = bclQualityEvaluationStrategy.reviseAndConditionallyLogQuality((byte)(UnsignedTypeUtil.uByteToInt(element) >>> 2));
}
-
- ++nextCluster;
- return new BclValue(base, quality);
+ this.queue = data;
}
- public void close() {
- CloserUtil.close(inputStream);
+ public static BclReader makeSeekable(final List<File> files, final BclQualityEvaluationStrategy bclQualityEvaluationStrategy, final int[] outputLengths) {
+ return new BclReader(files, outputLengths, bclQualityEvaluationStrategy, true);
}
- public void seek(final long virtualFilePointer) {
- if (!(inputStream instanceof BlockCompressedInputStream)) {
- throw new UnsupportedOperationException("Seeking only allowed on bzgf");
- } else {
- final BlockCompressedInputStream bcis = (BlockCompressedInputStream)inputStream;
- try {
- ((BlockCompressedInputStream) inputStream).seek(virtualFilePointer);
- } catch (IOException e) {
- throw new PicardException("Problem seeking in " + filePath, e);
+ public int seek(final List<File> files, final TileIndex tileIndex, final int currentTile) {
+ int count = 0;
+ int numClustersInTile = 0;
+ for (final InputStream inputStream : streams) {
+ final TileIndex.TileIndexRecord tileIndexRecord = tileIndex.findTile(currentTile);
+ final BclIndexReader bclIndexReader = new BclIndexReader(files.get(count));
+ final long virtualFilePointer = bclIndexReader.get(tileIndexRecord.getZeroBasedTileNumber());
+ if (!(inputStream instanceof BlockCompressedInputStream)) {
+ throw new UnsupportedOperationException("Seeking only allowed on bzgf");
+ } else {
+ try {
+ if (tileIndex.getNumTiles() != bclIndexReader.getNumTiles()) {
+ throw new PicardException(String.format("%s.getNumTiles(%d) != %s.getNumTiles(%d)",
+ tileIndex.getFile().getAbsolutePath(), tileIndex.getNumTiles(), bclIndexReader.getBciFile().getAbsolutePath(), bclIndexReader.getNumTiles()));
+ }
+ ((BlockCompressedInputStream) inputStream).seek(virtualFilePointer);
+ numClustersInTile = tileIndexRecord.getNumClustersInTile();
+ } catch (final IOException e) {
+ throw new PicardException("Problem seeking to " + virtualFilePointer, e);
+ }
}
+ count++;
}
- }
-
- public void remove() {
- throw new UnsupportedOperationException();
+ return numClustersInTile;
}
}
diff --git a/src/java/net/sf/picard/io/IoUtil.java b/src/java/net/sf/picard/io/IoUtil.java
index 0fade1f..d279035 100644
--- a/src/java/net/sf/picard/io/IoUtil.java
+++ b/src/java/net/sf/picard/io/IoUtil.java
@@ -500,18 +500,6 @@ public class IoUtil extends net.sf.samtools.util.IOUtil {
return str.trim().replaceAll("[\\s!\"#$%&'()*/:;<=>?@\\[\\]\\\\^`{|}~]", "_");
}
- /** Returns the name of the file minus the extension (i.e. text after the last "." in the filename). */
- public static String basename(final File f) {
- final String full = f.getName();
- final int index = full.lastIndexOf(".");
- if (index > 0 && index > full.lastIndexOf(File.separator)) {
- return full.substring(0, index);
- }
- else {
- return full;
- }
- }
-
/** Returns the name of the file extension (i.e. text after the last "." in the filename) including the . */
public static String fileSuffix(final File f) {
final String full = f.getName();
@@ -534,7 +522,7 @@ public class IoUtil extends net.sf.samtools.util.IOUtil {
if (f != null) f = f.getCanonicalFile();
}
return canonicalPath;
- } catch (IOException ioe) {
+ } catch (final IOException ioe) {
throw new RuntimeException("Error getting full canonical path for " +
file + ": " + ioe.getMessage(), ioe);
}
@@ -556,7 +544,7 @@ public class IoUtil extends net.sf.samtools.util.IOUtil {
return builder.toString();
}
- catch (IOException ioe) {
+ catch (final IOException ioe) {
throw new RuntimeIOException("Error reading stream", ioe);
}
}
@@ -586,14 +574,14 @@ public class IoUtil extends net.sf.samtools.util.IOUtil {
if (next == null) in.close();
return tmp;
}
- catch (IOException ioe) { throw new RuntimeIOException(ioe); }
+ catch (final IOException ioe) { throw new RuntimeIOException(ioe); }
}
/** Closes the underlying input stream. Not required if end of stream has already been hit. */
@Override public void close() throws IOException { CloserUtil.close(in); }
};
}
- catch (IOException e) {
+ catch (final IOException e) {
throw new RuntimeIOException(e);
}
}
@@ -690,7 +678,7 @@ class CustomGzipOutputStream extends GZIPOutputStream {
this.def.setLevel(compressionLevel);
}
- CustomGzipOutputStream(OutputStream outputStream, final int compressionLevel) throws IOException {
+ CustomGzipOutputStream(final OutputStream outputStream, final int compressionLevel) throws IOException {
super(outputStream);
this.def.setLevel(compressionLevel);
}
diff --git a/src/java/net/sf/picard/metrics/MetricsFile.java b/src/java/net/sf/picard/metrics/MetricsFile.java
index b32c9a2..fa7761d 100644
--- a/src/java/net/sf/picard/metrics/MetricsFile.java
+++ b/src/java/net/sf/picard/metrics/MetricsFile.java
@@ -27,6 +27,7 @@ package net.sf.picard.metrics;
import net.sf.picard.PicardException;
import net.sf.picard.util.FormatUtil;
import net.sf.picard.util.Histogram;
+import net.sf.samtools.util.CloserUtil;
import net.sf.samtools.util.StringUtil;
import java.io.*;
@@ -267,7 +268,7 @@ public class MetricsFile<BEAN extends MetricBase, HKEY extends Comparable> {
/** Gets the type of the metrics bean being used. */
private Class<?> getBeanType() {
- if (this.metrics == null || this.metrics.isEmpty()) {
+ if (this.metrics.isEmpty()) {
return null;
} else {
return this.metrics.get(0).getClass();
@@ -300,7 +301,7 @@ public class MetricsFile<BEAN extends MetricBase, HKEY extends Comparable> {
try {
header = (Header) loadClass(className, true).newInstance();
}
- catch (Exception e) {
+ catch (final Exception e) {
throw new PicardException("Error load and/or instantiating an instance of " + className, e);
}
}
@@ -334,7 +335,7 @@ public class MetricsFile<BEAN extends MetricBase, HKEY extends Comparable> {
try {
type = loadClass(className, true);
}
- catch (ClassNotFoundException cnfe) {
+ catch (final ClassNotFoundException cnfe) {
throw new PicardException("Could not locate class with name " + className, cnfe);
}
@@ -346,7 +347,7 @@ public class MetricsFile<BEAN extends MetricBase, HKEY extends Comparable> {
try {
fields[i] = type.getField(fieldNames[i]);
}
- catch (Exception e) {
+ catch (final Exception e) {
throw new PicardException("Could not get field with name " + fieldNames[i] +
" from class " + type.getName());
}
@@ -358,11 +359,11 @@ public class MetricsFile<BEAN extends MetricBase, HKEY extends Comparable> {
break;
}
else {
- String[] values = line.split(SEPARATOR, -1);
+ final String[] values = line.split(SEPARATOR, -1);
BEAN bean = null;
try { bean = (BEAN) type.newInstance(); }
- catch (Exception e) { throw new PicardException("Error instantiating a " + type.getName(), e); }
+ catch (final Exception e) { throw new PicardException("Error instantiating a " + type.getName(), e); }
for (int i=0; i<fields.length; ++i) {
Object value = null;
@@ -371,7 +372,7 @@ public class MetricsFile<BEAN extends MetricBase, HKEY extends Comparable> {
}
try { fields[i].set(bean, value); }
- catch (Exception e) {
+ catch (final Exception e) {
throw new PicardException("Error setting field " + fields[i].getName() +
" on class of type " + type.getName(), e);
}
@@ -393,7 +394,7 @@ public class MetricsFile<BEAN extends MetricBase, HKEY extends Comparable> {
Class<?> keyClass = null;
try { keyClass = loadClass(keyClassName, true); }
- catch (ClassNotFoundException cnfe) { throw new PicardException("Could not load class with name " + keyClassName); }
+ catch (final ClassNotFoundException cnfe) { throw new PicardException("Could not load class with name " + keyClassName); }
// Read the next line with the bin and value labels
final String[] labels = in.readLine().split(SEPARATOR);
@@ -413,9 +414,12 @@ public class MetricsFile<BEAN extends MetricBase, HKEY extends Comparable> {
}
}
}
- catch (IOException ioe) {
+ catch (final IOException ioe) {
throw new PicardException("Could not read metrics from reader.", ioe);
}
+ finally{
+ CloserUtil.close(in);
+ }
}
/** Attempts to load a class, taking into account that some classes have "migrated" from the broad to sf. */
diff --git a/src/java/net/sf/picard/reference/AbstractFastaSequenceFile.java b/src/java/net/sf/picard/reference/AbstractFastaSequenceFile.java
index 9f7f9b4..2f006b8 100644
--- a/src/java/net/sf/picard/reference/AbstractFastaSequenceFile.java
+++ b/src/java/net/sf/picard/reference/AbstractFastaSequenceFile.java
@@ -55,11 +55,13 @@ abstract class AbstractFastaSequenceFile implements ReferenceSequenceFile {
try {
final SAMTextHeaderCodec codec = new SAMTextHeaderCodec();
- final SAMFileHeader header = codec.decode(new BufferedLineReader(new FileInputStream(dictionary)),
+ final BufferedLineReader reader = new BufferedLineReader(new FileInputStream(dictionary));
+ final SAMFileHeader header = codec.decode(reader,
dictionary.toString());
if (header.getSequenceDictionary() != null && header.getSequenceDictionary().size() > 0) {
this.sequenceDictionary = header.getSequenceDictionary();
}
+ reader.close();
}
catch (Exception e) {
throw new PicardException("Could not open sequence dictionary file: " + dictionary, e);
diff --git a/src/java/net/sf/picard/reference/FastaSequenceIndex.java b/src/java/net/sf/picard/reference/FastaSequenceIndex.java
index 267d460..5c1b43d 100644
--- a/src/java/net/sf/picard/reference/FastaSequenceIndex.java
+++ b/src/java/net/sf/picard/reference/FastaSequenceIndex.java
@@ -141,6 +141,7 @@ public class FastaSequenceIndex implements Iterable<FastaSequenceIndexEntry> {
// Build sequence structure
add(new FastaSequenceIndexEntry(contig,location,size,basesPerLine,bytesPerLine, sequenceIndex++) );
}
+ scanner.close();
} catch (FileNotFoundException e) {
throw new PicardException("Fasta index file should be found but is not: " + indexFile, e);
}
diff --git a/src/java/net/sf/picard/reference/ReferenceSequenceFile.java b/src/java/net/sf/picard/reference/ReferenceSequenceFile.java
index 2969842..53235cc 100644
--- a/src/java/net/sf/picard/reference/ReferenceSequenceFile.java
+++ b/src/java/net/sf/picard/reference/ReferenceSequenceFile.java
@@ -26,6 +26,8 @@ package net.sf.picard.reference;
import net.sf.samtools.SAMSequenceDictionary;
+import java.io.IOException;
+
/**
* An interface for working with files of reference sequences regardless of the file format
* being used.
@@ -82,4 +84,6 @@ public interface ReferenceSequenceFile {
* @return Reference name, file name, or something other human-readable representation.
*/
public String toString();
+
+ public void close() throws IOException;
}
diff --git a/src/java/net/sf/picard/reference/ReferenceSequenceFileWalker.java b/src/java/net/sf/picard/reference/ReferenceSequenceFileWalker.java
index 61155f8..55f5cf9 100644
--- a/src/java/net/sf/picard/reference/ReferenceSequenceFileWalker.java
+++ b/src/java/net/sf/picard/reference/ReferenceSequenceFileWalker.java
@@ -27,6 +27,7 @@ import net.sf.picard.PicardException;
import net.sf.samtools.SAMSequenceDictionary;
import java.io.File;
+import java.io.IOException;
/**
* Manages a ReferenceSequenceFile. Loads the requested sequence, ensuring that
@@ -93,4 +94,8 @@ public class ReferenceSequenceFileWalker {
public SAMSequenceDictionary getSequenceDictionary() {
return referenceSequenceFile.getSequenceDictionary();
}
+
+ public void close() throws IOException {
+ referenceSequenceFile.close();
+ }
}
diff --git a/src/java/net/sf/picard/sam/AbstractAlignmentMerger.java b/src/java/net/sf/picard/sam/AbstractAlignmentMerger.java
index 507c8cd..97c86d3 100644
--- a/src/java/net/sf/picard/sam/AbstractAlignmentMerger.java
+++ b/src/java/net/sf/picard/sam/AbstractAlignmentMerger.java
@@ -50,10 +50,12 @@ import net.sf.samtools.SAMTag;
import net.sf.samtools.SAMUtils;
import net.sf.samtools.SamPairUtil;
import net.sf.samtools.util.CloseableIterator;
+import net.sf.samtools.util.CloserUtil;
import net.sf.samtools.util.SequenceUtil;
import net.sf.samtools.util.SortingCollection;
import java.io.File;
+import java.io.IOException;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.ArrayList;
@@ -112,6 +114,7 @@ public abstract class AbstractAlignmentMerger {
private int maxRecordsInRam = MAX_RECORDS_IN_RAM;
private final PrimaryAlignmentSelectionStrategy primaryAlignmentSelectionStrategy;
private boolean keepAlignerProperPairFlags = false;
+ private boolean addMateCigar = false;
private final SamRecordFilter alignmentFilter = new SamRecordFilter() {
public boolean filterOut(final SAMRecord record) {
@@ -155,6 +158,7 @@ public abstract class AbstractAlignmentMerger {
* output will be coordinate-sorted
* @param primaryAlignmentSelectionStrategy What to do when there are multiple primary alignments, or multiple
* alignments but none primary, for a read or read pair.
+ * @param addMateCigar True if we are to add or maintain the mate CIGAR (MC) tag, false if we are to remove or not include.
*/
public AbstractAlignmentMerger(final File unmappedBamFile, final File targetBamFile,
final File referenceFasta, final boolean clipAdapters,
@@ -164,7 +168,8 @@ public abstract class AbstractAlignmentMerger {
final Integer read1BasesTrimmed, final Integer read2BasesTrimmed,
final List<SamPairUtil.PairOrientation> expectedOrientations,
final SAMFileHeader.SortOrder sortOrder,
- final PrimaryAlignmentSelectionStrategy primaryAlignmentSelectionStrategy) {
+ final PrimaryAlignmentSelectionStrategy primaryAlignmentSelectionStrategy,
+ final boolean addMateCigar) {
IoUtil.assertFileIsReadable(unmappedBamFile);
IoUtil.assertFileIsWritable(targetBamFile);
IoUtil.assertFileIsReadable(referenceFasta);
@@ -211,6 +216,8 @@ public abstract class AbstractAlignmentMerger {
this.expectedOrientations = expectedOrientations;
this.primaryAlignmentSelectionStrategy = primaryAlignmentSelectionStrategy;
+
+ this.addMateCigar = addMateCigar;
}
/** Allows the caller to override the maximum records in RAM. */
@@ -467,7 +474,7 @@ public abstract class AbstractAlignmentMerger {
if (firstAligned != null) transferAlignmentInfoToFragment(firstUnaligned, firstAligned);
if (secondAligned != null) transferAlignmentInfoToFragment(secondUnaligned, secondAligned);
if (isClipOverlappingReads()) clipForOverlappingReads(firstUnaligned, secondUnaligned);
- SamPairUtil.setMateInfo(secondUnaligned, firstUnaligned, header);
+ SamPairUtil.setMateInfo(secondUnaligned, firstUnaligned, header, addMateCigar);
if (!keepAlignerProperPairFlags) {
SamPairUtil.setProperPairFlags(secondUnaligned, firstUnaligned, expectedOrientations);
}
@@ -596,14 +603,15 @@ public abstract class AbstractAlignmentMerger {
}
// If the read's mate maps off the end of the alignment, clip it
- if (rec.getReadPairedFlag() && !rec.getMateUnmappedFlag() && null != rec.getMateCigar()) {
- final Cigar mateCigar = createNewCigarIfMapsOffEndOfReference(rec.getHeader(),
+ if (SAMUtils.hasMateCigar(rec)) {
+ Cigar mateCigar = SAMUtils.getMateCigar(rec);
+ mateCigar = createNewCigarIfMapsOffEndOfReference(rec.getHeader(),
rec.getMateUnmappedFlag(),
rec.getMateReferenceIndex(),
- rec.getMateAlignmentEnd(),
- rec.getMateCigar().getReadLength(),
- rec.getMateCigar());
- if (null != mateCigar) rec.setAttribute(SAMTag.MC.name(), mateCigar);
+ SAMUtils.getMateAlignmentEnd(rec), // NB: this could be computed without another call to getMateCigar
+ mateCigar.getReadLength(),
+ mateCigar);
+ if (null != mateCigar) rec.setAttribute(SAMTag.MC.name(), mateCigar.toString());
}
}
@@ -683,4 +691,8 @@ public abstract class AbstractAlignmentMerger {
public void setIncludeSecondaryAlignments(final boolean includeSecondaryAlignments) {
this.includeSecondaryAlignments = includeSecondaryAlignments;
}
+
+ public void close() {
+ CloserUtil.close(this.refSeq);
+ }
}
diff --git a/src/java/net/sf/picard/sam/AddCommentsToBam.java b/src/java/net/sf/picard/sam/AddCommentsToBam.java
new file mode 100644
index 0000000..22cc1f8
--- /dev/null
+++ b/src/java/net/sf/picard/sam/AddCommentsToBam.java
@@ -0,0 +1,57 @@
+package net.sf.picard.sam;
+
+import net.sf.picard.PicardException;
+import net.sf.picard.cmdline.CommandLineProgram;
+import net.sf.picard.cmdline.Option;
+import net.sf.picard.cmdline.StandardOptionDefinitions;
+import net.sf.picard.cmdline.Usage;
+import net.sf.picard.io.IoUtil;
+import net.sf.samtools.BamFileIoUtils;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMFileReader;
+
+import java.io.File;
+import java.util.List;
+
+/**
+ * A tool to add comments to a BAM file header. Effectively copies the BAM file except for the addition of the @CO records
+ * in the header. This tool does not support SAM files.
+ *
+ * @author jgentry
+ */
+public class AddCommentsToBam extends CommandLineProgram {
+ @Usage public final String USAGE = "Adds one or more comments to the header of a specified BAM file. Copies the file with the " +
+ "modified header to a specified output file. Note that a block copying method is used to ensure efficient transfer to the " +
+ "output file. SAM files are not supported";
+ @Option(shortName= StandardOptionDefinitions.INPUT_SHORT_NAME, doc="Input BAM file to add a comment to the header")
+ public File INPUT;
+
+ @Option(shortName=StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc="Output BAM file to write results")
+ public File OUTPUT;
+
+ @Option(shortName="C", doc="Comments to add to the BAM file")
+ public List<String> COMMENT;
+
+ public static void main(final String[] args) { new AddCommentsToBam().instanceMainWithExit(args); }
+
+ protected int doWork() {
+ IoUtil.assertFileIsReadable(INPUT);
+ IoUtil.assertFileIsWritable(OUTPUT);
+
+ if (INPUT.getAbsolutePath().endsWith(".sam")) {
+ throw new PicardException("SAM files are not supported");
+ }
+
+ final SAMFileHeader samFileHeader = new SAMFileReader(INPUT).getFileHeader();
+ for (final String comment : COMMENT) {
+ if (comment.contains("\n")) {
+ throw new PicardException("Comments can not contain a new line");
+ }
+ samFileHeader.addComment(comment);
+ }
+
+ BamFileIoUtils.reheaderBamFile(samFileHeader, INPUT, OUTPUT, CREATE_MD5_FILE, CREATE_INDEX);
+
+ return 0;
+ }
+}
diff --git a/src/java/net/sf/picard/sam/BuildBamIndex.java b/src/java/net/sf/picard/sam/BuildBamIndex.java
index 63f034c..249c2bb 100755
--- a/src/java/net/sf/picard/sam/BuildBamIndex.java
+++ b/src/java/net/sf/picard/sam/BuildBamIndex.java
@@ -87,7 +87,7 @@ public class BuildBamIndex extends CommandLineProgram {
baseFileName = inputFile.getAbsolutePath();
}
- if (baseFileName.endsWith(".bam")) {
+ if (baseFileName.endsWith(BamFileIoUtils.BAM_FILE_EXTENSION)) {
final int index = baseFileName.lastIndexOf(".");
OUTPUT = new File(baseFileName.substring(0, index) + BAMIndex.BAMIndexSuffix);
diff --git a/src/java/net/sf/picard/sam/FilterSamReads.java b/src/java/net/sf/picard/sam/FilterSamReads.java
index 228ce51..046e3c0 100644
--- a/src/java/net/sf/picard/sam/FilterSamReads.java
+++ b/src/java/net/sf/picard/sam/FilterSamReads.java
@@ -23,7 +23,7 @@
*/
/**
- * $Id: FilterSamReads.java 1235 2012-07-21 12:49:32Z tfenne $
+ * $Id: FilterSamReads.java 1950 2014-04-28 21:41:46Z geoffjentry $
*/
package net.sf.picard.sam;
@@ -43,6 +43,7 @@ import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMFileWriterFactory;
import net.sf.samtools.SAMRecord;
+import net.sf.samtools.util.IOUtil;
import java.io.BufferedWriter;
import java.io.File;
@@ -53,7 +54,7 @@ import java.text.DecimalFormat;
* From a SAM or BAM file, produce a new SAM or BAM by filtering aligned reads or a list of read
* names provided in a file (one readname per line)
* <p/>
- * $Id: FilterSamReads.java 1235 2012-07-21 12:49:32Z tfenne $
+ * $Id: FilterSamReads.java 1950 2014-04-28 21:41:46Z geoffjentry $
*/
public class FilterSamReads extends CommandLineProgram {
@@ -148,7 +149,7 @@ public class FilterSamReads extends CommandLineProgram {
private void writeReadsFile(final File samOrBamFile) throws IOException {
final SAMFileReader reader = new SAMFileReader(samOrBamFile);
final File readsFile =
- new File(OUTPUT.getParentFile(), IoUtil.basename(samOrBamFile) + ".reads");
+ new File(OUTPUT.getParentFile(), IOUtil.basename(samOrBamFile) + ".reads");
IoUtil.assertFileIsWritable(readsFile);
final BufferedWriter bw = IoUtil.openFileForBufferedWriting(readsFile, false);
diff --git a/src/java/net/sf/picard/sam/FixMateInformation.java b/src/java/net/sf/picard/sam/FixMateInformation.java
index 3a566e7..e78f193 100644
--- a/src/java/net/sf/picard/sam/FixMateInformation.java
+++ b/src/java/net/sf/picard/sam/FixMateInformation.java
@@ -25,7 +25,26 @@
package net.sf.picard.sam;
import net.sf.picard.PicardException;
+import net.sf.picard.cmdline.CommandLineProgram;
+import net.sf.picard.cmdline.Option;
+import net.sf.picard.cmdline.StandardOptionDefinitions;
import net.sf.picard.cmdline.Usage;
+import net.sf.picard.io.IoUtil;
+import net.sf.picard.util.Log;
+import net.sf.picard.util.PeekableIterator;
+import net.sf.picard.util.ProgressLogger;
+import net.sf.samtools.BAMRecordCodec;
+import net.sf.samtools.BamFileIoUtils;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMFileHeader.SortOrder;
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMFileWriterFactory;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMRecordQueryNameComparator;
+import net.sf.samtools.SamPairUtil;
+import net.sf.samtools.util.RuntimeIOException;
+import net.sf.samtools.util.SortingCollection;
import java.io.File;
import java.io.IOException;
@@ -33,18 +52,6 @@ import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
-import net.sf.picard.util.PeekableIterator;
-import net.sf.picard.util.ProgressLogger;
-import net.sf.samtools.*;
-import net.sf.samtools.SAMFileHeader.SortOrder;
-import net.sf.picard.util.Log;
-import net.sf.samtools.util.RuntimeIOException;
-import net.sf.picard.cmdline.CommandLineProgram;
-import net.sf.picard.cmdline.Option;
-import net.sf.picard.cmdline.StandardOptionDefinitions;
-import net.sf.picard.io.IoUtil;
-import net.sf.samtools.util.SortingCollection;
-
/**
* Class to fix mate pair information for all reads in a SAM file. Will run in fairly limited
* memory unless there are lots of mate pairs that are far apart from each other in the file.
@@ -68,6 +75,9 @@ public class FixMateInformation extends CommandLineProgram {
doc="Optional sort order if the OUTPUT file should be sorted differently than the INPUT file.")
public SortOrder SORT_ORDER;
+ @Option(shortName="MC", optional=true, doc="Adds the mate CIGAR tag (MC) if true, does not if false.")
+ public Boolean ADD_MATE_CIGAR = true;
+
private static final Log log = Log.getInstance(FixMateInformation.class);
protected SAMFileWriter out;
@@ -104,7 +114,7 @@ public class FixMateInformation extends CommandLineProgram {
try {
IoUtil.assertFileIsWritable(soleInput);
IoUtil.assertDirectoryIsWritable(dir);
- OUTPUT = File.createTempFile(soleInput.getName() + ".being_fixed.", ".bam", dir);
+ OUTPUT = File.createTempFile(soleInput.getName() + ".being_fixed.", BamFileIoUtils.BAM_FILE_EXTENSION, dir);
}
catch (IOException ioe) {
throw new RuntimeIOException("Could not create tmp file in " + dir.getAbsolutePath());
@@ -197,7 +207,7 @@ public class FixMateInformation extends CommandLineProgram {
if (rec2 != null && rec1.getReadName().equals(rec2.getReadName())) {
iterator.next(); // consume the peeked record
- SamPairUtil.setMateInfo(rec1, rec2, header);
+ SamPairUtil.setMateInfo(rec1, rec2, header, ADD_MATE_CIGAR);
writeAlignment(rec1);
writeAlignment(rec2);
progress.record(rec1, rec2);
diff --git a/src/java/net/sf/picard/sam/GatherBamFiles.java b/src/java/net/sf/picard/sam/GatherBamFiles.java
new file mode 100644
index 0000000..1bfdbb6
--- /dev/null
+++ b/src/java/net/sf/picard/sam/GatherBamFiles.java
@@ -0,0 +1,97 @@
+package net.sf.picard.sam;
+
+import net.sf.picard.cmdline.CommandLineProgram;
+import net.sf.picard.cmdline.Option;
+import net.sf.picard.cmdline.StandardOptionDefinitions;
+import net.sf.picard.cmdline.Usage;
+import net.sf.picard.io.IoUtil;
+import net.sf.picard.util.Log;
+import net.sf.samtools.*;
+
+import net.sf.samtools.util.CloserUtil;
+
+import java.io.File;
+import java.util.List;
+
+/**
+ * Program to perform a rapid "gather" operation on BAM files after a scatter operations where
+ * the same process has been performed on different regions of a BAM file creating many smaller
+ * BAM files that now need to be concatenated back together.
+ *
+ * @author Tim Fennell
+ */
+public class GatherBamFiles extends CommandLineProgram {
+ @Usage public final String USAGE = "Concatenates one or more BAM files together as efficiently as possible. Assumes that the " +
+ "list of BAM files provided as INPUT are in the order that they should be concatenated and simply concatenates the bodies " +
+ "of the BAM files while retaining the header from the first file. Operates via copying of the gzip blocks directly for speed " +
+ "but also supports generation of an MD5 on the output and indexing of the output BAM file. Only support BAM files, does not " +
+ "support SAM files.";
+
+ @Option(shortName=StandardOptionDefinitions.INPUT_SHORT_NAME,
+ doc="One or more BAM files or text files containing lists of BAM files one per line.")
+ public List<File> INPUT;
+
+ @Option(shortName=StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc="The output BAM file to write.")
+ public File OUTPUT;
+
+ private static final Log log = Log.getInstance(GatherBamFiles.class);
+
+ // Stock main method.
+ public static void main(final String[] args) {
+ final GatherBamFiles gatherer = new GatherBamFiles();
+ gatherer.CREATE_INDEX = true;
+ gatherer.instanceMainWithExit(args);
+ }
+
+ @Override
+ protected int doWork() {
+ final List<File> inputs = IoUtil.unrollFiles(INPUT, BamFileIoUtils.BAM_FILE_EXTENSION, ".sam");
+ for (final File f: inputs) IoUtil.assertFileIsReadable(f);
+ IoUtil.assertFileIsWritable(OUTPUT);
+
+ if (determineBlockCopyingStatus(inputs)) {
+ BamFileIoUtils.gatherWithBlockCopying(inputs, OUTPUT, CREATE_INDEX, CREATE_MD5_FILE);
+ }
+ else {
+ gatherNormally(inputs, OUTPUT, CREATE_INDEX, CREATE_MD5_FILE);
+ }
+
+ return 0;
+ }
+
+ private boolean determineBlockCopyingStatus(final List<File> inputs) {
+ boolean useBlockCopying = true;
+ for (final File f : inputs) {
+ if (!BamFileIoUtils.isBamFile(f)) {
+ useBlockCopying = false;
+ }
+ }
+ return useBlockCopying;
+ }
+
+ /**
+ * Simple implementation of a gather operations that uses SAMFileReaders and Writers in order to concatenate
+ * multiple BAM files.
+ */
+ private static void gatherNormally(final List<File> inputs, final File output, final boolean createIndex, final boolean createMd5) {
+ final SAMFileHeader header;
+ {
+ final SAMFileReader tmp = new SAMFileReader(inputs.get(0));
+ header = tmp.getFileHeader();
+ tmp.close();
+ }
+
+ final SAMFileWriter out = new SAMFileWriterFactory().setCreateIndex(createIndex).setCreateMd5File(createMd5).makeSAMOrBAMWriter(header, true, output);
+
+ for (final File f : inputs) {
+ log.info("Gathering " + f.getAbsolutePath());
+ final SAMFileReader in = new SAMFileReader(f);
+ for (final SAMRecord rec : in) out.addAlignment(rec);
+ CloserUtil.close(in);
+ }
+
+ out.close();
+ }
+
+
+}
diff --git a/src/java/net/sf/picard/sam/MarkDuplicates.java b/src/java/net/sf/picard/sam/MarkDuplicates.java
index b10abcf..929aa03 100644
--- a/src/java/net/sf/picard/sam/MarkDuplicates.java
+++ b/src/java/net/sf/picard/sam/MarkDuplicates.java
@@ -68,7 +68,7 @@ public class MarkDuplicates extends AbstractDuplicateFindingAlgorithm {
public List<File> INPUT;
@Option(shortName=StandardOptionDefinitions.OUTPUT_SHORT_NAME,
- doc="The output file to right marked records to")
+ doc="The output file to write marked records to")
public File OUTPUT;
@Option(shortName="M",
diff --git a/src/java/net/sf/picard/sam/MergeBamAlignment.java b/src/java/net/sf/picard/sam/MergeBamAlignment.java
index 53dfc99..8884102 100644
--- a/src/java/net/sf/picard/sam/MergeBamAlignment.java
+++ b/src/java/net/sf/picard/sam/MergeBamAlignment.java
@@ -179,6 +179,9 @@ public class MergeBamAlignment extends CommandLineProgram {
@Option(doc="If false, do not write secondary alignments to output.")
public boolean INCLUDE_SECONDARY_ALIGNMENTS = true;
+ @Option(shortName="MC", optional=true, doc="Adds the mate CIGAR tag (MC) if true, does not if false.")
+ public Boolean ADD_MATE_CIGAR = true;
+
private static final Log log = Log.getInstance(MergeBamAlignment.class);
/**
@@ -233,12 +236,14 @@ public class MergeBamAlignment extends CommandLineProgram {
ALIGNED_READS_ONLY, ALIGNED_BAM, MAX_INSERTIONS_OR_DELETIONS,
ATTRIBUTES_TO_RETAIN, ATTRIBUTES_TO_REMOVE, READ1_TRIM, READ2_TRIM,
READ1_ALIGNED_BAM, READ2_ALIGNED_BAM, EXPECTED_ORIENTATIONS, SORT_ORDER,
- PRIMARY_ALIGNMENT_STRATEGY.newInstance());
+ PRIMARY_ALIGNMENT_STRATEGY.newInstance(), ADD_MATE_CIGAR);
merger.setClipOverlappingReads(CLIP_OVERLAPPING_READS);
merger.setMaxRecordsInRam(MAX_RECORDS_IN_RAM);
merger.setKeepAlignerProperPairFlags(ALIGNER_PROPER_PAIR_FLAGS);
merger.setIncludeSecondaryAlignments(INCLUDE_SECONDARY_ALIGNMENTS);
merger.mergeAlignment();
+ merger.close();
+
return 0;
}
diff --git a/src/java/net/sf/picard/sam/ReplaceSamHeader.java b/src/java/net/sf/picard/sam/ReplaceSamHeader.java
index 1f06dc0..a69f537 100644
--- a/src/java/net/sf/picard/sam/ReplaceSamHeader.java
+++ b/src/java/net/sf/picard/sam/ReplaceSamHeader.java
@@ -57,6 +57,7 @@ public class ReplaceSamHeader extends CommandLineProgram {
public static void main(final String[] argv) {
new ReplaceSamHeader().instanceMainWithExit(argv);
}
+
/**
* Do the work after command line has been parsed.
* RuntimeException may be thrown by this method, and are reported appropriately.
@@ -65,34 +66,49 @@ public class ReplaceSamHeader extends CommandLineProgram {
*/
@Override
protected int doWork() {
+ IoUtil.assertFileIsReadable(INPUT);
+ IoUtil.assertFileIsReadable(HEADER);
+ IoUtil.assertFileIsWritable(OUTPUT);
+
+ final SAMFileReader headerReader = new SAMFileReader(HEADER);
+ final SAMFileHeader replacementHeader = headerReader.getFileHeader();
+ headerReader.close();
+
final SAMFileReader.ValidationStringency originalStringency = SAMFileReader.getDefaultValidationStringency();
SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.SILENT);
+
try {
- IoUtil.assertFileIsReadable(INPUT);
- IoUtil.assertFileIsReadable(HEADER);
- IoUtil.assertFileIsWritable(OUTPUT);
- final SAMFileReader headerReader = new SAMFileReader(HEADER);
- final SAMFileHeader replacementHeader = headerReader.getFileHeader();
- final SAMFileReader recordReader = new SAMFileReader(INPUT);
- if (replacementHeader.getSortOrder() != recordReader.getFileHeader().getSortOrder()) {
- throw new PicardException("Sort orders of INPUT (" + recordReader.getFileHeader().getSortOrder().name() +
- ") and HEADER (" + replacementHeader.getSortOrder().name() + ") do not agree.");
+ if (BamFileIoUtils.isBamFile(INPUT)) {
+ blockCopyReheader(replacementHeader);
+ } else {
+ standardReheader(replacementHeader);
}
- final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(replacementHeader, true, OUTPUT);
-
- final ProgressLogger progress = new ProgressLogger(Log.getInstance(ReplaceSamHeader.class));
- for (final SAMRecord rec : recordReader) {
- rec.setHeader(replacementHeader);
- writer.addAlignment(rec);
- progress.record(rec);
- }
- writer.close();
- headerReader.close();
- recordReader.close();
- }
- finally {
+ } finally {
SAMFileReader.setDefaultValidationStringency(originalStringency);
}
+
return 0;
}
+
+ private void standardReheader(final SAMFileHeader replacementHeader) {
+ final SAMFileReader recordReader = new SAMFileReader(INPUT);
+ if (replacementHeader.getSortOrder() != recordReader.getFileHeader().getSortOrder()) {
+ throw new PicardException("Sort orders of INPUT (" + recordReader.getFileHeader().getSortOrder().name() +
+ ") and HEADER (" + replacementHeader.getSortOrder().name() + ") do not agree.");
+ }
+ final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(replacementHeader, true, OUTPUT);
+
+ final ProgressLogger progress = new ProgressLogger(Log.getInstance(ReplaceSamHeader.class));
+ for (final SAMRecord rec : recordReader) {
+ rec.setHeader(replacementHeader);
+ writer.addAlignment(rec);
+ progress.record(rec);
+ }
+ writer.close();
+ recordReader.close();
+ }
+
+ private void blockCopyReheader(final SAMFileHeader replacementHeader) {
+ BamFileIoUtils.reheaderBamFile(replacementHeader, INPUT, OUTPUT, CREATE_MD5_FILE, CREATE_INDEX);
+ }
}
diff --git a/src/java/net/sf/picard/sam/RevertOriginalBaseQualitiesAndAddMateCigar.java b/src/java/net/sf/picard/sam/RevertOriginalBaseQualitiesAndAddMateCigar.java
index ed5fffd..d90f623 100644
--- a/src/java/net/sf/picard/sam/RevertOriginalBaseQualitiesAndAddMateCigar.java
+++ b/src/java/net/sf/picard/sam/RevertOriginalBaseQualitiesAndAddMateCigar.java
@@ -9,7 +9,16 @@ import net.sf.picard.io.IoUtil;
import net.sf.picard.util.Log;
import net.sf.picard.util.PeekableIterator;
import net.sf.picard.util.ProgressLogger;
-import net.sf.samtools.*;
+import net.sf.samtools.BAMRecordCodec;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMFileWriterFactory;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMRecordQueryNameComparator;
+import net.sf.samtools.SAMUtils;
+import net.sf.samtools.SamPairUtil;
+import net.sf.samtools.SamPairUtil;
import net.sf.samtools.util.CloserUtil;
import net.sf.samtools.util.SortingCollection;
@@ -67,7 +76,7 @@ public class RevertOriginalBaseQualitiesAndAddMateCigar extends CommandLineProgr
boolean foundPairedMappedReads = false;
// Check if we can skip this file since it does not have OQ tags and the mate cigar tag is already there.
- final CanSkipSamFile skipSamFile = RevertOriginalBaseQualitiesAndAddMateCigar.canSkipSAMFile(INPUT, MAX_RECORDS_TO_EXAMINE);
+ final CanSkipSamFile skipSamFile = RevertOriginalBaseQualitiesAndAddMateCigar.canSkipSAMFile(INPUT, MAX_RECORDS_TO_EXAMINE, RESTORE_ORIGINAL_QUALITIES);
log.info(skipSamFile.getMessage(MAX_RECORDS_TO_EXAMINE));
if (skipSamFile.canSkip()) return 0;
@@ -145,7 +154,7 @@ public class RevertOriginalBaseQualitiesAndAddMateCigar extends CommandLineProgr
// we must find both records, and then always update the mate cigar
if (null != firstRecord && null != secondRecord) {
// Update mate info
- SamPairUtil.setMateInfo(firstRecord, secondRecord, outHeader);
+ SamPairUtil.setMateInfo(firstRecord, secondRecord, outHeader, true);
numMateCigarsAdded+=2;
}
@@ -188,9 +197,10 @@ public class RevertOriginalBaseQualitiesAndAddMateCigar extends CommandLineProgr
* Checks if we can skip the SAM/BAM file when reverting origin base qualities and adding mate cigars.
* @param inputFile the SAM/BAM input file
* @param maxRecordsToExamine the maximum number of records to examine before quitting
+ * @param revertOriginalBaseQualities true if we are to revert original base qualities, false otherwise
* @return whether we can skip or not, and the explanation why.
*/
- public static CanSkipSamFile canSkipSAMFile(final File inputFile, final int maxRecordsToExamine) {
+ public static CanSkipSamFile canSkipSAMFile(final File inputFile, final int maxRecordsToExamine, boolean revertOriginalBaseQualities) {
final SAMFileReader in = new SAMFileReader(inputFile, true);
final Iterator<SAMRecord> iterator = in.iterator();
int numRecordsExamined = 0;
@@ -199,7 +209,7 @@ public class RevertOriginalBaseQualitiesAndAddMateCigar extends CommandLineProgr
while (iterator.hasNext() && numRecordsExamined < maxRecordsToExamine) {
final SAMRecord record = iterator.next();
- if (null != record.getOriginalBaseQualities()) {
+ if (revertOriginalBaseQualities && null != record.getOriginalBaseQualities()) {
// has OQ, break and return case #2
returnType = CanSkipSamFile.CANNOT_SKIP_FOUND_OQ;
break;
@@ -207,7 +217,7 @@ public class RevertOriginalBaseQualitiesAndAddMateCigar extends CommandLineProgr
// check if mate pair and its mate is mapped
if (record.getReadPairedFlag() && !record.getMateUnmappedFlag()) {
- if (null == record.getMateCigar()) {
+ if (null == SAMUtils.getMateCigar(record)) {
// has no MC, break and return case #2
returnType = CanSkipSamFile.CANNOT_SKIP_FOUND_NO_MC;
break;
diff --git a/src/java/net/sf/picard/sam/SamAlignmentMerger.java b/src/java/net/sf/picard/sam/SamAlignmentMerger.java
index 85dba7a..42a8e49 100644
--- a/src/java/net/sf/picard/sam/SamAlignmentMerger.java
+++ b/src/java/net/sf/picard/sam/SamAlignmentMerger.java
@@ -79,6 +79,7 @@ public class SamAlignmentMerger extends AbstractAlignmentMerger {
* output will be coordinate-sorted
* @param primaryAlignmentSelectionStrategy How to handle multiple alignments for a fragment or read pair,
* in which none are primary, or more than one is marked primary
+ * @param addMateCigar True if we are to add or maintain the mate CIGAR (MC) tag, false if we are to remove or not include.
*/
public SamAlignmentMerger(final File unmappedBamFile, final File targetBamFile, final File referenceFasta,
final SAMProgramRecord programRecord, final boolean clipAdapters, final boolean bisulfiteSequence,
@@ -89,11 +90,12 @@ public class SamAlignmentMerger extends AbstractAlignmentMerger {
final List<File> read1AlignedSamFile, final List<File> read2AlignedSamFile,
final List<SamPairUtil.PairOrientation> expectedOrientations,
final SortOrder sortOrder,
- final PrimaryAlignmentSelectionStrategy primaryAlignmentSelectionStrategy) {
+ final PrimaryAlignmentSelectionStrategy primaryAlignmentSelectionStrategy,
+ final boolean addMateCigar) {
super(unmappedBamFile, targetBamFile, referenceFasta, clipAdapters, bisulfiteSequence,
alignedReadsOnly, programRecord, attributesToRetain, attributesToRemove, read1BasesTrimmed,
- read2BasesTrimmed, expectedOrientations, sortOrder, primaryAlignmentSelectionStrategy);
+ read2BasesTrimmed, expectedOrientations, sortOrder, primaryAlignmentSelectionStrategy, addMateCigar);
if ((alignedSamFile == null || alignedSamFile.size() == 0) &&
(read1AlignedSamFile == null || read1AlignedSamFile.size() == 0 ||
@@ -167,7 +169,6 @@ public class SamAlignmentMerger extends AbstractAlignmentMerger {
super.mergeAlignment();
}
}
-
/**
* Reads the aligned SAM records into a SortingCollection and returns an iterator over that collection
*/
diff --git a/src/java/net/sf/picard/sam/SamFileValidator.java b/src/java/net/sf/picard/sam/SamFileValidator.java
index 46695af..5708cd7 100644
--- a/src/java/net/sf/picard/sam/SamFileValidator.java
+++ b/src/java/net/sf/picard/sam/SamFileValidator.java
@@ -292,7 +292,7 @@ public class SamFileValidator {
}
private void validateReadGroup(final SAMRecord record, final SAMFileHeader header) {
- SAMReadGroupRecord rg = record.getReadGroup();
+ final SAMReadGroupRecord rg = record.getReadGroup();
if (rg == null) {
addError(new SAMValidationError(Type.RECORD_MISSING_READ_GROUP,
"A record is missing a read group", record.getReadName()));
@@ -361,7 +361,7 @@ public class SamFileValidator {
private boolean validateCigar(final SAMRecord record, final long recordNumber, final boolean isReadCigar) {
final ValidationStringency savedStringency = record.getValidationStringency();
record.setValidationStringency(ValidationStringency.LENIENT);
- final List<SAMValidationError> errors = isReadCigar ? record.validateCigar(recordNumber) : record.validateMateCigar(recordNumber);
+ final List<SAMValidationError> errors = isReadCigar ? record.validateCigar(recordNumber) : SAMUtils.validateMateCigar(record, recordNumber);
record.setValidationStringency(savedStringency);
if (errors == null) {
return true;
@@ -470,7 +470,7 @@ public class SamFileValidator {
if (fileHeader.getReadGroups().isEmpty()) {
addError(new SAMValidationError(Type.MISSING_READ_GROUP, "Read groups is empty", null));
}
- List<SAMProgramRecord> pgs = fileHeader.getProgramRecords();
+ final List<SAMProgramRecord> pgs = fileHeader.getProgramRecords();
for (int i = 0; i < pgs.size() - 1; i++) {
for (int j = i + 1; j < pgs.size(); j++) {
if (pgs.get(i).getProgramGroupId().equals(pgs.get(j).getProgramGroupId())) {
@@ -480,13 +480,23 @@ public class SamFileValidator {
}
}
- List<SAMReadGroupRecord> rgs = fileHeader.getReadGroups();
- for (int i = 0; i < rgs.size() - 1; i++) {
- for (int j = i + 1; j < rgs.size(); j++) {
- if (rgs.get(i).getReadGroupId().equals(rgs.get(j).getReadGroupId())) {
- addError(new SAMValidationError(Type.DUPLICATE_READ_GROUP_ID, "Duplicate " +
- "read group id: " + rgs.get(i).getReadGroupId(), null));
- }
+ final List<SAMReadGroupRecord> rgs = fileHeader.getReadGroups();
+ final Set<String> readGroupIDs = new HashSet<String>();
+
+ for (final SAMReadGroupRecord record : rgs) {
+ final String readGroupID = record.getReadGroupId();
+ if (readGroupIDs.contains(readGroupID)) {
+ addError(new SAMValidationError(Type.DUPLICATE_READ_GROUP_ID, "Duplicate " +
+ "read group id: " + readGroupID, null));
+ } else {
+ readGroupIDs.add(readGroupID);
+ }
+
+ final String platformValue = record.getPlatform();
+ if (platformValue == null || "".equals(platformValue)) {
+ addError(new SAMValidationError(Type.MISSING_PLATFORM_VALUE,
+ "A platform (PL) attribute was not found for read group ",
+ readGroupID));
}
}
diff --git a/src/java/net/sf/picard/util/AdapterMarker.java b/src/java/net/sf/picard/util/AdapterMarker.java
new file mode 100644
index 0000000..ac1476c
--- /dev/null
+++ b/src/java/net/sf/picard/util/AdapterMarker.java
@@ -0,0 +1,341 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2014 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+package net.sf.picard.util;
+
+import net.sf.picard.sam.ReservedTagConstants;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.util.CollectionUtil;
+import net.sf.samtools.util.SequenceUtil;
+import net.sf.samtools.util.StringUtil;
+
+import java.util.ArrayList;
+import java.util.Comparator;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.concurrent.atomic.AtomicReference;
+
+/**
+ * Store one or more AdapterPairs to use to mark adapter sequence of SAMRecords. This is a very compute-intensive process, so
+ * this class implements two heuristics to reduce computation:
+ * - Adapter sequences are truncated, and then any adapter pairs that become identical after truncation are collapsed into a single pair.
+ * - After a specified number of reads with adapter sequence has been seen, prune the list of adapter pairs to include only the most
+ * frequently seen adapters. For a flowcell, there should only be a single adapter pair found.
+ *
+ * Note that the AdapterPair object returned by all the adapterTrim* methods will not be one of the original AdapterPairs
+ * passed to the ctor, but rather will be one of the truncated copies.
+ */
+public class AdapterMarker {
+ public static final int DEFAULT_ADAPTER_LENGTH = 30;
+ public static final int DEFAULT_PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN = 100;
+ public static final int DEFAULT_NUM_ADAPTERS_TO_KEEP = 1;
+
+ // It is assumed that these are set once during execution, before the class is used to mark any adapters, but this is not enforced.
+ private int thresholdForSelectingAdaptersToKeep = DEFAULT_PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN;
+ private int numAdaptersToKeep = DEFAULT_NUM_ADAPTERS_TO_KEEP;
+ private int minSingleEndMatchBases = ClippingUtility.MIN_MATCH_BASES;
+ private int minPairMatchBases = ClippingUtility.MIN_MATCH_PE_BASES;
+ private double maxSingleEndErrorRate = ClippingUtility.MAX_ERROR_RATE;
+ private double maxPairErrorRate = ClippingUtility.MAX_PE_ERROR_RATE;
+
+ // This is AtomicReference because one thread could be matching adapters while the threshold has been crossed in another
+ // thread and the array is being replaced.
+ private final AtomicReference<AdapterPair[]> adapters = new AtomicReference<AdapterPair[]>();
+
+ // All the members below are only accessed within a synchronized block.
+ private boolean thresholdReached = false;
+ private int numAdaptersSeen = 0;
+ private final CollectionUtil.DefaultingMap<AdapterPair, Integer> seenCounts = new CollectionUtil.DefaultingMap<AdapterPair, Integer>(0);
+
+ /**
+ * Truncates adapters to DEFAULT_ADAPTER_LENGTH
+ * @param originalAdapters These should be in order from longest & most likely to shortest & least likely.
+ */
+ public AdapterMarker(final AdapterPair... originalAdapters) {
+ this(DEFAULT_ADAPTER_LENGTH, originalAdapters);
+ }
+
+ /**
+ * @param adapterLength Truncate adapters to this length.
+ * @param originalAdapters These should be in order from longest & most likely to shortest & least likely.
+ */
+ public AdapterMarker(final int adapterLength, final AdapterPair... originalAdapters) {
+ // Truncate each AdapterPair to the given length, and then combine any that end up the same after truncation.
+ final ArrayList<TruncatedAdapterPair> truncatedAdapters = new ArrayList<TruncatedAdapterPair>();
+ for (final AdapterPair adapter : originalAdapters) {
+ final TruncatedAdapterPair truncatedAdapter = makeTruncatedAdapterPair(adapter, adapterLength);
+ final int matchingIndex = truncatedAdapters.indexOf(truncatedAdapter);
+ if (matchingIndex == -1) {
+ truncatedAdapters.add(truncatedAdapter);
+ } else {
+ final TruncatedAdapterPair matchingAdapter = truncatedAdapters.get(matchingIndex);
+ matchingAdapter.setName(matchingAdapter.getName() + "|" + adapter.getName());
+ }
+ }
+ adapters.set(truncatedAdapters.toArray(new AdapterPair[truncatedAdapters.size()]));
+ }
+
+ public int getNumAdaptersToKeep() {
+ return numAdaptersToKeep;
+ }
+
+ /**
+ * After seeing the thresholdForSelectingAdapters number of adapters, keep up to this many of the original adapters.
+ */
+ public synchronized AdapterMarker setNumAdaptersToKeep(final int numAdaptersToKeep) {
+ if (numAdaptersToKeep <= 0) {
+ throw new IllegalArgumentException(String.format("numAdaptersToKeep should be positive: %d", numAdaptersToKeep));
+ }
+ this.numAdaptersToKeep = numAdaptersToKeep;
+ return this;
+ }
+
+ public int getThresholdForSelectingAdaptersToKeep() {
+ return thresholdForSelectingAdaptersToKeep;
+ }
+
+ /**
+ * When this number of adapters have been matched, discard the least-frequently matching ones.
+ * @param thresholdForSelectingAdaptersToKeep set to -1 to never discard any adapters.
+ */
+ public synchronized AdapterMarker setThresholdForSelectingAdaptersToKeep(final int thresholdForSelectingAdaptersToKeep) {
+ this.thresholdForSelectingAdaptersToKeep = thresholdForSelectingAdaptersToKeep;
+ return this;
+ }
+
+ public int getMinSingleEndMatchBases() {
+ return minSingleEndMatchBases;
+ }
+
+ /**
+ *
+ * @param minSingleEndMatchBases When marking a single-end read, adapter must match at least this many bases.
+ */
+ public synchronized AdapterMarker setMinSingleEndMatchBases(final int minSingleEndMatchBases) {
+ this.minSingleEndMatchBases = minSingleEndMatchBases;
+ return this;
+ }
+
+ public int getMinPairMatchBases() {
+ return minPairMatchBases;
+ }
+
+ /**
+ *
+ * @param minPairMatchBases When marking a paired-end read, adapter must match at least this many bases.
+ */
+ public synchronized AdapterMarker setMinPairMatchBases(final int minPairMatchBases) {
+ this.minPairMatchBases = minPairMatchBases;
+ return this;
+ }
+
+ public double getMaxSingleEndErrorRate() {
+ return maxSingleEndErrorRate;
+ }
+
+ /**
+ * @param maxSingleEndErrorRate For single-end read, no more than this fraction of the bases that align with the adapter can
+ * mismatch the adapter and still be considered an adapter match.
+ */
+ public synchronized AdapterMarker setMaxSingleEndErrorRate(final double maxSingleEndErrorRate) {
+ this.maxSingleEndErrorRate = maxSingleEndErrorRate;
+ return this;
+ }
+
+ public double getMaxPairErrorRate() {
+ return maxPairErrorRate;
+ }
+
+ /**
+ * @param maxPairErrorRate For paired-end read, no more than this fraction of the bases that align with the adapter can
+ * mismatch the adapter and still be considered an adapter match.
+ */
+ public synchronized AdapterMarker setMaxPairErrorRate(final double maxPairErrorRate) {
+ this.maxPairErrorRate = maxPairErrorRate;
+ return this;
+ }
+
+ public AdapterPair adapterTrimIlluminaSingleRead(final SAMRecord read) {
+ return adapterTrimIlluminaSingleRead(read, minSingleEndMatchBases, maxSingleEndErrorRate);
+ }
+
+ public AdapterPair adapterTrimIlluminaPairedReads(final SAMRecord read1, final SAMRecord read2) {
+ return adapterTrimIlluminaPairedReads(read1, read2, minPairMatchBases, maxPairErrorRate);
+ }
+
+ /**
+ * Overrides defaults for minMatchBases and maxErrorRate
+ */
+ public AdapterPair adapterTrimIlluminaSingleRead(final SAMRecord read, final int minMatchBases, final double maxErrorRate) {
+ final AdapterPair ret = ClippingUtility.adapterTrimIlluminaSingleRead(read, minMatchBases, maxErrorRate, adapters.get());
+ if (ret != null) tallyFoundAdapter(ret);
+ return ret;
+ }
+
+ /**
+ * Overrides defaults for minMatchBases and maxErrorRate
+ */
+ public AdapterPair adapterTrimIlluminaPairedReads(final SAMRecord read1, final SAMRecord read2,
+ final int minMatchBases, final double maxErrorRate) {
+ final AdapterPair ret = ClippingUtility.adapterTrimIlluminaPairedReads(read1, read2, minMatchBases, maxErrorRate, adapters.get());
+ if (ret != null) tallyFoundAdapter(ret);
+ return ret;
+ }
+
+ /** For unit testing only */
+ AdapterPair[] getAdapters() {
+ return adapters.get();
+ }
+
+ private TruncatedAdapterPair makeTruncatedAdapterPair(final AdapterPair adapterPair, final int adapterLength) {
+ return new TruncatedAdapterPair("truncated " + adapterPair.getName(),
+ substringAndRemoveTrailingNs(adapterPair.get3PrimeAdapterInReadOrder(), adapterLength),
+ substringAndRemoveTrailingNs(adapterPair.get5PrimeAdapterInReadOrder(), adapterLength));
+ }
+
+ /**
+ * Truncate to the given length, and in addition truncate any trailing Ns.
+ */
+ private String substringAndRemoveTrailingNs(final String s, int length) {
+ length = Math.min(length, s.length());
+ final byte[] bytes = StringUtil.stringToBytes(s);
+ while (length > 0 && SequenceUtil.isNoCall(bytes[length - 1])) {
+ length--;
+ }
+ return s.substring(0, length);
+ }
+
+ /**
+ * Keep track of every time an adapter is found, until it is time to prune the list of adapters.
+ */
+ private void tallyFoundAdapter(final AdapterPair foundAdapter) {
+ // If caller does not want adapter pruning, do nothing.
+ if (thresholdForSelectingAdaptersToKeep < 1) return;
+ synchronized (this) {
+ // Already pruned adapter list, so nothing more to do.
+ if (thresholdReached) return;
+
+ // Tally this adapter
+ seenCounts.put(foundAdapter, seenCounts.get(foundAdapter) + 1);
+
+ // Keep track of the number of times an adapter has been seen.
+ numAdaptersSeen += 1;
+
+ // Reached the threshold for pruning the list.
+ if (numAdaptersSeen >= thresholdForSelectingAdaptersToKeep) {
+
+ // Sort adapters by number of times each has been seen.
+ final TreeMap<Integer, AdapterPair> sortedAdapters = new TreeMap<Integer, AdapterPair>(new Comparator<Integer>() {
+ @Override
+ public int compare(final Integer integer, final Integer integer2) {
+ // Reverse of natural ordering
+ return integer2.compareTo(integer);
+ }
+ });
+ for (final Map.Entry<AdapterPair, Integer> entry : seenCounts.entrySet()) {
+ sortedAdapters.put(entry.getValue(), entry.getKey());
+ }
+
+ // Keep the #numAdaptersToKeep adapters that have been seen the most, plus any ties.
+ final ArrayList<AdapterPair> bestAdapters = new ArrayList<AdapterPair>(numAdaptersToKeep);
+ int countOfLastAdapter = Integer.MAX_VALUE;
+ for (final Map.Entry<Integer, AdapterPair> entry : sortedAdapters.entrySet()) {
+ if (bestAdapters.size() >= numAdaptersToKeep) {
+ if (entry.getKey() == countOfLastAdapter) {
+ bestAdapters.add(entry.getValue());
+ } else {
+ break;
+ }
+ } else {
+ countOfLastAdapter = entry.getKey();
+ bestAdapters.add(entry.getValue());
+ }
+ }
+ // Replace the existing list with the pruned list.
+ thresholdReached = true;
+ adapters.set(bestAdapters.toArray(new AdapterPair[bestAdapters.size()]));
+ }
+ }
+ }
+
+ private static class TruncatedAdapterPair implements AdapterPair {
+ String name;
+ final String fivePrime, threePrime, fivePrimeReadOrder;
+ final byte[] fivePrimeBytes, threePrimeBytes, fivePrimeReadOrderBytes;
+
+ private TruncatedAdapterPair(final String name, final String threePrimeReadOrder, final String fivePrimeReadOrder) {
+ this.name = name;
+ this.threePrime = threePrimeReadOrder;
+ this.threePrimeBytes = StringUtil.stringToBytes(threePrimeReadOrder);
+ this.fivePrimeReadOrder = fivePrimeReadOrder;
+ this.fivePrimeReadOrderBytes = StringUtil.stringToBytes(fivePrimeReadOrder);
+ this.fivePrime = SequenceUtil.reverseComplement(fivePrimeReadOrder);
+ this.fivePrimeBytes = StringUtil.stringToBytes(this.fivePrime);
+ }
+
+ public String get3PrimeAdapter(){ return threePrime; }
+ public String get5PrimeAdapter(){ return fivePrime; }
+ public String get3PrimeAdapterInReadOrder(){ return threePrime; }
+ public String get5PrimeAdapterInReadOrder() { return fivePrimeReadOrder; }
+ public byte[] get3PrimeAdapterBytes() { return threePrimeBytes; }
+ public byte[] get5PrimeAdapterBytes() { return fivePrimeBytes; }
+ public byte[] get3PrimeAdapterBytesInReadOrder() { return threePrimeBytes; }
+ public byte[] get5PrimeAdapterBytesInReadOrder() { return fivePrimeReadOrderBytes; }
+
+ public String getName() { return this.name; }
+
+ public void setName(final String name) {
+ this.name = name;
+ }
+
+ // WARNING: These methods ignore the name member!
+ @Override
+ public boolean equals(final Object o) {
+ if (this == o) return true;
+ if (o == null || getClass() != o.getClass()) return false;
+
+ final TruncatedAdapterPair that = (TruncatedAdapterPair) o;
+
+ if (!fivePrime.equals(that.fivePrime)) return false;
+ if (!threePrime.equals(that.threePrime)) return false;
+
+ return true;
+ }
+
+ @Override
+ public int hashCode() {
+ int result = fivePrime.hashCode();
+ result = 31 * result + threePrime.hashCode();
+ return result;
+ }
+
+ @Override
+ public String toString() {
+ return "TruncatedAdapterPair{" +
+ "fivePrimeReadOrder='" + fivePrimeReadOrder + '\'' +
+ ", threePrime='" + threePrime + '\'' +
+ ", name='" + name + '\'' +
+ '}';
+ }
+ }
+}
diff --git a/src/java/net/sf/picard/util/BasicInputParser.java b/src/java/net/sf/picard/util/BasicInputParser.java
index a84d529..4d6576f 100644
--- a/src/java/net/sf/picard/util/BasicInputParser.java
+++ b/src/java/net/sf/picard/util/BasicInputParser.java
@@ -31,6 +31,7 @@ import java.util.Arrays;
import java.util.ArrayList;
import net.sf.samtools.util.BufferedLineReader;
+import net.sf.samtools.util.CloserUtil;
import net.sf.samtools.util.RuntimeIOException;
/**
@@ -134,6 +135,9 @@ public class BasicInputParser extends AbstractInputParser
if (reader != null) {
reader.close();
}
+ for(final InputStream stream : inputs){
+ CloserUtil.close(stream);
+ }
}
/**
diff --git a/src/java/net/sf/picard/util/IlluminaUtil.java b/src/java/net/sf/picard/util/IlluminaUtil.java
index 4a901ab..d1772c6 100644
--- a/src/java/net/sf/picard/util/IlluminaUtil.java
+++ b/src/java/net/sf/picard/util/IlluminaUtil.java
@@ -31,7 +31,7 @@ import java.io.Closeable;
import java.util.List;
/**
- * Misc utilities for working with Illuina specific files and data
+ * Misc utilities for working with Illumina specific files and data
*
* @author jburke at broadinstitute.org
*/
@@ -124,36 +124,41 @@ public class IlluminaUtil {
return (byte)(qualityAsCharacter & 0xff);
}
+ // Strings indented below to make these easier to compare visually.
/** Describes adapters used on each pair of strands */
public static enum IlluminaAdapterPair implements AdapterPair {
- PAIRED_END("AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT", //58 bases)
- "AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG"), // 61 bases
+ PAIRED_END( "AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT", //58 bases)
+ "AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG"), // 61 bases
- INDEXED ("AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT",
- "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG"), // note 8 N's // 67 bases
+ INDEXED ( "AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT",
+ "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG"), // note 8 N's // 67 bases
- SINGLE_END ("AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT",
- "AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG"),
+ SINGLE_END ( "AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT",
+ "AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG"),
- ALTERNATIVE_SINGLE_END("AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACGATC",
- "TCGTATGCCGTCTTCTGCTTG"),
+ NEXTERA_V1( "AATGATACGGCGACCACCGAGATCTACACGCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG",
+ "CTGTCTCTTATACACATCTCTGAGCGGGCTGGCAAGGCAGACCGNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG"),
+
+ NEXTERA_V2( "AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG",
+ "CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG"),
- NEXTERA_V1("AATGATACGGCGACCACCGAGATCTACACGCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG",
- "CTGTCTCTTATACACATCTCTGAGCGGGCTGGCAAGGCAGACCGNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG"),
+ DUAL_INDEXED( "AATGATACGGCGACCACCGAGATCTNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT",
+ "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG"),
- NEXTERA_V2("AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG",
- "CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG"),
+ FLUIDIGM( "AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA",
+ "AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG"),
- DUAL_INDEXED("AATGATACGGCGACCACCGAGATCTNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT",
- "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG"),
+ TRUSEQ_SMALLRNA( "AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATC",
+ "TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG"),
- FLUIDIGM("AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA",
- "AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG"),
+ // This one is at the end of the list because its 3' is a subset of several of the 3's above.
+ // There are unit tests that try all AdapterPairs, and this one should go at the end os
+ // it is checked last.
+ ALTERNATIVE_SINGLE_END("AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACGATC",
+ "TCGTATGCCGTCTTCTGCTTG"),
- TRUSEQ_SMALLRNA("AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATC",
- "TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG")
- ;
+ ;
final String fivePrime, threePrime, fivePrimeReadOrder;
final byte[] fivePrimeBytes, threePrimeBytes, fivePrimeReadOrderBytes;
diff --git a/src/java/net/sf/picard/util/IntervalList.java b/src/java/net/sf/picard/util/IntervalList.java
index 740a333..22d959c 100644
--- a/src/java/net/sf/picard/util/IntervalList.java
+++ b/src/java/net/sf/picard/util/IntervalList.java
@@ -25,10 +25,13 @@ package net.sf.picard.util;
import net.sf.picard.PicardException;
import net.sf.picard.io.IoUtil;
-import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMSequenceDictionary;
-import net.sf.samtools.SAMTextHeaderCodec;
+import net.sf.samtools.*;
+import net.sf.samtools.util.CollectionUtil;
+import net.sf.samtools.util.SequenceUtil;
import net.sf.samtools.util.StringLineReader;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.VCFFileReader;
+import net.sf.samtools.util.StringUtil;
import java.io.*;
import java.util.*;
@@ -41,13 +44,14 @@ import java.util.*;
* A SAM style header must be present in the file which lists the sequence records
* against which the intervals are described. After the header the file then contains
* records one per line in text format with the following values tab-separated:
- * - Sequence name
- * - Start position (1-based)
- * - End position (1-based, end inclusive)
- * - Strand (either + or -)
- * - Interval name (an, ideally unique, name for the interval)
+ * Sequence name,
+ * Start position (1-based),
+ * End position (1-based, end inclusive),
+ * Strand (either + or -),
+ * Interval name (an, ideally unique, name for the interval),
*
* @author Tim Fennell
+ * @author Yossi Farjoun
*/
public class IntervalList implements Iterable<Interval> {
private final SAMFileHeader header;
@@ -72,13 +76,46 @@ public class IntervalList implements Iterable<Interval> {
/** Adds an interval to the list of intervals. */
public void add(final Interval interval) { this.intervals.add(interval); }
+ /** Adds a Collection of intervals to the list of intervals. */
+ public void addall(final Collection<Interval> intervals) {
+ this.intervals.addAll(intervals);
+ }
+
/** Sorts the internal collection of intervals by coordinate. */
+ @Deprecated // Use sorted() instead of sort(). The sort() function modifies the object in-place and
+ // is therefore difficult to work with. sorted() returns a new IntervalList that is sorted
public void sort() {
Collections.sort(this.intervals, new IntervalCoordinateComparator(this.header));
this.header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
}
+ /** returns an independent sorted IntervalList*/
+ public IntervalList sorted() {
+ final IntervalList sorted = IntervalList.copyOf(this);
+ Collections.sort(sorted.intervals, new IntervalCoordinateComparator(sorted.header));
+ sorted.header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
+ return sorted;
+ }
+
+ /** Returned an independent IntervalList that is sorted and uniquified. */
+ public IntervalList uniqued() {
+ return uniqued(true);
+ }
+
+ /**
+ * Returned an independent IntervalList that is sorted and uniquified.
+ * @param concatenateNames If false, interval names are not concatenated when merging intervals to save space.
+ */
+ public IntervalList uniqued(final boolean concatenateNames) {
+ final List<Interval> tmp = getUniqueIntervals(sorted(), concatenateNames);
+ final IntervalList value = new IntervalList(this.header.clone());
+ value.intervals.addAll(tmp);
+ return value;
+ }
+
/** Sorts and uniques the list of intervals held within this interval list. */
+ @Deprecated//use uniqued() instead. This function modifies the object in-place and
+ // is therefore difficult to work with.
public void unique() {
unique(true);
}
@@ -87,6 +124,8 @@ public class IntervalList implements Iterable<Interval> {
* Sorts and uniques the list of intervals held within this interval list.
* @param concatenateNames If false, interval names are not concatenated when merging intervals to save space.
*/
+ @Deprecated//use uniqued() instead. This function modifies the object in-place and
+ // is therefore difficult to work with
public void unique(final boolean concatenateNames) {
sort();
final List<Interval> tmp = getUniqueIntervals(concatenateNames);
@@ -108,43 +147,93 @@ public class IntervalList implements Iterable<Interval> {
*
* @return the set of unique intervals condensed from the contained intervals
*/
+ @Deprecated//use uniqued().getIntervals() instead. This function modifies the object in-place and
+ // is therefore difficult to work with
public List<Interval> getUniqueIntervals() {
return getUniqueIntervals(true);
}
+ //NO SIDE EFFECTS HERE!
/**
* Merges list of intervals and reduces them like net.sf.picard.util.IntervalList#getUniqueIntervals()
* @param concatenateNames If false, the merged interval has the name of the earlier interval. This keeps name shorter.
*/
- public List<Interval> getUniqueIntervals(final boolean concatenateNames) {
- if (getHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
- sort();
+ public static List<Interval> getUniqueIntervals(final IntervalList list, final boolean concatenateNames) {
+
+ final List<Interval> intervals;
+ if (list.getHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
+ intervals = list.sorted().intervals;
+ }
+ else {
+ intervals = list.intervals;
}
+
final List<Interval> unique = new ArrayList<Interval>();
- final ListIterator<Interval> iterator = this.intervals.listIterator();
- Interval previous = iterator.next();
-
- while (iterator.hasNext()) {
- final Interval next = iterator.next();
- if (previous.intersects(next) || previous.abuts(next)) {
- final String intervalName = (concatenateNames? previous.getName() + "|" + next.getName(): previous.getName());
- previous = new Interval(previous.getSequence(),
- previous.getStart(),
- Math.max(previous.getEnd(), next.getEnd()),
- previous.isNegativeStrand(),
- intervalName);
+ final TreeSet<Interval> toBeMerged = new TreeSet<Interval>();
+ Interval current = null;
+
+ for (final Interval next : intervals) {
+ if (current == null) {
+ toBeMerged.add(next);
+ current = next;
+ }
+ else if (current.intersects(next) || current.abuts(next)) {
+ toBeMerged.add(next);
+ current = new Interval(current.getSequence(), current.getStart(), Math.max(current.getEnd(), next.getEnd()), false , "");
}
else {
- unique.add(previous);
- previous = next;
+ // Emit merged/unique interval
+ unique.add(merge(toBeMerged, concatenateNames));
+
+ // Set current == next for next iteration
+ toBeMerged.clear();
+ current = next;
+ toBeMerged.add(current);
}
}
- if (previous != null) unique.add(previous);
-
+ if (toBeMerged.size() > 0) unique.add(merge(toBeMerged, concatenateNames));
return unique;
}
+ /**
+ * Merges list of intervals and reduces them like net.sf.picard.util.IntervalList#getUniqueIntervals()
+ * @param concatenateNames If false, the merged interval has the name of the earlier interval. This keeps name shorter.
+ */
+ @Deprecated //use uniqued(concatenateNames).getIntervals() or the static version instead to avoid changing the underlying object.
+ /**
+ * Merges list of intervals and reduces them like net.sf.picard.util.IntervalList#getUniqueIntervals()
+ * @param concatenateNames If false, the merged interval has the name of the earlier interval. This keeps name shorter.
+ */
+ public List<Interval> getUniqueIntervals(final boolean concatenateNames) {
+ if (getHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
+ sort();
+ }
+
+ return getUniqueIntervals(this, concatenateNames);
+ }
+
+ /** Merges a sorted collection of intervals and optionally concatenates unique names or takes the first name. */
+ static Interval merge(final SortedSet<Interval> intervals, final boolean concatenateNames) {
+ final String chrom = intervals.first().getSequence();
+ int start = intervals.first().getStart();
+ int end = intervals.last().getEnd();
+ final boolean neg = intervals.first().isNegativeStrand();
+ final LinkedHashSet<String> names = new LinkedHashSet<String>();
+ final String name;
+
+ for (final Interval i : intervals) {
+ if (i.getName() != null) names.add(i.getName());
+ start = Math.min(start, i.getStart());
+ end = Math.max(end, i.getEnd());
+ }
+
+ if (concatenateNames) { name = StringUtil.join("|", names); }
+ else { name = names.iterator().next(); }
+
+ return new Interval(chrom, start, end, neg, name);
+ }
+
/** Gets the (potentially redundant) sum of the length of the intervals in the list. */
public long getBaseCount() {
return Interval.countBases(this.intervals);
@@ -152,7 +241,7 @@ public class IntervalList implements Iterable<Interval> {
/** Gets the count of unique bases represented by the intervals in the list. */
public long getUniqueBaseCount() {
- return Interval.countBases(getUniqueIntervals());
+ return uniqued().getBaseCount();
}
/** Returns the count of intervals in the list. */
@@ -161,12 +250,71 @@ public class IntervalList implements Iterable<Interval> {
}
/**
+ * Parse a VCF file and convert to an IntervalList The name field of the IntervalList is taken from the ID field of the variant, if it exists. if not,
+ * creates a name of the format interval-n where n is a running number that increments only on un-named intervals
+ * @param file
+ * @return
+ */
+ public static IntervalList fromVcf(final File file){
+ final VCFFileReader vcfFileReader = new VCFFileReader(file, false);
+ final IntervalList intervalList = IntervalList.fromVcf(vcfFileReader);
+ vcfFileReader.close();
+ return intervalList;
+ }
+
+ /**
+ * Converts a vcf to an IntervalList. The name field of the IntervalList is taken from the ID field of the variant, if it exists. if not,
+ * creates a name of the format interval-n where n is a running number that increments only on un-named intervals
+ * @param vcf the vcfReader to be used for the conversion
+ * @return an IntervalList constructed from input vcf
+ */
+ public static IntervalList fromVcf(final VCFFileReader vcf){
+
+ //grab the dictionary from the VCF and use it in the IntervalList
+ final SAMSequenceDictionary dict = vcf.getFileHeader().getSequenceDictionary();
+ final SAMFileHeader samFileHeader = new SAMFileHeader();
+ samFileHeader.setSequenceDictionary(dict);
+ final IntervalList list = new IntervalList( samFileHeader);
+
+ int intervals=0;
+ for(final VariantContext vc : vcf){
+ if(!vc.isFiltered()){
+ String name = vc.getID();
+ if(".".equals(name) || name == null)
+ name = "interval-" + (++intervals);
+ list.add(new Interval(vc.getChr(), vc.getStart(), vc.getEnd(), false, name));
+ }
+ }
+
+ return list;
+ }
+
+ /** creates a independent copy of the given IntervalList
+ *
+ * @param list
+ * @return
+ */
+ public static IntervalList copyOf(final IntervalList list){
+ final IntervalList clone = new IntervalList(list.header.clone());
+ clone.intervals.addAll(list.intervals);
+ return clone;
+ }
+
+ /**
* Parses an interval list from a file.
* @param file the file containing the intervals
* @return an IntervalList object that contains the headers and intervals from the file
*/
public static IntervalList fromFile(final File file) {
- return fromReader(IoUtil.openFileForBufferedReading(file));
+ final BufferedReader reader=IoUtil.openFileForBufferedReading(file);
+ final IntervalList list = fromReader(reader);
+ try {
+ reader.close();
+ } catch (final IOException e) {
+ throw new PicardException(String.format("Failed to close file %s after reading",file));
+ }
+
+ return list;
}
/**
@@ -198,6 +346,9 @@ public class IntervalList implements Iterable<Interval> {
final IntervalList list = new IntervalList(codec.decode(headerReader, "BufferedReader"));
final SAMSequenceDictionary dict = list.getHeader().getSequenceDictionary();
+ //there might not be any lines after the header, in which case we should return an empty list
+ if(line == null) return list;
+
// Then read in the intervals
final FormatUtil format = new FormatUtil();
do {
@@ -234,11 +385,11 @@ public class IntervalList implements Iterable<Interval> {
return list;
}
- catch (IOException ioe) {
+ catch (final IOException ioe) {
throw new PicardException("Error parsing interval list.", ioe);
}
finally {
- try { in.close(); } catch (Exception e) { /* do nothing */ }
+ try { in.close(); } catch (final Exception e) { /* do nothing */ }
}
}
@@ -267,19 +418,202 @@ public class IntervalList implements Iterable<Interval> {
out.write('\t');
out.write(interval.isPositiveStrand() ? '+' : '-');
out.write('\t');
- out.write(interval.getName());
+ if(interval.getName() != null){
+ out.write(interval.getName());
+ }
+ else{
+ out.write(".");
+ }
out.newLine();
}
out.flush();
out.close();
}
- catch (IOException ioe) {
+ catch (final IOException ioe) {
throw new PicardException("Error writing out interval list to file: " + file.getAbsolutePath(), ioe);
}
}
-}
+ /**
+ * A utility function for generating the intersection of two IntervalLists, checks for equal dictionaries.
+ *
+ * @param list1 the first IntervalList
+ * @param list2 the second IntervalList
+ * @return the intersection of list1 and list2.
+ */
+
+ public static IntervalList intersection(final IntervalList list1, final IntervalList list2) {
+
+ final IntervalList result;
+ // Ensure that all the sequence dictionaries agree and merge the lists
+ SequenceUtil.assertSequenceDictionariesEqual(list1.getHeader().getSequenceDictionary(),
+ list2.getHeader().getSequenceDictionary());
+
+ result = new IntervalList(list1.getHeader().clone());
+
+ final OverlapDetector<Interval> detector = new OverlapDetector<Interval>(0, 0);
+
+ detector.addAll(list1.getIntervals(), list1.getIntervals());
+
+ for (final Interval i : list2.getIntervals()) {
+ final Collection<Interval> as = detector.getOverlaps(i);
+ for (final Interval j : as) {
+ final Interval tmp = i.intersect(j);
+
+ result.add(tmp);
+ }
+ }
+ return result.uniqued();
+
+ }
+
+ /**
+ * A utility function for intersecting a list of IntervalLists, checks for equal dictionaries.
+ *
+ * @param lists the list of IntervalList
+ * @return the intersection of all the IntervalLists in lists.
+ */
+
+
+ public static IntervalList intersection(final Collection<IntervalList> lists) {
+
+ IntervalList intersection = null;
+ for (final IntervalList list : lists) {
+ if(intersection == null){
+ intersection = list;
+ }
+ else{
+ intersection = intersection(intersection, list);
+ }
+ }
+ return intersection;
+ }
+
+
+
+
+ /**
+ * A utility function for merging a list of IntervalLists, checks for equal dictionaries.
+ * Merging does not look for overlapping intervals nor uniquify
+ *
+ * @param lists a list of IntervalList
+ * @return the union of all the IntervalLists in lists.
+ */
+ public static IntervalList concatenate(final Collection<IntervalList> lists) {
+ if(lists.isEmpty()){
+ throw new PicardException("Cannot concatenate an empty list of IntervalLists.");
+ }
+
+ // Ensure that all the sequence dictionaries agree and merge the lists
+ final SAMFileHeader header = lists.iterator().next().getHeader().clone();
+ header.setSortOrder(SAMFileHeader.SortOrder.unsorted);
+
+ final IntervalList merged = new IntervalList(header);
+
+ for (final IntervalList in : lists) {
+ SequenceUtil.assertSequenceDictionariesEqual(merged.getHeader().getSequenceDictionary(),
+ in.getHeader().getSequenceDictionary());
+
+ merged.addall(in.intervals);
+ }
+ return merged;
+ }
+
+
+
+ /**
+ * A utility function for finding the union of a list of IntervalLists, checks for equal dictionaries.
+ * also looks for overlapping intervals, uniquifies, and sorts (by coordinate)
+ *
+ * @param lists the list of IntervalList
+ * @return the union of all the IntervalLists in lists.
+ */
+ public static IntervalList union(final Collection<IntervalList> lists) {
+ final IntervalList merged = concatenate(lists);
+ return merged.uniqued();
+ }
+
+
+ public static IntervalList union(final IntervalList list1, final IntervalList list2) {
+ final Collection<IntervalList> duo = CollectionUtil.makeList(list1, list2);
+ return IntervalList.union(duo);
+ }
+
+
+ /** inverts an IntervalList and returns one that has exactly all the bases in the dictionary that the original one does not.
+ *
+ * @param list an IntervalList
+ * @return an IntervalList that is complementary to list
+ */
+ public static IntervalList invert(final IntervalList list) {
+ final IntervalList inverse = new IntervalList(list.header.clone());
+
+ final ListMap<Integer,Interval> map = new ListMap<Integer,Interval>();
+
+ //add all the intervals (uniqued and therefore also sorted) to a ListMap from sequenceIndex to a list of Intervals
+ for(final Interval i : list.uniqued().getIntervals()){
+ map.add(list.getHeader().getSequenceIndex(i.getSequence()),i);
+ }
+
+ int intervals = 0; // a counter to supply newly-created intervals with a name
+
+
+ //iterate over the contigs in the dictionary
+ for (final SAMSequenceRecord samSequenceRecord : list.getHeader().getSequenceDictionary().getSequences()) {
+ final Integer sequenceIndex = samSequenceRecord.getSequenceIndex();
+ final String sequenceName = samSequenceRecord.getSequenceName();
+ final int sequenceLength = samSequenceRecord.getSequenceLength();
+
+ Integer lastCoveredPosition = 0; //start at beginning of sequence
+ //iterate over list of intervals that are in sequence
+ if (map.containsKey(sequenceIndex)) // if there are intervals in the ListMap on this contig, iterate over them (in order)
+ for (final Interval i : map.get(sequenceIndex)) {
+ if (i.getStart() > lastCoveredPosition + 1) //if there's space between the last interval and the current one, add an interval between them
+ inverse.add(new Interval(sequenceName, lastCoveredPosition + 1, i.getStart() - 1, false, "interval-" + (++intervals)));
+ lastCoveredPosition = i.getEnd(); //update the last covered position
+ }
+ //finally, if there's room between the last covered position and the end of the sequence, add an interval
+ if (sequenceLength > lastCoveredPosition) //if there's space between the last interval and the next
+ // one, add an interval. This also covers the case that there are no intervals in the ListMap for a contig.
+ inverse.add(new Interval(sequenceName, lastCoveredPosition + 1, sequenceLength, false, "interval-" + (++intervals)));
+ }
+
+ return inverse;
+ }
+
+
+ /**
+ * A utility function for subtracting a collection of IntervalLists from another. Resulting loci are those that are in the first collection
+ * but not the second.
+ *
+ * @param listsToSubtractFrom the collection of IntervalList from which to subtract intervals
+ * @param listsToSubtract the collection of intervals to subtract
+ * @return an IntervalLists comprising all loci that are in first collection but not second.
+ */
+ public static IntervalList subtract(final Collection<IntervalList> listsToSubtractFrom, final Collection<IntervalList> listsToSubtract) {
+ return intersection(
+ union(listsToSubtractFrom),
+ invert(union(listsToSubtract)));
+ }
+
+
+ /**
+ * A utility function for finding the difference between two IntervalLists.
+ *
+ * @param lists1 the first collection of IntervalLists
+ * @param lists2 the second collection of IntervalLists
+ * @return the difference between the two intervals, i.e. the loci that are only in one IntervalList but not both
+ */
+ public static IntervalList difference(final Collection<IntervalList> lists1, final Collection<IntervalList> lists2) {
+ return union(
+ subtract(lists1, lists2),
+ subtract(lists2, lists1));
+ }
+
+
+
+}
/**
* Comparator that orders intervals based on their sequence index, by coordinate
* then by strand and finally by name.
diff --git a/src/java/net/sf/picard/util/IntervalListTools.java b/src/java/net/sf/picard/util/IntervalListTools.java
index 9befcf9..9fc75a3 100644
--- a/src/java/net/sf/picard/util/IntervalListTools.java
+++ b/src/java/net/sf/picard/util/IntervalListTools.java
@@ -1,20 +1,19 @@
package net.sf.picard.util;
import net.sf.picard.PicardException;
+import net.sf.picard.cmdline.CommandLineParser;
+import net.sf.picard.cmdline.CommandLineProgram;
import net.sf.picard.cmdline.Option;
import net.sf.picard.cmdline.StandardOptionDefinitions;
import net.sf.picard.cmdline.Usage;
import net.sf.picard.io.IoUtil;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMProgramRecord;
-import net.sf.samtools.util.SequenceUtil;
import java.io.File;
import java.text.DecimalFormat;
import java.util.*;
-import net.sf.picard.cmdline.CommandLineProgram;
-
/**
* Little class to aid working with interval lists.
*
@@ -22,7 +21,7 @@ import net.sf.picard.cmdline.CommandLineProgram;
*/
public class IntervalListTools extends CommandLineProgram {
@Usage public final String USAGE = getStandardUsagePreamble() + " General tool for manipulating interval lists, " +
- "including sorting, merging, padding, uniqueifying. Default operation if given one or more inputs is to " +
+ "including sorting, merging, padding, uniqueifying, and other set-theoretic operations. Default operation if given one or more inputs is to " +
"merge and sort them. Other options are controlled by arguments.";
@Option(shortName=StandardOptionDefinitions.INPUT_SHORT_NAME,
@@ -31,11 +30,11 @@ public class IntervalListTools extends CommandLineProgram {
public List<File> INPUT;
@Option(doc="The output interval list file to write (if SCATTER_COUNT is 1) or the directory into which " +
- "to write the scattered interval sub-directories (if SCATTER_COUNT > 1)", shortName= StandardOptionDefinitions.OUTPUT_SHORT_NAME, optional=true)
+ "to write the scattered interval sub-directories (if SCATTER_COUNT > 1)", shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, optional = true)
public File OUTPUT;
@Option(doc="The amount to pad each end of the intervals by before other operations are undertaken. Negative numbers are allowed " +
- "and indicate intervals should be shrunk. Resulting intervals < 0 bases long will be removed.", optional=true)
+ "and indicate intervals should be shrunk. Resulting intervals < 0 bases long will be removed. Padding is applied to the interval lists <b> before </b> the ACTION is performed.", optional=true)
public int PADDING = 0;
@Option(doc="If true, merge overlapping and adjacent intervals to create a list of unique intervals. Implies SORT=true")
@@ -44,13 +43,73 @@ public class IntervalListTools extends CommandLineProgram {
@Option(doc="If true, sort the resulting interval list by coordinate.")
public boolean SORT = true;
- @Option(doc="One or more lines of comment to add to the header of the output file.", optional=true)
+ @Option(doc = "Action to take on inputs.")
+ public Action ACTION = Action.CONCAT;
+
+ @Option(shortName = "SI", doc = "Second set of intervals for SUBTRACT and DIFFERENCE operations.", optional = true)
+ public List<File> SECOND_INPUT;
+
+ @Option(doc="One or more lines of comment to add to the header of the output file.", optional = true)
public List<String> COMMENT = null;
@Option(doc="The number of files into which to scatter the resulting list by locus.")
public int SCATTER_COUNT = 1;
- private final Log log = Log.getInstance(IntervalListTools.class);
+ @Option(doc = "Produce the inverse list", optional = true)
+ public boolean INVERT = false;
+
+ private static final Log log = Log.getInstance(IntervalListTools.class);
+
+ public enum Action implements CommandLineParser.ClpEnum{
+
+ CONCAT("The concatenation of all the INPUTs, no sorting or merging of overlapping/abutting intervals implied. Will result in an unsorted list unless requested otherwise.") {
+ @Override
+ IntervalList act(final List<IntervalList> list, final List<IntervalList> unused) {
+ if(!unused.isEmpty()) throw new IllegalArgumentException(String.format("Second List found when action was %s. Ignoring second list.",this.name()));
+ return IntervalList.concatenate(list);
+ }
+ },
+ UNION ("Like CONCATENATE but with UNIQUE and SORT implied, the result being the set-wise union of all INPUTS.") {
+ @Override
+ IntervalList act(final List<IntervalList> list, final List<IntervalList> unused) {
+ if(!unused.isEmpty()) throw new IllegalArgumentException(String.format("Second List found when action was %s. Ignoring second list.",this.name()));
+ return IntervalList.union(list);
+ }
+ },
+ INTERSECT ("The sorted, uniqued set of all loci that are contained in all of the INPUTs.") {
+ @Override
+ IntervalList act(final List<IntervalList> list, final List<IntervalList> unused) {
+ if(!unused.isEmpty()) throw new IllegalArgumentException(String.format("Second List found when action was %s. Ignoring second list.",this.name()));
+ return IntervalList.intersection(list);
+ }
+ },
+ SUBTRACT ("Subtracts SECOND_INPUT from INPUT. The resulting loci are there in INPUT that are not in SECOND_INPUT") {
+ @Override
+ IntervalList act(final List<IntervalList> list1, final List<IntervalList> list2) {
+ return IntervalList.subtract(list1, list2);
+
+ }
+ },
+ SYMDIFF ("Find loci that are in INPUT or SECOND_INPUT but are not in both." ) {
+ @Override
+ IntervalList act(final List<IntervalList> list1, final List<IntervalList> list2) {
+ return IntervalList.difference(list1, list2);
+ }
+ };
+
+
+ String helpdoc;
+ Action(final String helpdoc){
+ this.helpdoc=helpdoc;
+ }
+
+ @Override
+ public String getHelpDoc() {
+ return helpdoc;
+ }
+ abstract IntervalList act(final List<IntervalList> list1, final List<IntervalList> list2);
+
+ }
// Stock main method
public static void main(final String[] args) {
@@ -61,6 +120,8 @@ public class IntervalListTools extends CommandLineProgram {
protected int doWork() {
// Check inputs
for (final File f : INPUT) IoUtil.assertFileIsReadable(f);
+ for (final File f : SECOND_INPUT) IoUtil.assertFileIsReadable(f);
+
if (OUTPUT != null) {
if (SCATTER_COUNT == 1) {
IoUtil.assertFileIsWritable(OUTPUT);
@@ -92,35 +153,51 @@ public class IntervalListTools extends CommandLineProgram {
}
}
- if (UNIQUE && !SORT ) {
- log.warn("UNIQUE=true requires sorting but SORT=false was specified. Sorting anyway!");
- SORT = true;
- }
+ // same for the second list
+ final List<IntervalList> secondLists = new ArrayList<IntervalList>();
+ for (final File f : SECOND_INPUT) {
+ final IntervalList list = IntervalList.fromFile(f);
+ if (PADDING != 0) {
+ final IntervalList out = new IntervalList(list.getHeader());
+ for (final Interval i : list) {
+ final int start = i.getStart() - PADDING;
+ final int end = i.getEnd() + PADDING;
+ if (start <= end) {
+ final Interval i2 = new Interval(i.getSequence(), start, end, i.isNegativeStrand(), i.getName());
+ out.add(i2);
+ }
+ }
- // Ensure that all the sequence dictionaries agree and merge the lists
- IntervalList merged= null;
- for (final IntervalList in : lists) {
- if (merged == null) {
- merged = in;
+ secondLists.add(out);
}
else {
- SequenceUtil.assertSequenceDictionariesEqual(merged.getHeader().getSequenceDictionary(),
- in.getHeader().getSequenceDictionary());
-
- for (final Interval i : in) {
- merged.add(i);
- }
+ secondLists.add(list);
}
}
- if (SORT) merged.sort();
- final List<Interval> finalIntervals = UNIQUE ? merged.getUniqueIntervals() : merged.getIntervals();
+ if (UNIQUE && !SORT ) {
+ log.warn("UNIQUE=true requires sorting but SORT=false was specified. Results will be sorted!");
+ }
+
+ final IntervalList result = ACTION.act(lists, secondLists);
+
+ if(INVERT){
+ SORT=false; // no need to sort, since return will be sorted by definition.
+ UNIQUE=false; //no need to unique since invert will already return a unique list.
+ }
+
+ final IntervalList possiblySortedResult = SORT ? result.sorted() : result;
+ final IntervalList possiblyInvertedResult = INVERT ? IntervalList.invert(possiblySortedResult) : possiblySortedResult;
+
+ //only get unique if this has been asked unless inverting (since the invert will return a unique list)
+ final List<Interval> finalIntervals = UNIQUE ? possiblyInvertedResult.uniqued().getIntervals() : possiblyInvertedResult.getIntervals();
+
// Decide on a PG ID and make a program group
- final SAMFileHeader header = merged.getHeader();
+ final SAMFileHeader header = result.getHeader();
final Set<String> pgs = new HashSet<String>();
for (final SAMProgramRecord pg : header.getProgramRecords()) pgs.add(pg.getId());
- for (int i=1; i<Integer.MAX_VALUE; ++i) {
+ for (int i = 1; i < Integer.MAX_VALUE; ++i) {
if (!pgs.contains(String.valueOf(i))) {
final SAMProgramRecord pg = new SAMProgramRecord(String.valueOf(i));
pg.setCommandLine(getCommandLine());
@@ -189,11 +266,12 @@ public class IntervalListTools extends CommandLineProgram {
// push both pieces onto locs, continue
// The last split is special -- when you have only one split left, it gets all of the remaining locs
// to deal with rounding issues
- final long idealSplitLength = Math.max((long)Math.floor(list.getUniqueBaseCount() / (1.0*SCATTER_COUNT)), 1);
+ final IntervalList uniquedList=list.uniqued();
+ final long idealSplitLength = Math.max((long)Math.floor(uniquedList.getBaseCount() / (1.0*SCATTER_COUNT)), 1);
int splitLength = 0;
- IntervalList split = new IntervalList(list.getHeader());
+ IntervalList split = new IntervalList(uniquedList.getHeader());
int index = 1; // The index of the next split file to write
- final Iterator<Interval> it = list.iterator();
+ final Iterator<Interval> it = uniquedList.iterator();
int totalIntervals = 0;
final DecimalFormat format = new DecimalFormat("0000");
@@ -209,7 +287,7 @@ public class IntervalListTools extends CommandLineProgram {
split.add(interval);
totalIntervals++;
split.write(createDirectoryAndGetScatterFile(format.format(index++)));
- split = new IntervalList(list.getHeader());
+ split = new IntervalList(uniquedList.getHeader());
splitLength = 0;
}
else {
@@ -221,7 +299,7 @@ public class IntervalListTools extends CommandLineProgram {
split.add(partial);
totalIntervals++;
split.write(createDirectoryAndGetScatterFile(format.format(index++)));
- split = new IntervalList(list.getHeader());
+ split = new IntervalList(uniquedList.getHeader());
consumed += amountToConsume;
splitLength = 0;
diff --git a/src/java/net/sf/picard/util/MathUtil.java b/src/java/net/sf/picard/util/MathUtil.java
index 7ffb8c9..73f1011 100644
--- a/src/java/net/sf/picard/util/MathUtil.java
+++ b/src/java/net/sf/picard/util/MathUtil.java
@@ -207,7 +207,16 @@ public class MathUtil {
for (final double next : arr) result += next;
return result;
}
-
+
+ /** Returns the sum of the elements in the array starting with start and ending before stop. */
+ public static long sum(final long[] arr, final int start, final int stop) {
+ long result = 0;
+ for (int i=start; i<stop; ++i) {
+ result += arr[i];
+ }
+ return result;
+ }
+
public static final LogMath LOG_2_MATH = new LogMath(2);
public static final LogMath NATURAL_LOG_MATH = new LogMath(Math.exp(1)) {
@Override
diff --git a/src/java/net/sf/picard/util/SamLocusIterator.java b/src/java/net/sf/picard/util/SamLocusIterator.java
index baf5571..39ca075 100644
--- a/src/java/net/sf/picard/util/SamLocusIterator.java
+++ b/src/java/net/sf/picard/util/SamLocusIterator.java
@@ -133,8 +133,8 @@ public class SamLocusIterator implements Iterable<SamLocusIterator.LocusInfo>, C
private final LinkedList<LocusInfo> accumulator = new LinkedList<LocusInfo>();
private int qualityScoreCutoff = Integer.MIN_VALUE;
-
private int mappingQualityScoreCutoff = Integer.MIN_VALUE;
+ private boolean includeNonPfReads = true;
/**
* If true, emit a LocusInfo for every locus in the target map, or if no target map,
@@ -277,7 +277,9 @@ public class SamLocusIterator implements Iterable<SamLocusIterator.LocusInfo>, C
}
// Skip over an unaligned read that has been forced to be sorted with the aligned reads
- if (rec.getReadUnmappedFlag()) {
+ if (rec.getReadUnmappedFlag()
+ || rec.getMappingQuality() < this.mappingQualityScoreCutoff
+ || (!this.includeNonPfReads && rec.getReadFailsVendorQualityCheckFlag())) {
samIterator.next();
continue;
}
@@ -361,8 +363,7 @@ public class SamLocusIterator implements Iterable<SamLocusIterator.LocusInfo>, C
rec.getAlignmentStart() + j));
}
// if the quality score cutoff is met, accumulate the base info
- if (rec.getBaseQualities()[readOffset] >= getQualityScoreCutoff() &&
- rec.getMappingQuality() >= getMappingQualityScoreCutoff()) {
+ if (rec.getBaseQualities()[readOffset] >= getQualityScoreCutoff()) {
accumulator.get(refOffset).add(rec, readOffset);
}
}
@@ -483,15 +484,14 @@ public class SamLocusIterator implements Iterable<SamLocusIterator.LocusInfo>, C
public int getMappingQualityScoreCutoff() {
return mappingQualityScoreCutoff;
}
+ public void setMappingQualityScoreCutoff(final int mappingQualityScoreCutoff) { this.mappingQualityScoreCutoff = mappingQualityScoreCutoff; }
- public void setMappingQualityScoreCutoff(final int mappingQualityScoreCutoff) {
- this.mappingQualityScoreCutoff = mappingQualityScoreCutoff;
- }
+ public boolean isIncludeNonPfReads() { return includeNonPfReads; }
+ public void setIncludeNonPfReads(final boolean includeNonPfReads) { this.includeNonPfReads = includeNonPfReads; }
public boolean isEmitUncoveredLoci() {
return emitUncoveredLoci;
}
-
public void setEmitUncoveredLoci(final boolean emitUncoveredLoci) {
this.emitUncoveredLoci = emitUncoveredLoci;
}
diff --git a/src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java b/src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java
index 01f3338..2f81e3b 100644
--- a/src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java
+++ b/src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java
@@ -8,17 +8,15 @@ import net.sf.picard.cmdline.Usage;
import net.sf.picard.io.IoUtil;
import net.sf.picard.util.Log;
import net.sf.picard.util.ProgressLogger;
-import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.util.CloseableIterator;
import net.sf.samtools.util.CloserUtil;
-import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
import org.broadinstitute.variant.variantcontext.writer.Options;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterBuilder;
import org.broadinstitute.variant.vcf.*;
import java.io.File;
@@ -67,11 +65,17 @@ public class MakeSitesOnlyVcf extends CommandLineProgram {
}
final ProgressLogger progress = new ProgressLogger(Log.getInstance(MakeSitesOnlyVcf.class), 10000);
- final EnumSet<Options> options = EnumSet.copyOf(VariantContextWriterFactory.DEFAULT_OPTIONS);
- if (CREATE_INDEX) options.add(Options.INDEX_ON_THE_FLY); else options.remove(Options.INDEX_ON_THE_FLY);
// Setup the site-only file writer
- final VariantContextWriter writer = VariantContextWriterFactory.create(OUTPUT, sequenceDictionary, options);
+ final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
+ .setOutputFile(OUTPUT)
+ .setReferenceDictionary(sequenceDictionary);
+ if (CREATE_INDEX)
+ builder.setOption(Options.INDEX_ON_THE_FLY);
+ else
+ builder.unsetOption(Options.INDEX_ON_THE_FLY);
+ final VariantContextWriter writer = builder.build();
+
final VCFHeader header = new VCFHeader(inputVcfHeader.getMetaDataInInputOrder(), SAMPLE);
writer.writeHeader(header);
diff --git a/src/java/net/sf/picard/vcf/MergeVcfs.java b/src/java/net/sf/picard/vcf/MergeVcfs.java
index d9a42c4..918f9f1 100644
--- a/src/java/net/sf/picard/vcf/MergeVcfs.java
+++ b/src/java/net/sf/picard/vcf/MergeVcfs.java
@@ -41,7 +41,7 @@ import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextComparator;
import org.broadinstitute.variant.variantcontext.writer.Options;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterBuilder;
import org.broadinstitute.variant.vcf.VCFFileReader;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFUtils;
@@ -134,8 +134,14 @@ public class MergeVcfs extends CommandLineProgram {
if (CREATE_INDEX && sequenceDictionary == null) {
throw new PicardException("A sequence dictionary must be available (either through the input file or by setting it explicitly) when creating indexed output.");
}
- final EnumSet<Options> options = CREATE_INDEX ? EnumSet.of(Options.INDEX_ON_THE_FLY) : EnumSet.noneOf(Options.class);
- final VariantContextWriter writer = VariantContextWriterFactory.create(OUTPUT, sequenceDictionary, options);
+
+ final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
+ .setOutputFile(OUTPUT)
+ .setReferenceDictionary(sequenceDictionary)
+ .clearOptions();
+ if (CREATE_INDEX)
+ builder.setOption(Options.INDEX_ON_THE_FLY);
+ final VariantContextWriter writer = builder.build();
writer.writeHeader(new VCFHeader(VCFUtils.smartMergeHeaders(headers, false), sampleList));
diff --git a/src/java/net/sf/picard/vcf/SplitVcfs.java b/src/java/net/sf/picard/vcf/SplitVcfs.java
index 1295bea..971a7b2 100644
--- a/src/java/net/sf/picard/vcf/SplitVcfs.java
+++ b/src/java/net/sf/picard/vcf/SplitVcfs.java
@@ -16,7 +16,7 @@ import net.sf.samtools.util.CloserUtil;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.writer.Options;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterBuilder;
import org.broadinstitute.variant.vcf.VCFFileReader;
import org.broadinstitute.variant.vcf.VCFHeader;
@@ -80,10 +80,14 @@ public class SplitVcfs extends CommandLineProgram {
throw new PicardException("A sequence dictionary must be available (either through the input file or by setting it explicitly) when creating indexed output.");
}
- final EnumSet<Options> options = CREATE_INDEX ? EnumSet.of(Options.INDEX_ON_THE_FLY) : EnumSet.noneOf(Options.class);
+ final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
+ .setReferenceDictionary(sequenceDictionary)
+ .clearOptions();
+ if (CREATE_INDEX)
+ builder.setOption(Options.INDEX_ON_THE_FLY);
- final VariantContextWriter snpWriter = VariantContextWriterFactory.create(SNP_OUTPUT, sequenceDictionary, options);
- final VariantContextWriter indelWriter = VariantContextWriterFactory.create(INDEL_OUTPUT, sequenceDictionary, options);
+ final VariantContextWriter snpWriter = builder.setOutputFile(SNP_OUTPUT).build();
+ final VariantContextWriter indelWriter = builder.setOutputFile(INDEL_OUTPUT).build();
snpWriter.writeHeader(fileHeader);
indelWriter.writeHeader(fileHeader);
diff --git a/src/java/net/sf/picard/vcf/VcfFormatConverter.java b/src/java/net/sf/picard/vcf/VcfFormatConverter.java
index 72b35b9..fc87825 100644
--- a/src/java/net/sf/picard/vcf/VcfFormatConverter.java
+++ b/src/java/net/sf/picard/vcf/VcfFormatConverter.java
@@ -39,7 +39,7 @@ import net.sf.samtools.util.CloserUtil;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.writer.Options;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterBuilder;
import org.broadinstitute.variant.vcf.VCFFileReader;
import org.broadinstitute.variant.vcf.VCFHeader;
@@ -91,10 +91,14 @@ public class VcfFormatConverter extends CommandLineProgram {
throw new PicardException("A sequence dictionary must be available in the input file when creating indexed output.");
}
- final EnumSet<Options> options = EnumSet.copyOf(VariantContextWriterFactory.DEFAULT_OPTIONS);
- if (CREATE_INDEX) options.add(Options.INDEX_ON_THE_FLY); else options.remove(Options.INDEX_ON_THE_FLY);
-
- final VariantContextWriter writer = VariantContextWriterFactory.create(OUTPUT, sequenceDictionary, options);
+ final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
+ .setOutputFile(OUTPUT)
+ .setReferenceDictionary(sequenceDictionary);
+ if (CREATE_INDEX)
+ builder.setOption(Options.INDEX_ON_THE_FLY);
+ else
+ builder.unsetOption(Options.INDEX_ON_THE_FLY);
+ final VariantContextWriter writer = builder.build();
writer.writeHeader(header);
final CloseableIterator<VariantContext> iterator = reader.iterator();
diff --git a/src/java/net/sf/samtools/AbstractSAMHeaderRecord.java b/src/java/net/sf/samtools/AbstractSAMHeaderRecord.java
index 7bd0a4b..4268341 100644
--- a/src/java/net/sf/samtools/AbstractSAMHeaderRecord.java
+++ b/src/java/net/sf/samtools/AbstractSAMHeaderRecord.java
@@ -101,4 +101,9 @@ public abstract class AbstractSAMHeaderRecord {
* @return list of predefined tags for the concrete SAMHeader record type.
*/
abstract Set<String> getStandardTags();
+
+ /** Simple to String that outputs the concrete class name and the set of attributes stored. */
+ @Override public String toString() {
+ return getClass().getSimpleName() + this.mAttributes.toString();
+ }
}
diff --git a/src/java/net/sf/samtools/BAMFileReader.java b/src/java/net/sf/samtools/BAMFileReader.java
index e0bf6d7..fe14aaa 100644
--- a/src/java/net/sf/samtools/BAMFileReader.java
+++ b/src/java/net/sf/samtools/BAMFileReader.java
@@ -38,7 +38,7 @@ import java.util.List;
import java.util.NoSuchElementException;
/**
- * Internal class for reading and querying BAM files.
+ * Class for reading and querying BAM files.
*/
class BAMFileReader extends SAMFileReader.ReaderImplementation {
// True if reading from a File rather than an InputStream
@@ -103,7 +103,7 @@ class BAMFileReader extends SAMFileReader.ReaderImplementation {
this.eagerDecode = eagerDecode;
this.mValidationStringency = validationStringency;
this.samRecordFactory = factory;
- readHeader(null);
+ this.mFileHeader = readHeader(this.mStream, this.mValidationStringency, null);
}
/**
@@ -159,7 +159,7 @@ class BAMFileReader extends SAMFileReader.ReaderImplementation {
this.eagerDecode = eagerDecode;
this.mValidationStringency = validationStringency;
this.samRecordFactory = factory;
- readHeader(source);
+ this.mFileHeader = readHeader(this.mStream, this.mValidationStringency, source);
mFirstRecordPointer = mCompressedInputStream.getFilePointer();
}
@@ -177,10 +177,18 @@ class BAMFileReader extends SAMFileReader.ReaderImplementation {
this.eagerDecode = eagerDecode;
this.mValidationStringency = validationStringency;
this.samRecordFactory = factory;
- readHeader(source);
+ this.mFileHeader = readHeader(this.mStream, this.mValidationStringency, source);
mFirstRecordPointer = mCompressedInputStream.getFilePointer();
}
+ /** Reads through the header and sequence records to find the virtual file offset of the first record in the BAM file. */
+ static long findVirtualOffsetOfFirstRecord(final File bam) throws IOException {
+ final BAMFileReader reader = new BAMFileReader(bam, null, false, ValidationStringency.SILENT, new DefaultSAMRecordFactory());
+ final long offset = reader.mFirstRecordPointer;
+ reader.close();
+ return offset;
+ }
+
/**
* If true, writes the source of every read into the source SAMRecords.
* @param enabled true to write source information into each SAMRecord.
@@ -193,7 +201,7 @@ class BAMFileReader extends SAMFileReader.ReaderImplementation {
* If true, uses the caching version of the index reader.
* @param enabled true to write source information into each SAMRecord.
*/
- public void enableIndexCaching(final boolean enabled) {
+ protected void enableIndexCaching(final boolean enabled) {
if(mIndex != null)
throw new SAMException("Unable to turn on index caching; index file has already been loaded.");
this.mEnableIndexCaching = enabled;
@@ -204,7 +212,7 @@ class BAMFileReader extends SAMFileReader.ReaderImplementation {
* This is slower but more scalable when accessing large numbers of BAM files sequentially.
* @param enabled True to use memory mapping, false to use regular I/O.
*/
- public void enableIndexMemoryMapping(final boolean enabled) {
+ protected void enableIndexMemoryMapping(final boolean enabled) {
if (mIndex != null) {
throw new SAMException("Unable to change index memory mapping; index file has already been loaded.");
}
@@ -220,7 +228,7 @@ class BAMFileReader extends SAMFileReader.ReaderImplementation {
/**
* @return true if ths is a BAM file, and has an index
*/
- public boolean hasIndex() {
+ protected boolean hasIndex() {
return (mIndexFile != null) || (mIndexStream != null);
}
@@ -228,7 +236,7 @@ class BAMFileReader extends SAMFileReader.ReaderImplementation {
* Retrieves the index for the given file type. Ensure that the index is of the specified type.
* @return An index of the given type.
*/
- public BAMIndex getIndex() {
+ protected BAMIndex getIndex() {
if(!hasIndex())
throw new SAMException("No index is available for this BAM file.");
if(mIndex == null) {
@@ -463,36 +471,38 @@ class BAMFileReader extends SAMFileReader.ReaderImplementation {
}
/**
- * Reads the header from the file or stream
+ * Reads the header of a BAM file from a stream
+ * @param stream A BinaryCodec to read the header from
+ * @param validationStringency Determines how stringent to be when validating the sam
* @param source Note that this is used only for reporting errors.
*/
- private void readHeader(final String source)
+ protected static SAMFileHeader readHeader(final BinaryCodec stream, final ValidationStringency validationStringency, final String source)
throws IOException {
final byte[] buffer = new byte[4];
- mStream.readBytes(buffer);
+ stream.readBytes(buffer);
if (!Arrays.equals(buffer, BAMFileConstants.BAM_MAGIC)) {
throw new IOException("Invalid BAM file header");
}
- final int headerTextLength = mStream.readInt();
- final String textHeader = mStream.readString(headerTextLength);
+ final int headerTextLength = stream.readInt();
+ final String textHeader = stream.readString(headerTextLength);
final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec();
- headerCodec.setValidationStringency(mValidationStringency);
- mFileHeader = headerCodec.decode(new StringLineReader(textHeader),
+ headerCodec.setValidationStringency(validationStringency);
+ final SAMFileHeader samFileHeader = headerCodec.decode(new StringLineReader(textHeader),
source);
- final int sequenceCount = mStream.readInt();
- if (mFileHeader.getSequenceDictionary().size() > 0) {
+ final int sequenceCount = stream.readInt();
+ if (samFileHeader.getSequenceDictionary().size() > 0) {
// It is allowed to have binary sequences but no text sequences, so only validate if both are present
- if (sequenceCount != mFileHeader.getSequenceDictionary().size()) {
+ if (sequenceCount != samFileHeader.getSequenceDictionary().size()) {
throw new SAMFormatException("Number of sequences in text header (" +
- mFileHeader.getSequenceDictionary().size() +
+ samFileHeader.getSequenceDictionary().size() +
") != number of sequences in binary header (" + sequenceCount + ") for file " + source);
}
for (int i = 0; i < sequenceCount; i++) {
- final SAMSequenceRecord binarySequenceRecord = readSequenceRecord(source);
- final SAMSequenceRecord sequenceRecord = mFileHeader.getSequence(i);
+ final SAMSequenceRecord binarySequenceRecord = readSequenceRecord(stream, source);
+ final SAMSequenceRecord sequenceRecord = samFileHeader.getSequence(i);
if (!sequenceRecord.getSequenceName().equals(binarySequenceRecord.getSequenceName())) {
throw new SAMFormatException("For sequence " + i + ", text and binary have different names in file " +
source);
@@ -503,28 +513,30 @@ class BAMFileReader extends SAMFileReader.ReaderImplementation {
}
}
} else {
- // If only binary sequences are present, copy them into mFileHeader
+ // If only binary sequences are present, copy them into samFileHeader
final List<SAMSequenceRecord> sequences = new ArrayList<SAMSequenceRecord>(sequenceCount);
for (int i = 0; i < sequenceCount; i++) {
- sequences.add(readSequenceRecord(source));
+ sequences.add(readSequenceRecord(stream, source));
}
- mFileHeader.setSequenceDictionary(new SAMSequenceDictionary(sequences));
+ samFileHeader.setSequenceDictionary(new SAMSequenceDictionary(sequences));
}
+
+ return samFileHeader;
}
/**
* Reads a single binary sequence record from the file or stream
* @param source Note that this is used only for reporting errors.
*/
- private SAMSequenceRecord readSequenceRecord(final String source) {
- final int nameLength = mStream.readInt();
+ private static SAMSequenceRecord readSequenceRecord(final BinaryCodec stream, final String source) {
+ final int nameLength = stream.readInt();
if (nameLength <= 1) {
throw new SAMFormatException("Invalid BAM file header: missing sequence name in file " + source);
}
- final String sequenceName = mStream.readString(nameLength - 1);
+ final String sequenceName = stream.readString(nameLength - 1);
// Skip the null terminator
- mStream.readByte();
- final int sequenceLength = mStream.readInt();
+ stream.readByte();
+ final int sequenceLength = stream.readInt();
return new SAMSequenceRecord(SAMSequenceRecord.truncateSequenceName(sequenceName), sequenceLength);
}
@@ -733,11 +745,10 @@ class BAMFileReader extends SAMFileReader.ReaderImplementation {
*/
private static File findIndexFile(final File dataFile) {
// If input is foo.bam, look for foo.bai
- final String bamExtension = ".bam";
File indexFile;
final String fileName = dataFile.getName();
- if (fileName.endsWith(bamExtension)) {
- final String bai = fileName.substring(0, fileName.length() - bamExtension.length()) + BAMIndex.BAMIndexSuffix;
+ if (fileName.endsWith(BamFileIoUtils.BAM_FILE_EXTENSION)) {
+ final String bai = fileName.substring(0, fileName.length() - BamFileIoUtils.BAM_FILE_EXTENSION.length()) + BAMIndex.BAMIndexSuffix;
indexFile = new File(dataFile.getParent(), bai);
if (indexFile.exists()) {
return indexFile;
@@ -745,7 +756,7 @@ class BAMFileReader extends SAMFileReader.ReaderImplementation {
}
// If foo.bai doesn't exist look for foo.bam.bai
- indexFile = new File(dataFile.getParent(), dataFile.getName() + ".bai");
+ indexFile = new File(dataFile.getParent(), dataFile.getName() + BAMIndex.BAMIndexSuffix);
if (indexFile.exists()) {
return indexFile;
} else {
diff --git a/src/java/net/sf/samtools/BAMFileWriter.java b/src/java/net/sf/samtools/BAMFileWriter.java
index 66a4c74..04dda87 100644
--- a/src/java/net/sf/samtools/BAMFileWriter.java
+++ b/src/java/net/sf/samtools/BAMFileWriter.java
@@ -24,41 +24,51 @@
package net.sf.samtools;
import net.sf.samtools.util.BinaryCodec;
+import net.sf.samtools.util.BlockCompressedFilePointerUtil;
+import net.sf.samtools.util.BlockCompressedInputStream;
import net.sf.samtools.util.BlockCompressedOutputStream;
+import net.sf.samtools.util.BlockCompressedStreamConstants;
+import net.sf.samtools.util.CloserUtil;
+import net.sf.samtools.util.IOUtil;
+import net.sf.samtools.util.RuntimeIOException;
import java.io.DataOutputStream;
import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
import java.io.OutputStream;
+import java.io.StringWriter;
+import java.io.Writer;
/**
* Concrete implementation of SAMFileWriter for writing gzipped BAM files.
*/
-public class BAMFileWriter extends SAMFileWriterImpl {
+class BAMFileWriter extends SAMFileWriterImpl {
private final BinaryCodec outputBinaryCodec;
private BAMRecordCodec bamRecordCodec = null;
private final BlockCompressedOutputStream blockCompressedOutputStream;
private BAMIndexer bamIndexer = null;
- public BAMFileWriter(final File path) {
+ protected BAMFileWriter(final File path) {
blockCompressedOutputStream = new BlockCompressedOutputStream(path);
outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
outputBinaryCodec.setOutputFileName(path.getAbsolutePath());
}
- public BAMFileWriter(final File path, final int compressionLevel) {
+ protected BAMFileWriter(final File path, final int compressionLevel) {
blockCompressedOutputStream = new BlockCompressedOutputStream(path, compressionLevel);
outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
outputBinaryCodec.setOutputFileName(path.getAbsolutePath());
}
- public BAMFileWriter(final OutputStream os, final File file) {
+ protected BAMFileWriter(final OutputStream os, final File file) {
blockCompressedOutputStream = new BlockCompressedOutputStream(os, file);
outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
outputBinaryCodec.setOutputFileName(getPathString(file));
}
- public BAMFileWriter(final OutputStream os, final File file, final int compressionLevel) {
+ protected BAMFileWriter(final OutputStream os, final File file, final int compressionLevel) {
blockCompressedOutputStream = new BlockCompressedOutputStream(os, file, compressionLevel);
outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
outputBinaryCodec.setOutputFileName(getPathString(file));
@@ -72,7 +82,7 @@ public class BAMFileWriter extends SAMFileWriterImpl {
}
/** @return absolute path, or null if arg is null. */
- private String getPathString(File path){
+ private String getPathString(final File path){
return (path != null) ? path.getAbsolutePath() : null;
}
@@ -88,9 +98,9 @@ public class BAMFileWriter extends SAMFileWriterImpl {
bamIndexer = createBamIndex(getFilename());
}
- private BAMIndexer createBamIndex(String path) {
+ private BAMIndexer createBamIndex(final String path) {
try {
- final String indexFileBase = path.endsWith(".bam") ?
+ final String indexFileBase = path.endsWith(BamFileIoUtils.BAM_FILE_EXTENSION) ?
path.substring(0, path.lastIndexOf(".")) : path;
final File indexFile = new File(indexFileBase + BAMIndex.BAMIndexSuffix);
if (indexFile.exists()) {
@@ -125,17 +135,7 @@ public class BAMFileWriter extends SAMFileWriterImpl {
}
protected void writeHeader(final String textHeader) {
- outputBinaryCodec.writeBytes(BAMFileConstants.BAM_MAGIC);
-
- // calculate and write the length of the SAM file header text and the header text
- outputBinaryCodec.writeString(textHeader, true, false);
-
- // write the sequences binarily. This is redundant with the text header
- outputBinaryCodec.writeInt(getFileHeader().getSequenceDictionary().size());
- for (final SAMSequenceRecord sequenceRecord: getFileHeader().getSequenceDictionary().getSequences()) {
- outputBinaryCodec.writeString(sequenceRecord.getSequenceName(), true, true);
- outputBinaryCodec.writeInt(sequenceRecord.getSequenceLength());
- }
+ writeHeader(outputBinaryCodec, getFileHeader(), textHeader);
}
protected void finish() {
@@ -153,4 +153,47 @@ public class BAMFileWriter extends SAMFileWriterImpl {
protected String getFilename() {
return outputBinaryCodec.getOutputFileName();
}
+
+ /**
+ * Writes a header to a BAM file. samFileHeader and headerText are redundant - one can be used to regenerate the other but in
+ * some instances we already have both so this allows us to save some cycles
+ */
+ protected static void writeHeader(final BinaryCodec outputBinaryCodec, final SAMFileHeader samFileHeader, final String headerText) {
+ outputBinaryCodec.writeBytes(BAMFileConstants.BAM_MAGIC);
+
+ // calculate and write the length of the SAM file header text and the header text
+ outputBinaryCodec.writeString(headerText, true, false);
+
+ // write the sequences binarily. This is redundant with the text header
+ outputBinaryCodec.writeInt(samFileHeader.getSequenceDictionary().size());
+ for (final SAMSequenceRecord sequenceRecord: samFileHeader.getSequenceDictionary().getSequences()) {
+ outputBinaryCodec.writeString(sequenceRecord.getSequenceName(), true, true);
+ outputBinaryCodec.writeInt(sequenceRecord.getSequenceLength());
+ }
+ }
+
+ /**
+ * Writes a header to a BAM file. Might need to regenerate the String version of the header, if one already has both the
+ * samFileHeader and the String, use the version of this method which takes both.
+ */
+ protected static void writeHeader(final BinaryCodec outputBinaryCodec, final SAMFileHeader samFileHeader) {
+ // Do not use SAMFileHeader.getTextHeader() as it is not updated when changes to the underlying object are made
+ final String headerString;
+ final Writer stringWriter = new StringWriter();
+ new SAMTextHeaderCodec().encode(stringWriter, samFileHeader, true);
+ headerString = stringWriter.toString();
+
+ writeHeader(outputBinaryCodec, samFileHeader, headerString);
+ }
+
+ protected static void writeHeader(final OutputStream outputStream, final SAMFileHeader samFileHeader) {
+ final BlockCompressedOutputStream blockCompressedOutputStream = new BlockCompressedOutputStream(outputStream, null);
+ final BinaryCodec outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
+ writeHeader(outputBinaryCodec, samFileHeader);
+ try {
+ blockCompressedOutputStream.flush();
+ } catch (final IOException ioe) {
+ throw new RuntimeIOException(ioe);
+ }
+ }
}
diff --git a/src/java/net/sf/samtools/BamFileIoUtils.java b/src/java/net/sf/samtools/BamFileIoUtils.java
new file mode 100644
index 0000000..e4d7406
--- /dev/null
+++ b/src/java/net/sf/samtools/BamFileIoUtils.java
@@ -0,0 +1,155 @@
+package net.sf.samtools;
+
+import net.sf.samtools.util.BlockCompressedFilePointerUtil;
+import net.sf.samtools.util.BlockCompressedInputStream;
+import net.sf.samtools.util.BlockCompressedOutputStream;
+import net.sf.samtools.util.BlockCompressedStreamConstants;
+import net.sf.samtools.util.CloserUtil;
+import net.sf.samtools.util.IOUtil;
+import net.sf.samtools.util.Md5CalculatingOutputStream;
+import net.sf.samtools.util.RuntimeIOException;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.List;
+
+public class BamFileIoUtils {
+ public static final String BAM_FILE_EXTENSION = ".bam";
+
+ public static boolean isBamFile(final File file) {
+ return ((file != null) && file.getName().endsWith(BAM_FILE_EXTENSION));
+ }
+
+ public static void reheaderBamFile(final SAMFileHeader samFileHeader, final File inputFile, final File outputFile) {
+ reheaderBamFile(samFileHeader, inputFile, outputFile, true, true);
+ }
+
+ /**
+ * Copy a BAM file but replacing the header
+ * @param samFileHeader The header to use in the new file
+ * @param inputFile The BAM file to copy, sans header
+ * @param outputFile The new BAM file, constructed with the new header and the content from inputFile
+ * @param createMd5 Whether or not to create an MD5 file for the new BAM
+ * @param createIndex Whether or not to create an index file for the new BAM
+ */
+ public static void reheaderBamFile(final SAMFileHeader samFileHeader, final File inputFile, final File outputFile, final boolean createMd5, final boolean createIndex) {
+ // TODO: In a future world where IoUtil and IOUtil are merged, de-comment these
+// IoUtil.assertFileIsReadable(inputFile);
+// IoUtil.assertFileIsWritable(outputFile);
+
+ try {
+ BlockCompressedInputStream.assertNonDefectiveFile(inputFile);
+ assertSortOrdersAreEqual(samFileHeader, inputFile);
+
+ final OutputStream outputStream = buildOutputStream(outputFile, createMd5, createIndex);
+
+ BAMFileWriter.writeHeader(outputStream, samFileHeader);
+ blockCopyBamFile(inputFile, outputStream, true, false);
+
+ CloserUtil.close(inputFile);
+ outputStream.close();
+ } catch (final IOException ioe) {
+ throw new RuntimeIOException(ioe);
+ }
+ }
+
+ /**
+ * Copy data from a BAM file to an OutputStream by directly copying the gzip blocks
+ *
+ * @param inputFile The file to be copied
+ * @param outputStream The stream to write the copied data to
+ * @param skipHeader If true, the header of the input file will not be copied to the output stream
+ * @param skipTerminator If true, the terminator block of the input file will not be written to the output stream
+ */
+ public static void blockCopyBamFile(final File inputFile, final OutputStream outputStream, final boolean skipHeader, final boolean skipTerminator) {
+ FileInputStream in = null;
+ try {
+ in = new FileInputStream(inputFile);
+
+ // a) It's good to check that the end of the file is valid and b) we need to know if there's a terminator block and not copy it if skipTerminator is true
+ final BlockCompressedInputStream.FileTermination term = BlockCompressedInputStream.checkTermination(inputFile);
+ if (term == BlockCompressedInputStream.FileTermination.DEFECTIVE)
+ throw new SAMException(inputFile.getAbsolutePath() + " does not have a valid GZIP block at the end of the file.");
+
+ if (skipHeader) {
+ final long vOffsetOfFirstRecord = SAMUtils.findVirtualOffsetOfFirstRecordInBam(inputFile);
+ final BlockCompressedInputStream blockIn = new BlockCompressedInputStream(inputFile);
+ blockIn.seek(vOffsetOfFirstRecord);
+ final long remainingInBlock = blockIn.available();
+
+ // If we found the end of the header then write the remainder of this block out as a
+ // new gzip block and then break out of the while loop
+ if (remainingInBlock >= 0) {
+ final BlockCompressedOutputStream blockOut = new BlockCompressedOutputStream(outputStream, null);
+ IOUtil.transferByStream(blockIn, blockOut, remainingInBlock);
+ blockOut.flush();
+ // Don't close blockOut because closing underlying stream would break everything
+ }
+
+ long pos = BlockCompressedFilePointerUtil.getBlockAddress(blockIn.getFilePointer());
+ blockIn.close();
+ while (pos > 0) {
+ pos -= in.skip(pos);
+ }
+ }
+
+ // Copy remainder of input stream into output stream
+ final long currentPos = in.getChannel().position();
+ final long length = inputFile.length();
+ final long skipLast = ((term == BlockCompressedInputStream.FileTermination.HAS_TERMINATOR_BLOCK) && skipTerminator) ?
+ BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK.length : 0;
+ final long bytesToWrite = length - skipLast - currentPos;
+
+ IOUtil.transferByStream(in, outputStream, bytesToWrite);
+ } catch (final IOException ioe) {
+ throw new RuntimeIOException(ioe);
+ } finally {
+ CloserUtil.close(in);
+ }
+ }
+
+ /**
+ * Assumes that all inputs and outputs are block compressed VCF files and copies them without decompressing and parsing
+ * most of the gzip blocks. Will decompress and parse blocks up to the one containing the end of the header in each file
+ * (often the first block) and re-compress any data remaining in that block into a new block in the output file. Subsequent
+ * blocks (excluding a terminator block if present) are copied directly from input to output.
+ */
+ public static void gatherWithBlockCopying(final List<File> bams, final File output, final boolean createIndex, final boolean createMd5) {
+ try {
+ OutputStream out = new FileOutputStream(output);
+ if (createMd5) out = new Md5CalculatingOutputStream(out, new File(output.getAbsolutePath() + ".md5"));
+ if (createIndex) out = new StreamInflatingIndexingOutputStream(out, new File(output.getParentFile(), IOUtil.basename(output) + BAMIndex.BAMIndexSuffix));
+ boolean isFirstFile = true;
+
+ for (final File f : bams) {
+ blockCopyBamFile(f, out, !isFirstFile, true);
+ isFirstFile = false;
+ }
+
+ // And lastly add the Terminator block and close up
+ out.write(BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK);
+ out.close();
+ }
+ catch (final IOException ioe) {
+ throw new RuntimeIOException(ioe);
+ }
+ }
+
+ private static OutputStream buildOutputStream(final File outputFile, final boolean createMd5, final boolean createIndex) throws IOException {
+ OutputStream outputStream = new FileOutputStream(outputFile);
+ if (createMd5) outputStream = new Md5CalculatingOutputStream(outputStream, new File(outputFile.getAbsolutePath() + ".md5"));
+ if (createIndex) outputStream = new StreamInflatingIndexingOutputStream(outputStream, new File(outputFile.getParentFile(), IOUtil.basename(outputFile) + BAMIndex.BAMIndexSuffix));
+ return outputStream;
+ }
+
+ private static void assertSortOrdersAreEqual(final SAMFileHeader newHeader, final File inputFile) throws IOException {
+ final SAMFileHeader origHeader = new SAMFileReader(inputFile).getFileHeader();
+ final SAMFileHeader.SortOrder newSortOrder = newHeader.getSortOrder();
+ if (newSortOrder != SAMFileHeader.SortOrder.unsorted && newSortOrder != origHeader.getSortOrder()) {
+ throw new SAMException("Sort order of new header does not match the original file, needs to be " + origHeader.getSortOrder());
+ }
+ }
+}
diff --git a/src/java/net/sf/samtools/Defaults.java b/src/java/net/sf/samtools/Defaults.java
index ed0b7eb..d4e5368 100644
--- a/src/java/net/sf/samtools/Defaults.java
+++ b/src/java/net/sf/samtools/Defaults.java
@@ -1,5 +1,7 @@
package net.sf.samtools;
+import java.io.File;
+
/**
* Embodies defaults for global values that affect how the SAM JDK operates. Defaults are encoded in the class
* and are also overridable using system properties.
@@ -35,6 +37,11 @@ public class Defaults {
* where the executable jar lives. */
public static final String INTEL_DEFLATER_SHARED_LIBRARY_PATH;
+ /** The reference FASTA file. If this is not set, the file is null. This file may be required for reading
+ * writing SAM files (ex. CRAM).
+ */
+ public static final File REFERENCE_FASTA;
+
static {
CREATE_INDEX = getBooleanProperty("create_index", false);
CREATE_MD5 = getBooleanProperty("create_md5", false);
@@ -48,6 +55,7 @@ public class Defaults {
} else {
NON_ZERO_BUFFER_SIZE = BUFFER_SIZE;
}
+ REFERENCE_FASTA = getFileProperty("reference_fasta", null);
}
/** Gets a string system property, prefixed with "samjdk." using the default if the property does not exist.*/
@@ -66,4 +74,11 @@ public class Defaults {
final String value = getStringProperty(name, new Integer(def).toString());
return Integer.parseInt(value);
}
+
+ /** Gets a File system property, prefixed with "samdjk." using the default if the property does not exist.*/
+ private static File getFileProperty(final String name, final String def) {
+ final String value = getStringProperty(name, def);
+ // TODO: assert that it is readable
+ return (null == value) ? null : new File(value);
+ }
}
diff --git a/src/java/net/sf/samtools/SAMFileWriterFactory.java b/src/java/net/sf/samtools/SAMFileWriterFactory.java
index 94fb183..e38cce1 100644
--- a/src/java/net/sf/samtools/SAMFileWriterFactory.java
+++ b/src/java/net/sf/samtools/SAMFileWriterFactory.java
@@ -247,7 +247,7 @@ public class SAMFileWriterFactory {
*/
public SAMFileWriter makeSAMOrBAMWriter(final SAMFileHeader header, final boolean presorted, final File outputFile) {
final String filename = outputFile.getName();
- if (filename.endsWith(".bam")) {
+ if (filename.endsWith(BamFileIoUtils.BAM_FILE_EXTENSION)) {
return makeBAMWriter(header, presorted, outputFile);
}
if (filename.endsWith(".sam")) {
diff --git a/src/java/net/sf/samtools/SAMRecord.java b/src/java/net/sf/samtools/SAMRecord.java
index 4f7da39..ded7ebe 100644
--- a/src/java/net/sf/samtools/SAMRecord.java
+++ b/src/java/net/sf/samtools/SAMRecord.java
@@ -367,7 +367,7 @@ public class SAMRecord implements Cloneable
} else {
try {
mReferenceName = mHeader.getSequence(referenceIndex).getSequenceName();
- } catch (NullPointerException e) {
+ } catch (final NullPointerException e) {
throw new IllegalArgumentException("Reference index " + referenceIndex + " not found in sequence dictionary.", e);
}
}
@@ -426,7 +426,7 @@ public class SAMRecord implements Cloneable
} else {
try {
mMateReferenceName = mHeader.getSequence(referenceIndex).getSequenceName();
- } catch (NullPointerException e) {
+ } catch (final NullPointerException e) {
throw new IllegalArgumentException("Reference index " + referenceIndex + " not found in sequence dictionary.", e);
}
}
@@ -472,32 +472,7 @@ public class SAMRecord implements Cloneable
* Invalid to call on an unmapped read.
*/
public int getUnclippedStart() {
- return getUnclippedStart(getAlignmentStart(), getCigar());
- }
-
- /**
- * @param alignmentStart The start (1-based) of the alignment
- * @param cigar The cigar containing the alignment information
- * @return the alignment start (1-based, inclusive) adjusted for clipped bases. For example if the read
- * has an alignment start of 100 but the first 4 bases were clipped (hard or soft clipped)
- * then this method will return 96.
- *
- * Invalid to call on an unmapped read.
- * Invalid to call with cigar = null
- */
- private int getUnclippedStart(final int alignmentStart, final Cigar cigar) {
- int unClippedStart = alignmentStart;
- for (final CigarElement cig : cigar.getCigarElements()) {
- final CigarOperator op = cig.getOperator();
- if (op == CigarOperator.SOFT_CLIP || op == CigarOperator.HARD_CLIP) {
- unClippedStart -= cig.getLength();
- }
- else {
- break;
- }
- }
-
- return unClippedStart;
+ return SAMUtils.getUnclippedStart(getAlignmentStart(), getCigar());
}
/**
@@ -508,36 +483,9 @@ public class SAMRecord implements Cloneable
* Invalid to call on an unmapped read.
*/
public int getUnclippedEnd() {
- return getUnclippedEnd(getAlignmentEnd(), getCigar());
+ return SAMUtils.getUnclippedEnd(getAlignmentEnd(), getCigar());
}
- /**
- * @param alignmentEnd The end (1-based) of the alignment
- * @param cigar The cigar containing the alignment information
- * @return the alignment end (1-based, inclusive) adjusted for clipped bases. For example if the read
- * has an alignment end of 100 but the last 7 bases were clipped (hard or soft clipped)
- * then this method will return 107.
- *
- * Invalid to call on an unmapped read.
- * Invalid to call with cigar = null
- */
- private int getUnclippedEnd(final int alignmentEnd, final Cigar cigar) {
- int unClippedEnd = alignmentEnd;
- final List<CigarElement> cigs = cigar.getCigarElements();
- for (int i=cigs.size() - 1; i>=0; --i) {
- final CigarElement cig = cigs.get(i);
- final CigarOperator op = cig.getOperator();
-
- if (op == CigarOperator.SOFT_CLIP || op == CigarOperator.HARD_CLIP) {
- unClippedEnd += cig.getLength();
- }
- else {
- break;
- }
- }
-
- return unClippedEnd;
- }
/**
* @return 1-based inclusive reference position of the unclipped sequence at a given offset,
@@ -585,58 +533,6 @@ public class SAMRecord implements Cloneable
}
/**
- * This method uses the MateCigar value as determined from the attribute MC. It must be non-null.
- * @return 1-based inclusive rightmost position of the clipped mate sequence, or 0 read if unmapped.
- */
- public int getMateAlignmentEnd() {
- if (getMateUnmappedFlag()) {
- throw new RuntimeException("getMateAlignmentEnd called on an unmapped mate.");
- }
- final Cigar mateCigar = getMateCigar();
- if (mateCigar == null) {
- throw new SAMException("Mate CIGAR (Tag MC) not found.");
- }
- return CoordMath.getEnd(getMateAlignmentStart(), mateCigar.getReferenceLength());
- }
-
- /**
- * @return the mate alignment start (1-based, inclusive) adjusted for clipped bases. For example if the mate
- * has an alignment start of 100 but the first 4 bases were clipped (hard or soft clipped)
- * then this method will return 96.
- *
- * Invalid to call on an unmapped read.
- */
- public int getMateUnclippedStart() {
- if (getMateUnmappedFlag())
- throw new RuntimeException("getMateUnclippedStart called on an unmapped mate.");
- final Cigar mateCigar = getMateCigar();
- if (mateCigar == null) {
- throw new SAMException("Mate CIGAR (Tag MC) not found.");
- }
- return getUnclippedStart(getMateAlignmentStart(), mateCigar);
- }
-
-
- /**
- * @return the mate alignment end (1-based, inclusive) adjusted for clipped bases. For example if the mate
- * has an alignment end of 100 but the last 7 bases were clipped (hard or soft clipped)
- * then this method will return 107.
- *
- * Invalid to call on an unmapped read.
- */
- public int getMateUnclippedEnd() {
- if (getMateUnmappedFlag()) {
- throw new RuntimeException("getMateUnclippedEnd called on an unmapped mate.");
- }
- final Cigar mateCigar = getMateCigar();
- if (mateCigar == null) {
- throw new SAMException("Mate CIGAR (Tag MC) not found.");
- }
- return getUnclippedEnd(getMateAlignmentEnd(), mateCigar);
- }
-
-
- /**
* @return insert size (difference btw 5' end of read & 5' end of mate), if possible, else 0.
* Negative if mate maps to lower position than read.
*/
@@ -686,7 +582,7 @@ public class SAMRecord implements Cloneable
mCigar = TextCigarCodec.getSingleton().decode(mCigarString);
if (getValidationStringency() != SAMFileReader.ValidationStringency.SILENT && !this.getReadUnmappedFlag()) {
// Don't know line number, and don't want to force read name to be decoded.
- SAMUtils.processValidationErrors(validateCigar(-1L), -1L, getValidationStringency());
+ SAMUtils.processValidationErrors(this.validateCigar(-1L), -1L, getValidationStringency());
}
}
return mCigar;
@@ -719,39 +615,6 @@ public class SAMRecord implements Cloneable
}
/**
- * Returns the Mate Cigar String as stored in the attribute 'MC'.
- * @return Mate Cigar String, or null if there is none.
- */
- public String getMateCigarString() {
- return getStringAttribute(SAMTag.MC.name());
- }
-
- /**
- * Returns the Mate Cigar or null if there is none.
- * @return Cigar object for the read's mate, or null if there is none.
- */
- public Cigar getMateCigar() {
- final String mateCigarString = getMateCigarString();
- Cigar mateCigar = null;
- if (mateCigarString != null) {
- mateCigar = TextCigarCodec.getSingleton().decode(mateCigarString);
- if (getValidationStringency() != SAMFileReader.ValidationStringency.SILENT) {
- final List<AlignmentBlock> alignmentBlocks = getAlignmentBlocks(mateCigar, getMateAlignmentStart(), "mate cigar");
- SAMUtils.processValidationErrors(validateCigar(mateCigar, getMateReferenceIndex(), alignmentBlocks, -1, "Mate CIGAR"), -1L, getValidationStringency());
- }
- }
- return mateCigar;
- }
-
- /**
- * @return number of cigar elements (number + operator) in the mate cigar string.
- */
- public int getMateCigarLength() {
- final Cigar mateCigar = getMateCigar();
- return (mateCigar != null) ? mateCigar.numCigarElements() : 0;
- }
-
- /**
* Get the SAMReadGroupRecord for this SAMRecord.
* @return The SAMReadGroupRecord from the SAMFileHeader for this SAMRecord, or null if
* 1) this record has no RG tag, or 2) the header doesn't contain the read group with
@@ -1501,61 +1364,12 @@ public class SAMRecord implements Cloneable
*/
public List<AlignmentBlock> getAlignmentBlocks() {
if (this.mAlignmentBlocks == null) {
- this.mAlignmentBlocks = getAlignmentBlocks(getCigar(), getAlignmentStart(), "read cigar");
+ this.mAlignmentBlocks = SAMUtils.getAlignmentBlocks(getCigar(), getAlignmentStart(), "read cigar");
}
return this.mAlignmentBlocks;
}
/**
- * Returns blocks of the mate sequence that have been aligned directly to the
- * reference sequence. Note that clipped portions of the mate and inserted and
- * deleted bases (vs. the reference) are not represented in the alignment blocks.
- */
- public List<AlignmentBlock> getMateAlignmentBlocks() {
- return getAlignmentBlocks(getMateCigar(), getMateAlignmentStart(), "mate cigar");
- }
-
- /**
- * Given a Cigar, Returns blocks of the sequence that have been aligned directly to the
- * reference sequence. Note that clipped portions, and inserted and deleted bases (vs. the reference)
- * are not represented in the alignment blocks.
- *
- * @param cigar The cigar containing the alignment information
- * @param alignmentStart The start (1-based) of the alignment
- * @param cigarTypeName The type of cigar passed - for error logging.
- * @return List of alignment blocks
- */
- private List<AlignmentBlock> getAlignmentBlocks(final Cigar cigar, final int alignmentStart, final String cigarTypeName) {
- if (cigar == null) return Collections.emptyList();
-
- final List<AlignmentBlock> alignmentBlocks = new ArrayList<AlignmentBlock>();
- int readBase = 1;
- int refBase = alignmentStart;
-
- for (final CigarElement e : cigar.getCigarElements()) {
- switch (e.getOperator()) {
- case H : break; // ignore hard clips
- case P : break; // ignore pads
- case S : readBase += e.getLength(); break; // soft clip read bases
- case N : refBase += e.getLength(); break; // reference skip
- case D : refBase += e.getLength(); break;
- case I : readBase += e.getLength(); break;
- case M :
- case EQ :
- case X :
- final int length = e.getLength();
- alignmentBlocks.add(new AlignmentBlock(readBase, refBase, length));
- readBase += length;
- refBase += length;
- break;
- default : throw new IllegalStateException("Case statement didn't deal with " + cigarTypeName + " op: " + e.getOperator());
- }
- }
- return Collections.unmodifiableList(alignmentBlocks);
- }
-
-
- /**
* Run all validations of CIGAR. These include validation that the CIGAR makes sense independent of
* placement, plus validation that CIGAR + placement yields all bases with M operator within the range of the reference.
* @param recordNumber For error reporting. -1 if not known.
@@ -1565,73 +1379,11 @@ public class SAMRecord implements Cloneable
List<SAMValidationError> ret = null;
if (getValidationStringency() != SAMFileReader.ValidationStringency.SILENT && !this.getReadUnmappedFlag()) {
- ret = validateCigar(getCigar(), getReferenceIndex(), getAlignmentBlocks(), recordNumber, "Read CIGAR");
- }
- return ret;
- }
-
- /**
- * Run all validations of the mate's CIGAR. These include validation that the CIGAR makes sense independent of
- * placement, plus validation that CIGAR + placement yields all bases with M operator within the range of the reference.
- * @param recordNumber For error reporting. -1 if not known.
- * @return List of errors, or null if no errors.
- */
- public List<SAMValidationError> validateMateCigar(final long recordNumber) {
- List<SAMValidationError> ret = null;
-
- if (getValidationStringency() != SAMFileReader.ValidationStringency.SILENT) {
- if (!this.getMateUnmappedFlag()) { // The mateCigar will be defined if the mate is mapped
- if (getMateCigarString() != null) {
- ret = validateCigar(getMateCigar(), getMateReferenceIndex(), getMateAlignmentBlocks(), recordNumber, "Mate CIGAR");
- }
- } else {
- if (getMateCigarString() != null) {
- // If the Mate is unmapped, and the Mate Cigar String (MC Attribute) exists, that is a validation error.
- ret = new ArrayList<SAMValidationError>();
- ret.add(new SAMValidationError(SAMValidationError.Type.MATE_CIGAR_STRING_INVALID_PRESENCE,
- "Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped", getReadName(), recordNumber));
- }
- }
+ ret = SAMUtils.validateCigar(this, getCigar(), getReferenceIndex(), getAlignmentBlocks(), recordNumber, "Read CIGAR");
}
-
return ret;
}
- /**
- * Run all validations of the mate's CIGAR. These include validation that the CIGAR makes sense independent of
- * placement, plus validation that CIGAR + placement yields all bases with M operator within the range of the reference.
- * @return List of errors, or null if no errors.
- * @param cigar The cigar containing the alignment information
- * @param referenceIndex The reference index
- * @param alignmentBlocks The alignment blocks (parsed from the cigar)
- * @param recordNumber For error reporting. -1 if not known.
- * @param cigarTypeName For error reporting. "Read CIGAR" or "Mate Cigar"
- * @return
- */
-
- private List<SAMValidationError> validateCigar(final Cigar cigar,
- final Integer referenceIndex,
- final List<AlignmentBlock> alignmentBlocks,
- final long recordNumber,
- final String cigarTypeName) {
- // Don't know line number, and don't want to force read name to be decoded.
- List<SAMValidationError> ret = cigar.isValid(getReadName(), recordNumber);
- if (referenceIndex != NO_ALIGNMENT_REFERENCE_INDEX) {
- final SAMSequenceRecord sequence = getHeader().getSequence(referenceIndex);
- final int referenceSequenceLength = sequence.getSequenceLength();
- for (final AlignmentBlock alignmentBlock : alignmentBlocks) {
- if (alignmentBlock.getReferenceStart() + alignmentBlock.getLength() - 1 > referenceSequenceLength) {
- if (ret == null) ret = new ArrayList<SAMValidationError>();
- ret.add(new SAMValidationError(SAMValidationError.Type.CIGAR_MAPS_OFF_REFERENCE,
- cigarTypeName + " M operator maps off end of reference", getReadName(), recordNumber));
- break;
- }
- }
- }
- return ret;
- }
-
-
@Override
public boolean equals(final Object o) {
if (this == o) return true;
@@ -1944,7 +1696,7 @@ public class SAMRecord implements Cloneable
/** Simple toString() that gives a little bit of useful info about the read. */
@Override
public String toString() {
- StringBuilder builder = new StringBuilder(64);
+ final StringBuilder builder = new StringBuilder(64);
builder.append(getReadName());
if (getReadPairedFlag()) {
if (getFirstOfPairFlag()) {
diff --git a/src/java/net/sf/samtools/SAMRecordSetBuilder.java b/src/java/net/sf/samtools/SAMRecordSetBuilder.java
index a93b999..7507239 100644
--- a/src/java/net/sf/samtools/SAMRecordSetBuilder.java
+++ b/src/java/net/sf/samtools/SAMRecordSetBuilder.java
@@ -29,7 +29,14 @@ import net.sf.samtools.util.RuntimeIOException;
import java.io.File;
import java.io.IOException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Random;
+import java.util.TreeSet;
/**
* Factory class for creating SAMRecords for testing purposes. Various methods can be called
* to add new SAM records (or pairs of records) to a list which can then be returned at
@@ -77,10 +84,15 @@ public class SAMRecordSetBuilder implements Iterable<SAMRecord> {
public SAMRecordSetBuilder(final boolean sortForMe, final SAMFileHeader.SortOrder sortOrder) {
this(sortForMe, sortOrder, true) ;
}
+
public SAMRecordSetBuilder(final boolean sortForMe, final SAMFileHeader.SortOrder sortOrder, final boolean addReadGroup) {
+ this(sortForMe, sortOrder, addReadGroup, DEFAULT_CHROMOSOME_LENGTH);
+ }
+
+ public SAMRecordSetBuilder(final boolean sortForMe, final SAMFileHeader.SortOrder sortOrder, final boolean addReadGroup, final int defaultChromosomeLength) {
final List<SAMSequenceRecord> sequences = new ArrayList<SAMSequenceRecord>();
for (final String chrom : chroms) {
- final SAMSequenceRecord sequenceRecord = new SAMSequenceRecord(chrom, DEFAULT_CHROMOSOME_LENGTH);
+ final SAMSequenceRecord sequenceRecord = new SAMSequenceRecord(chrom, defaultChromosomeLength);
sequences.add(sequenceRecord);
}
@@ -102,6 +114,7 @@ public class SAMRecordSetBuilder implements Iterable<SAMRecord> {
if (addReadGroup) {
final SAMReadGroupRecord readGroupRecord = new SAMReadGroupRecord(READ_GROUP_ID);
readGroupRecord.setSample(SAMPLE);
+ readGroupRecord.setPlatform("ILLUMINA");
final List<SAMReadGroupRecord> readGroups = new ArrayList<SAMReadGroupRecord>();
readGroups.add(readGroupRecord);
this.header.setReadGroups(readGroups);
@@ -337,7 +350,7 @@ public class SAMRecordSetBuilder implements Iterable<SAMRecord> {
end2.setSecondOfPairFlag(true);
// set mate info
- SamPairUtil.setMateInfo(end1, end2, header);
+ SamPairUtil.setMateInfo(end1, end2, header, true);
recordsList.add(end1);
recordsList.add(end2);
diff --git a/src/java/net/sf/samtools/SAMTag.java b/src/java/net/sf/samtools/SAMTag.java
index 8854f29..d5eeef5 100644
--- a/src/java/net/sf/samtools/SAMTag.java
+++ b/src/java/net/sf/samtools/SAMTag.java
@@ -28,5 +28,5 @@ package net.sf.samtools;
*/
public enum SAMTag {
RG, LB, PU, PG, AS, SQ, MQ, NM, H0, H1, H2, UQ, PQ, NH, IH, HI, MD, CS, CQ, CM, R2, Q2, S2, CC, CP, SM, AM, MF,
- E2, U2, OQ, FZ, SA, MC
+ E2, U2, OQ, FZ, SA, MC, BC
}
diff --git a/src/java/net/sf/samtools/SAMUtils.java b/src/java/net/sf/samtools/SAMUtils.java
index 2dfdd05..5517ea8 100644
--- a/src/java/net/sf/samtools/SAMUtils.java
+++ b/src/java/net/sf/samtools/SAMUtils.java
@@ -23,9 +23,12 @@
*/
package net.sf.samtools;
+import net.sf.samtools.util.CoordMath;
+import net.sf.samtools.util.RuntimeEOFException;
import net.sf.samtools.util.StringUtil;
import java.io.File;
+import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.math.BigInteger;
import java.security.MessageDigest;
@@ -627,4 +630,296 @@ public final class SAMUtils
return m1 + m2;
}
+
+ /**
+ * Returns the virtual file offset of the first record in a BAM file - i.e. the virtual file
+ * offset after skipping over the text header and the sequence records.
+ */
+ public static long findVirtualOffsetOfFirstRecordInBam(final File bamFile) {
+ try { return BAMFileReader.findVirtualOffsetOfFirstRecord(bamFile); }
+ catch (final IOException ioe) { throw new RuntimeEOFException(ioe); }
+ }
+
+ /**
+ * Given a Cigar, Returns blocks of the sequence that have been aligned directly to the
+ * reference sequence. Note that clipped portions, and inserted and deleted bases (vs. the reference)
+ * are not represented in the alignment blocks.
+ *
+ * @param cigar The cigar containing the alignment information
+ * @param alignmentStart The start (1-based) of the alignment
+ * @param cigarTypeName The type of cigar passed - for error logging.
+ * @return List of alignment blocks
+ */
+ public static List<AlignmentBlock> getAlignmentBlocks(final Cigar cigar, final int alignmentStart, final String cigarTypeName) {
+ if (cigar == null) return Collections.emptyList();
+
+ final List<AlignmentBlock> alignmentBlocks = new ArrayList<AlignmentBlock>();
+ int readBase = 1;
+ int refBase = alignmentStart;
+
+ for (final CigarElement e : cigar.getCigarElements()) {
+ switch (e.getOperator()) {
+ case H : break; // ignore hard clips
+ case P : break; // ignore pads
+ case S : readBase += e.getLength(); break; // soft clip read bases
+ case N : refBase += e.getLength(); break; // reference skip
+ case D : refBase += e.getLength(); break;
+ case I : readBase += e.getLength(); break;
+ case M :
+ case EQ :
+ case X :
+ final int length = e.getLength();
+ alignmentBlocks.add(new AlignmentBlock(readBase, refBase, length));
+ readBase += length;
+ refBase += length;
+ break;
+ default : throw new IllegalStateException("Case statement didn't deal with " + cigarTypeName + " op: " + e.getOperator());
+ }
+ }
+ return Collections.unmodifiableList(alignmentBlocks);
+ }
+
+ /**
+ * @param alignmentStart The start (1-based) of the alignment
+ * @param cigar The cigar containing the alignment information
+ * @return the alignment start (1-based, inclusive) adjusted for clipped bases. For example if the read
+ * has an alignment start of 100 but the first 4 bases were clipped (hard or soft clipped)
+ * then this method will return 96.
+ *
+ * Invalid to call on an unmapped read.
+ * Invalid to call with cigar = null
+ */
+ public static int getUnclippedStart(final int alignmentStart, final Cigar cigar) {
+ int unClippedStart = alignmentStart;
+ for (final CigarElement cig : cigar.getCigarElements()) {
+ final CigarOperator op = cig.getOperator();
+ if (op == CigarOperator.SOFT_CLIP || op == CigarOperator.HARD_CLIP) {
+ unClippedStart -= cig.getLength();
+ }
+ else {
+ break;
+ }
+ }
+
+ return unClippedStart;
+ }
+
+ /**
+ * @param alignmentEnd The end (1-based) of the alignment
+ * @param cigar The cigar containing the alignment information
+ * @return the alignment end (1-based, inclusive) adjusted for clipped bases. For example if the read
+ * has an alignment end of 100 but the last 7 bases were clipped (hard or soft clipped)
+ * then this method will return 107.
+ *
+ * Invalid to call on an unmapped read.
+ * Invalid to call with cigar = null
+ */
+ public static int getUnclippedEnd(final int alignmentEnd, final Cigar cigar) {
+ int unClippedEnd = alignmentEnd;
+ final List<CigarElement> cigs = cigar.getCigarElements();
+ for (int i=cigs.size() - 1; i>=0; --i) {
+ final CigarElement cig = cigs.get(i);
+ final CigarOperator op = cig.getOperator();
+
+ if (op == CigarOperator.SOFT_CLIP || op == CigarOperator.HARD_CLIP) {
+ unClippedEnd += cig.getLength();
+ }
+ else {
+ break;
+ }
+ }
+
+ return unClippedEnd;
+ }
+
+ /**
+ * Returns the Mate Cigar String as stored in the attribute 'MC'.
+ * @param rec the SAM record
+ * @return Mate Cigar String, or null if there is none.
+ */
+ public static String getMateCigarString(final SAMRecord rec) {
+ return rec.getStringAttribute(SAMTag.MC.name());
+ }
+
+ /**
+ * Returns the Mate Cigar or null if there is none.
+ * @param rec the SAM record
+ * @param withValidation true if we are to validate the mate cigar before returning, false otherwise.
+ * @return Cigar object for the read's mate, or null if there is none.
+ */
+ public static Cigar getMateCigar(final SAMRecord rec, final boolean withValidation) {
+ final String mateCigarString = getMateCigarString(rec);
+ Cigar mateCigar = null;
+ if (mateCigarString != null) {
+ mateCigar = TextCigarCodec.getSingleton().decode(mateCigarString);
+ if (withValidation && rec.getValidationStringency() != SAMFileReader.ValidationStringency.SILENT) {
+ final List<AlignmentBlock> alignmentBlocks = getAlignmentBlocks(mateCigar, rec.getMateAlignmentStart(), "mate cigar");
+ SAMUtils.processValidationErrors(validateCigar(rec, mateCigar, rec.getMateReferenceIndex(), alignmentBlocks, -1, "Mate CIGAR"), -1L, rec.getValidationStringency());
+ }
+ }
+ return mateCigar;
+ }
+
+ /**
+ * Returns the Mate Cigar or null if there is none. No validation is done on the returned cigar.
+ * @param rec the SAM record
+ * @return Cigar object for the read's mate, or null if there is none.
+ */
+ public static Cigar getMateCigar(final SAMRecord rec) {
+ return getMateCigar(rec, false);
+ }
+
+ /**
+ * @param rec the SAM record
+ * @return number of cigar elements (number + operator) in the mate cigar string.
+ */
+ public static int getMateCigarLength(final SAMRecord rec) {
+ final Cigar mateCigar = getMateCigar(rec);
+ return (mateCigar != null) ? mateCigar.numCigarElements() : 0;
+ }
+
+ /**
+ * This method uses the MateCigar value as determined from the attribute MC. It must be non-null.
+ * @param rec the SAM record
+ * @return 1-based inclusive rightmost position of the clipped mate sequence, or 0 read if unmapped.
+ */
+ public static int getMateAlignmentEnd(final SAMRecord rec) {
+ if (rec.getMateUnmappedFlag()) {
+ throw new RuntimeException("getMateAlignmentEnd called on an unmapped mate.");
+ }
+ final Cigar mateCigar = SAMUtils.getMateCigar(rec);
+ if (mateCigar == null) {
+ throw new SAMException("Mate CIGAR (Tag MC) not found.");
+ }
+ return CoordMath.getEnd(rec.getMateAlignmentStart(), mateCigar.getReferenceLength());
+ }
+
+ /**
+ * @param rec the SAM record
+ * @return the mate alignment start (1-based, inclusive) adjusted for clipped bases. For example if the mate
+ * has an alignment start of 100 but the first 4 bases were clipped (hard or soft clipped)
+ * then this method will return 96.
+ *
+ * Invalid to call on an unmapped read.
+ */
+ public static int getMateUnclippedStart(final SAMRecord rec) {
+ if (rec.getMateUnmappedFlag())
+ throw new RuntimeException("getMateUnclippedStart called on an unmapped mate.");
+ final Cigar mateCigar = getMateCigar(rec);
+ if (mateCigar == null) {
+ throw new SAMException("Mate CIGAR (Tag MC) not found.");
+ }
+ return SAMUtils.getUnclippedStart(rec.getMateAlignmentStart(), mateCigar);
+ }
+
+
+ /**
+ * @param rec the SAM record
+ * @return the mate alignment end (1-based, inclusive) adjusted for clipped bases. For example if the mate
+ * has an alignment end of 100 but the last 7 bases were clipped (hard or soft clipped)
+ * then this method will return 107.
+ *
+ * Invalid to call on an unmapped read.
+ */
+ public static int getMateUnclippedEnd(final SAMRecord rec) {
+ if (rec.getMateUnmappedFlag()) {
+ throw new RuntimeException("getMateUnclippedEnd called on an unmapped mate.");
+ }
+ final Cigar mateCigar = SAMUtils.getMateCigar(rec);
+ if (mateCigar == null) {
+ throw new SAMException("Mate CIGAR (Tag MC) not found.");
+ }
+ return SAMUtils.getUnclippedEnd(getMateAlignmentEnd(rec), mateCigar);
+ }
+
+ /**
+ * @param rec the SAM record
+ * Returns blocks of the mate sequence that have been aligned directly to the
+ * reference sequence. Note that clipped portions of the mate and inserted and
+ * deleted bases (vs. the reference) are not represented in the alignment blocks.
+ */
+ public static List<AlignmentBlock> getMateAlignmentBlocks(final SAMRecord rec) {
+ return getAlignmentBlocks(getMateCigar(rec), rec.getMateAlignmentStart(), "mate cigar");
+ }
+
+ /**
+ * Run all validations of the mate's CIGAR. These include validation that the CIGAR makes sense independent of
+ * placement, plus validation that CIGAR + placement yields all bases with M operator within the range of the reference.
+ * @param rec the SAM record
+ * @param cigar The cigar containing the alignment information
+ * @param referenceIndex The reference index
+ * @param alignmentBlocks The alignment blocks (parsed from the cigar)
+ * @param recordNumber For error reporting. -1 if not known.
+ * @param cigarTypeName For error reporting. "Read CIGAR" or "Mate Cigar"
+ * @return List of errors, or null if no errors.
+ */
+
+ public static List<SAMValidationError> validateCigar(final SAMRecord rec,
+ final Cigar cigar,
+ final Integer referenceIndex,
+ final List<AlignmentBlock> alignmentBlocks,
+ final long recordNumber,
+ final String cigarTypeName) {
+ // Don't know line number, and don't want to force read name to be decoded.
+ List<SAMValidationError> ret = cigar.isValid(rec.getReadName(), recordNumber);
+ if (referenceIndex != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
+ final SAMSequenceRecord sequence = rec.getHeader().getSequence(referenceIndex);
+ final int referenceSequenceLength = sequence.getSequenceLength();
+ for (final AlignmentBlock alignmentBlock : alignmentBlocks) {
+ if (alignmentBlock.getReferenceStart() + alignmentBlock.getLength() - 1 > referenceSequenceLength) {
+ if (ret == null) ret = new ArrayList<SAMValidationError>();
+ ret.add(new SAMValidationError(SAMValidationError.Type.CIGAR_MAPS_OFF_REFERENCE,
+ cigarTypeName + " M operator maps off end of reference", rec.getReadName(), recordNumber));
+ break;
+ }
+ }
+ }
+ return ret;
+ }
+
+ /**
+ * Run all validations of the mate's CIGAR. These include validation that the CIGAR makes sense independent of
+ * placement, plus validation that CIGAR + placement yields all bases with M operator within the range of the reference.
+ * @param rec the SAM record
+ * @param recordNumber For error reporting. -1 if not known.
+ * @return List of errors, or null if no errors.
+ */
+ public static List<SAMValidationError> validateMateCigar(final SAMRecord rec, final long recordNumber) {
+ List<SAMValidationError> ret = null;
+
+ if (rec.getValidationStringency() != SAMFileReader.ValidationStringency.SILENT) {
+ if (rec.getReadPairedFlag() && !rec.getMateUnmappedFlag()) { // The mateCigar will be defined if the mate is mapped
+ if (getMateCigarString(rec) != null) {
+ ret = SAMUtils.validateCigar(rec, getMateCigar(rec), rec.getMateReferenceIndex(), getMateAlignmentBlocks(rec), recordNumber, "Mate CIGAR");
+ }
+ } else {
+ if (getMateCigarString(rec) != null) {
+ ret = new ArrayList<SAMValidationError>();
+ if (rec.getMateUnmappedFlag()) {
+ // If the Mate is unmapped, and the Mate Cigar String (MC Attribute) exists, that is a validation error.
+ ret.add(new SAMValidationError(SAMValidationError.Type.MATE_CIGAR_STRING_INVALID_PRESENCE,
+ "Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped", rec.getReadName(), recordNumber));
+ }
+ else {
+ // If the Mate is not paired, and the Mate Cigar String (MC Attribute) exists, that is a validation error.
+ ret.add(new SAMValidationError(SAMValidationError.Type.MATE_CIGAR_STRING_INVALID_PRESENCE,
+ "Mate CIGAR String (MC Attribute) present for a read that is not paired", rec.getReadName(), recordNumber));
+ }
+ }
+ }
+ }
+
+ return ret;
+ }
+
+ /**
+ * Checks to see if it is valid for this record to have a mate CIGAR (MC) and then if there is a mate CIGAR available. This is done by
+ * checking that this record is paired, its mate is mapped, and that it returns a non-null mate CIGAR.
+ * @param rec
+ * @return
+ */
+ public static boolean hasMateCigar(SAMRecord rec) {
+ // NB: use getMateCigarString rather than getMateCigar to avoid validation.
+ return (rec.getReadPairedFlag() && !rec.getMateUnmappedFlag() && null != SAMUtils.getMateCigarString(rec));
+ }
}
diff --git a/src/java/net/sf/samtools/SAMValidationError.java b/src/java/net/sf/samtools/SAMValidationError.java
index 4968477..3690d81 100644
--- a/src/java/net/sf/samtools/SAMValidationError.java
+++ b/src/java/net/sf/samtools/SAMValidationError.java
@@ -173,7 +173,7 @@ public class SAMValidationError {
/** Unsigned integer tag value is deprecated in BAM. */
TAG_VALUE_TOO_LARGE,
- /** Invalide virtualFilePointer in index */
+ /** Invalid virtualFilePointer in index */
INVALID_INDEX_FILE_POINTER,
/** PI tag value is not numeric. */
@@ -182,6 +182,12 @@ public class SAMValidationError {
/** Same read group id appears more than once */
DUPLICATE_READ_GROUP_ID,
+ /** The read group is missing its PL (platform unit) field */
+ MISSING_PLATFORM_VALUE,
+
+ /** The read group has an invalid value set for its PL field */
+ INVALID_PLATFORM_VALUE,
+
/** Same program group id appears more than once */
DUPLICATE_PROGRAM_GROUP_ID,
diff --git a/src/java/net/sf/samtools/SamPairUtil.java b/src/java/net/sf/samtools/SamPairUtil.java
index 9ff366f..e93028f 100644
--- a/src/java/net/sf/samtools/SamPairUtil.java
+++ b/src/java/net/sf/samtools/SamPairUtil.java
@@ -179,26 +179,34 @@ public class SamPairUtil {
/**
* Write the mate info for two SAMRecords
+ * @param rec1 the first SAM record
+ * @param rec2 the second SAM record
+ * @param header the SAM file header
+ * @param setMateCigar true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.
*/
- public static void setMateInfo(final SAMRecord rec1, final SAMRecord rec2, final SAMFileHeader header) {
+ public static void setMateInfo(final SAMRecord rec1, final SAMRecord rec2, final SAMFileHeader header, final boolean setMateCigar) {
// If neither read is unmapped just set their mate info
if (!rec1.getReadUnmappedFlag() && !rec2.getReadUnmappedFlag()) {
-
rec1.setMateReferenceIndex(rec2.getReferenceIndex());
rec1.setMateAlignmentStart(rec2.getAlignmentStart());
rec1.setMateNegativeStrandFlag(rec2.getReadNegativeStrandFlag());
rec1.setMateUnmappedFlag(false);
rec1.setAttribute(SAMTag.MQ.name(), rec2.getMappingQuality());
- // TODO: Consider re-enabling when mate cigar issues are resolved
- // rec1.setAttribute(SAMTag.MC.name(), rec2.getCigarString());
rec2.setMateReferenceIndex(rec1.getReferenceIndex());
rec2.setMateAlignmentStart(rec1.getAlignmentStart());
rec2.setMateNegativeStrandFlag(rec1.getReadNegativeStrandFlag());
rec2.setMateUnmappedFlag(false);
rec2.setAttribute(SAMTag.MQ.name(), rec1.getMappingQuality());
- // TODO: Consider re-enabling when mate cigar issues are resolved
- // rec2.setAttribute(SAMTag.MC.name(), rec1.getCigarString());
+
+ if (setMateCigar) {
+ rec1.setAttribute(SAMTag.MC.name(), rec2.getCigarString());
+ rec2.setAttribute(SAMTag.MC.name(), rec1.getCigarString());
+ }
+ else {
+ rec1.setAttribute(SAMTag.MC.name(), null);
+ rec2.setAttribute(SAMTag.MC.name(), null);
+ }
}
// Else if they're both unmapped set that straight
else if (rec1.getReadUnmappedFlag() && rec2.getReadUnmappedFlag()) {
@@ -209,8 +217,7 @@ public class SamPairUtil {
rec1.setMateNegativeStrandFlag(rec2.getReadNegativeStrandFlag());
rec1.setMateUnmappedFlag(true);
rec1.setAttribute(SAMTag.MQ.name(), null);
- // TODO: Consider re-enabling when mate cigar issues are resolved
- // rec1.setAttribute(SAMTag.MC.name(), null);
+ rec1.setAttribute(SAMTag.MC.name(), null);
rec1.setInferredInsertSize(0);
rec2.setReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
@@ -220,8 +227,7 @@ public class SamPairUtil {
rec2.setMateNegativeStrandFlag(rec1.getReadNegativeStrandFlag());
rec2.setMateUnmappedFlag(true);
rec2.setAttribute(SAMTag.MQ.name(), null);
- // TODO: Consider re-enabling when mate cigar issues are resolved
- // rec2.setAttribute(SAMTag.MC.name(), null);
+ rec2.setAttribute(SAMTag.MC.name(), null);
rec2.setInferredInsertSize(0);
}
// And if only one is mapped copy it's coordinate information to the mate
@@ -236,8 +242,7 @@ public class SamPairUtil {
mapped.setMateNegativeStrandFlag(unmapped.getReadNegativeStrandFlag());
mapped.setMateUnmappedFlag(true);
// For the mapped read, set it's mateCigar to null, since the other read must be unmapped
- // TODO: Consider re-enabling when mate cigar issues are resolved
- // mapped.setAttribute(SAMTag.MC.name(), null);
+ mapped.setAttribute(SAMTag.MC.name(), null);
mapped.setInferredInsertSize(0);
unmapped.setMateReferenceIndex(mapped.getReferenceIndex());
@@ -245,8 +250,8 @@ public class SamPairUtil {
unmapped.setMateNegativeStrandFlag(mapped.getReadNegativeStrandFlag());
unmapped.setMateUnmappedFlag(false);
// For the unmapped read, set it's mateCigar to the mate's Cigar, since the mate must be mapped
- // TODO: Consider re-enabling when mate cigar issues are resolved
- // unmapped.setAttribute(SAMTag.MC.name(), mapped.getCigarString());
+ if (setMateCigar) unmapped.setAttribute(SAMTag.MC.name(), mapped.getCigarString());
+ else unmapped.setAttribute(SAMTag.MC.name(), null);
unmapped.setInferredInsertSize(0);
}
@@ -256,6 +261,16 @@ public class SamPairUtil {
}
/**
+ * Write the mate info for two SAMRecords. This will always clear/remove any mate cigar tag that is present.
+ * @param rec1 the first SAM record
+ * @param rec2 the second SAM record
+ * @param header the SAM file header
+ */
+ public static void setMateInfo(final SAMRecord rec1, final SAMRecord rec2, final SAMFileHeader header) {
+ setMateInfo(rec1, rec2, header, false);
+ }
+
+ /**
* Sets mate pair information appropriately on a supplemental SAMRecord (e.g. from a split alignment)
* using the primary alignment of the read's mate.
* @param supplemental a supplemental alignment for the mate pair of the primary supplied
@@ -270,10 +285,27 @@ public class SamPairUtil {
supplemental.setInferredInsertSize(-matePrimary.getInferredInsertSize());
}
+ /**
+ * This method will clear any mate cigar already present.
+ */
public static void setProperPairAndMateInfo(final SAMRecord rec1, final SAMRecord rec2,
final SAMFileHeader header,
final List<PairOrientation> exepectedOrientations) {
- setMateInfo(rec1, rec2, header);
+ setProperPairAndMateInfo(rec1, rec2, header, exepectedOrientations, false);
+ }
+
+ /**
+ * @param rec1
+ * @param rec2
+ * @param header
+ * @param exepectedOrientations
+ * @param addMateCigar true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.
+ */
+ public static void setProperPairAndMateInfo(final SAMRecord rec1, final SAMRecord rec2,
+ final SAMFileHeader header,
+ final List<PairOrientation> exepectedOrientations,
+ final boolean addMateCigar) {
+ setMateInfo(rec1, rec2, header, addMateCigar);
setProperPairFlags(rec1, rec2, exepectedOrientations);
}
diff --git a/src/java/net/sf/samtools/StreamInflatingIndexingOutputStream.java b/src/java/net/sf/samtools/StreamInflatingIndexingOutputStream.java
new file mode 100644
index 0000000..a422e9d
--- /dev/null
+++ b/src/java/net/sf/samtools/StreamInflatingIndexingOutputStream.java
@@ -0,0 +1,80 @@
+package net.sf.samtools;
+
+
+import net.sf.samtools.util.RuntimeIOException;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.io.PipedInputStream;
+import java.io.PipedOutputStream;
+
+/**
+ * OutputStream implementation that writes output to an underlying output stream while also copying the
+ * same bytes to a PipedOutputStream that routes the data back into an Indexer to generate a BAMIndex
+ * by inflating and decoding the stream and feeding the SAMRecords to a BAMIndexer.
+ */
+class StreamInflatingIndexingOutputStream extends OutputStream {
+ private final OutputStream s1;
+ private final PipedOutputStream s2;
+ private final Thread thread;
+
+ public StreamInflatingIndexingOutputStream(final OutputStream s1, final File indexFile) {
+ try {
+ this.s1 = s1;
+ this.s2 = new PipedOutputStream();
+ final PipedInputStream pin = new PipedInputStream(this.s2, Defaults.NON_ZERO_BUFFER_SIZE);
+ this.thread = new Thread(new Indexer(indexFile, pin), "BamIndexingThread");
+ this.thread.start();
+ }
+ catch (final IOException ioe) {
+ throw new RuntimeIOException(ioe);
+ }
+ }
+
+ @Override public final void write(final int b) throws IOException { this.s1.write(b); this.s2.write(b); }
+ @Override public final void write(final byte[] b) throws IOException { this.s1.write(b); this.s2.write(b); }
+ @Override public final void write(final byte[] b, final int off, final int len) throws IOException { this.s1.write(b, off, len); this.s2.write(b, off, len); }
+ @Override public final void flush() throws IOException { this.s1.flush(); this.s2.flush(); }
+
+ @Override public final void close() throws IOException {
+ this.s1.close();
+ this.s2.close();
+
+ try { this.thread.join(); }
+ catch (final InterruptedException ie) { throw new RuntimeException(ie); }
+ }
+}
+
+/**
+ * A little class that takes an InputStream from which it reads a BAM file, generates
+ * a BAMIndex and then writes the index to the File provided. All operations are designed
+ * to be carried out in a separate thread.
+ */
+class Indexer implements Runnable {
+ private final File index;
+ private final InputStream stream;
+
+ /** Constructs an indexer that reads from the stream provided and writes an index to the File provided. */
+ Indexer(final File index, final InputStream stream) {
+ this.index = index;
+ this.stream = stream;
+ }
+
+ /** Runnable implementation that reads the entire stream and writes the index. */
+ @Override
+ public void run() {
+ final SAMFileReader in = new SAMFileReader(this.stream);
+ in.enableFileSource(true);
+ in.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
+ in.enableCrcChecking(false);
+ final BAMIndexer indexer = new BAMIndexer(this.index, in.getFileHeader());
+ for (final SAMRecord rec : in) {
+ indexer.processAlignment(rec);
+ }
+
+ indexer.finish();
+ in.close();
+ }
+}
diff --git a/src/java/net/sf/samtools/TagValueAndUnsignedArrayFlag.java b/src/java/net/sf/samtools/TagValueAndUnsignedArrayFlag.java
index 11cba95..c5ca6da 100644
--- a/src/java/net/sf/samtools/TagValueAndUnsignedArrayFlag.java
+++ b/src/java/net/sf/samtools/TagValueAndUnsignedArrayFlag.java
@@ -26,7 +26,7 @@ package net.sf.samtools;
/**
* CVO to use as a method return value.
*/
-class TagValueAndUnsignedArrayFlag {
+public class TagValueAndUnsignedArrayFlag {
public final Object value;
public final boolean isUnsignedArray;
diff --git a/src/java/net/sf/samtools/TextTagCodec.java b/src/java/net/sf/samtools/TextTagCodec.java
index 9502e1b..5157c40 100644
--- a/src/java/net/sf/samtools/TextTagCodec.java
+++ b/src/java/net/sf/samtools/TextTagCodec.java
@@ -39,7 +39,7 @@ import java.text.ParseException;
* variables in order to reduce object creation, but it should not ever be the case that the same
* instance is used in multiple threads.
*/
-class TextTagCodec {
+public class TextTagCodec {
private static final int NUM_TAG_FIELDS = 3;
/**
@@ -53,7 +53,7 @@ class TextTagCodec {
* @param value Tag value as approriate Object subclass.
* @return SAM text String representation, i.e. name:type:value
*/
- String encode(final String tagName, Object value) {
+ public String encode(final String tagName, Object value) {
final StringBuilder sb = new StringBuilder(tagName);
sb.append(':');
char tagType = BinaryTagCodec.getTagValueType(value);
@@ -130,13 +130,13 @@ class TextTagCodec {
}
/**
- * Encode a standard tag, which should not have a type field.
+ * Encode a standard header tag, which should not have a type field.
* @param tagName 2-character String.
* @param value Not necessarily a String. Some of these are integers but the type is implied by
* the tagName. Converted to String with toString().
* @return Colon-separated text representation suitable for a SAM header, i.e. name:value.
*/
- String encodeUntypedTag(final String tagName, final Object value) {
+ public String encodeUntypedTag(final String tagName, final Object value) {
final StringBuilder sb = new StringBuilder(tagName);
sb.append(':');
sb.append(value.toString());
@@ -149,7 +149,7 @@ class TextTagCodec {
* @return Tag name as 2-character String, and tag value in appropriate class based on tag type.
* If value is an unsigned array, then the value is a TagValueAndUnsignedArrayFlag object.
*/
- Map.Entry<String, Object> decode(final String tag) {
+ public Map.Entry<String, Object> decode(final String tag) {
final int numFields = StringUtil.splitConcatenateExcessTokens(tag, fields, ':');
if (numFields != TextTagCodec.NUM_TAG_FIELDS) {
throw new SAMFormatException("Not enough fields in tag '" + tag + "'");
diff --git a/src/java/net/sf/samtools/util/BlockCompressedInputStream.java b/src/java/net/sf/samtools/util/BlockCompressedInputStream.java
index f5a3926..a66a4b2 100755
--- a/src/java/net/sf/samtools/util/BlockCompressedInputStream.java
+++ b/src/java/net/sf/samtools/util/BlockCompressedInputStream.java
@@ -35,6 +35,7 @@ import java.nio.ByteOrder;
import java.util.Arrays;
import net.sf.samtools.FileTruncatedException;
+import net.sf.samtools.SAMException;
import net.sf.samtools.seekablestream.SeekableBufferedStream;
import net.sf.samtools.seekablestream.SeekableFileStream;
import net.sf.samtools.seekablestream.SeekableHTTPStream;
@@ -492,6 +493,12 @@ public class BlockCompressedInputStream extends InputStream implements LocationA
}
}
+ public static void assertNonDefectiveFile(final File file) throws IOException {
+ if (checkTermination(file) == FileTermination.DEFECTIVE) {
+ throw new SAMException(file.getAbsolutePath() + " does not have a valid GZIP block at the end of the file.");
+ }
+ }
+
private static boolean preambleEqual(final byte[] preamble, final byte[] buf, final int startOffset, final int length) {
for (int i = 0; i < length; ++i) {
if (preamble[i] != buf[i + startOffset]) {
diff --git a/src/java/net/sf/samtools/util/CloseableIterator.java b/src/java/net/sf/samtools/util/CloseableIterator.java
index fc023a8..13d9a3a 100755
--- a/src/java/net/sf/samtools/util/CloseableIterator.java
+++ b/src/java/net/sf/samtools/util/CloseableIterator.java
@@ -23,6 +23,7 @@
*/
package net.sf.samtools.util;
+import java.io.Closeable;
import java.util.Iterator;
/**
@@ -31,15 +32,14 @@ import java.util.Iterator;
* The consumer of a CloseableIterator should ensure that the close() method is always called,
* for example by putting such a call in a finally block. Two conventions should be followed
* by all implementors of CloseableIterator:
- * 1) The close() method should be idempotent. Calling close() twice should have no effect.
+ * 1) The close() method should be idempotent: calling close() twice should have no effect.
* 2) When hasNext() returns false, the iterator implementation should automatically close itself.
* The latter makes it somewhat safer for consumers to use the for loop syntax for iteration:
* for (Type obj : getCloseableIterator()) { ... }
*
* We do not inherit from java.io.Closeable because IOExceptions are a pain to deal with.
*/
-public interface CloseableIterator<T>
- extends Iterator<T> {
+public interface CloseableIterator<T> extends Iterator<T>, Closeable {
public void close();
}
diff --git a/src/java/net/sf/samtools/util/IOUtil.java b/src/java/net/sf/samtools/util/IOUtil.java
index 6873083..aff1209 100644
--- a/src/java/net/sf/samtools/util/IOUtil.java
+++ b/src/java/net/sf/samtools/util/IOUtil.java
@@ -58,6 +58,25 @@ public class IOUtil {
}
/**
+ * Transfers from the input stream to the output stream using stream operations and a buffer.
+ */
+ public static void transferByStream(final InputStream in, final OutputStream out, final long bytes) {
+ final byte[] buffer = new byte[Defaults.NON_ZERO_BUFFER_SIZE];
+ long remaining = bytes;
+
+ try {
+ while (remaining > 0) {
+ final int read = in.read(buffer, 0, (int) Math.min(buffer.length, remaining));
+ out.write(buffer, 0, read);
+ remaining -= read;
+ }
+ }
+ catch (final IOException ioe) {
+ throw new RuntimeIOException(ioe);
+ }
+ }
+
+ /**
* @return If Defaults.BUFFER_SIZE > 0, wrap os in BufferedOutputStream, else return os itself.
*/
public static OutputStream maybeBufferOutputStream(final OutputStream os) {
@@ -186,4 +205,16 @@ public class IOUtil {
if (tmp.endsWith(File.separatorChar + user)) return new File(tmp);
else return new File(tmp, user);
}
+
+ /** Returns the name of the file minus the extension (i.e. text after the last "." in the filename). */
+ public static String basename(final File f) {
+ final String full = f.getName();
+ final int index = full.lastIndexOf(".");
+ if (index > 0 && index > full.lastIndexOf(File.separator)) {
+ return full.substring(0, index);
+ }
+ else {
+ return full;
+ }
+ }
}
diff --git a/src/java/net/sf/samtools/util/LineReader.java b/src/java/net/sf/samtools/util/LineReader.java
index 91ac6f1..5f09b81 100644
--- a/src/java/net/sf/samtools/util/LineReader.java
+++ b/src/java/net/sf/samtools/util/LineReader.java
@@ -23,10 +23,12 @@
*/
package net.sf.samtools.util;
+import java.io.Closeable;
+
/**
* Interface allows for implementations that read lines from a String, an ASCII file, or somewhere else.
*/
-public interface LineReader {
+public interface LineReader extends Closeable{
/**
* Read a line and remove the line terminator
diff --git a/src/java/org/broad/tribble/AbstractFeatureReader.java b/src/java/org/broad/tribble/AbstractFeatureReader.java
index 1192f90..8dd9008 100644
--- a/src/java/org/broad/tribble/AbstractFeatureReader.java
+++ b/src/java/org/broad/tribble/AbstractFeatureReader.java
@@ -22,8 +22,13 @@ import org.broad.tribble.index.Index;
import org.broad.tribble.util.ParsingUtils;
import org.broad.tribble.util.TabixUtils;
+import java.io.File;
import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
import java.util.Iterator;
+import java.util.Set;
/**
* jrobinso
@@ -44,6 +49,8 @@ public abstract class AbstractFeatureReader<T extends Feature, SOURCE> implement
private static ComponentMethods methods = new ComponentMethods();
+ public static final Set<String> BLOCK_COMPRESSED_EXTENSIONS = Collections.unmodifiableSet(new HashSet<String>(Arrays.asList(".gz", ".gzip", ".bgz", ".bgzf")));
+
/**
* Calls {@link #getFeatureReader(String, FeatureCodec, boolean)} with {@code requireIndex} = true
*/
@@ -126,6 +133,28 @@ public abstract class AbstractFeatureReader<T extends Feature, SOURCE> implement
}
/**
+ * Whether a filename ends in one of the BLOCK_COMPRESSED_EXTENSIONS
+ * @param fileName
+ * @return
+ */
+ public static boolean hasBlockCompressedExtension (final String fileName) {
+ for (final String extension : BLOCK_COMPRESSED_EXTENSIONS) {
+ if (fileName.toLowerCase().endsWith(extension))
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Whether the name of a file ends in one of the BLOCK_COMPRESSED_EXTENSIONS
+ * @param file
+ * @return
+ */
+ public static boolean hasBlockCompressedExtension (final File file) {
+ return hasBlockCompressedExtension(file.getName());
+ }
+
+ /**
* get the header
*
* @return the header object we've read-in
@@ -148,7 +177,7 @@ public abstract class AbstractFeatureReader<T extends Feature, SOURCE> implement
if(indexPath == null){
indexPath = ParsingUtils.appendToPath(resourcePath, TabixUtils.STANDARD_INDEX_EXTENSION);
}
- return resourcePath.endsWith(".gz") && ParsingUtils.resourceExists(indexPath);
+ return hasBlockCompressedExtension(resourcePath) && ParsingUtils.resourceExists(indexPath);
}
}
}
diff --git a/src/java/org/broad/tribble/index/IndexFactory.java b/src/java/org/broad/tribble/index/IndexFactory.java
index f92281f..f3730c0 100644
--- a/src/java/org/broad/tribble/index/IndexFactory.java
+++ b/src/java/org/broad/tribble/index/IndexFactory.java
@@ -25,6 +25,7 @@ package org.broad.tribble.index;
import net.sf.samtools.Defaults;
import net.sf.samtools.SAMSequenceDictionary;
+import net.sf.samtools.util.BlockCompressedInputStream;
import org.broad.tribble.*;
import org.broad.tribble.index.interval.IntervalIndexCreator;
import org.broad.tribble.index.interval.IntervalTreeIndex;
@@ -38,6 +39,7 @@ import org.broad.tribble.readers.PositionalBufferedStream;
import org.broad.tribble.util.LittleEndianInputStream;
import org.broad.tribble.util.LittleEndianOutputStream;
import org.broad.tribble.util.ParsingUtils;
+import org.broad.tribble.util.TabixUtils;
import java.io.*;
import java.lang.reflect.Constructor;
@@ -158,6 +160,9 @@ public class IndexFactory {
if (indexFile.endsWith(".gz")) {
inputStream = new GZIPInputStream(inputStream);
}
+ else if (indexFile.endsWith(TabixUtils.STANDARD_INDEX_EXTENSION)) {
+ inputStream = new BlockCompressedInputStream(inputStream);
+ }
// Must be buffered, because getIndexType uses mark and reset
bufferedInputStream = new BufferedInputStream(inputStream, Defaults.NON_ZERO_BUFFER_SIZE);
final Class indexClass = IndexType.getIndexType(bufferedInputStream).getIndexType();
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/src/java/org/broad/tribble/util/ftp/.gitignore
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to src/java/org/broad/tribble/util/ftp/.gitignore
diff --git a/src/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterBuilder.java b/src/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterBuilder.java
new file mode 100644
index 0000000..e7c3b2d
--- /dev/null
+++ b/src/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterBuilder.java
@@ -0,0 +1,466 @@
+/*
+* Copyright (c) 2014 The Broad Institute
+*
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+*
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+*
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.variant.variantcontext.writer;
+
+import net.sf.samtools.Defaults;
+import net.sf.samtools.SAMSequenceDictionary;
+import net.sf.samtools.util.BlockCompressedOutputStream;
+import net.sf.samtools.util.IOUtil;
+import net.sf.samtools.util.Md5CalculatingOutputStream;
+import net.sf.samtools.util.RuntimeIOException;
+import org.broad.tribble.AbstractFeatureReader;
+import org.broad.tribble.index.IndexCreator;
+import org.broad.tribble.index.tabix.TabixFormat;
+import org.broad.tribble.index.tabix.TabixIndexCreator;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.OutputStream;
+import java.util.EnumSet;
+
+/**
+ * Created with IntelliJ IDEA.
+ * User: thibault
+ * Date: 3/7/14
+ * Time: 2:07 PM
+ *
+ * Provides methods for creating VariantContextWriters using the Builder pattern.
+ * Replaces VariantContextWriterFactory.
+ *
+ * The caller must choose an output file or an output stream for the VariantContextWriter to write to.
+ * When a file is chosen, the output stream is created implicitly based on Defaults and options passed to the builder.
+ * When a stream is chosen, it is passed unchanged to the VariantContextWriter.
+ *
+ * Example: Create a series of files with buffering and indexing on the fly.
+ * Determine the appropriate file type based on filename.
+ *
+ * VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
+ * .setReferenceDictionary(refDict)
+ * .setOption(Options.INDEX_ON_THE_FLY)
+ * .setBuffer(8192);
+ *
+ * VariantContextWriter sample1_writer = builder
+ * .setOutputFile("sample1.vcf")
+ * .build();
+ * VariantContextWriter sample2_writer = builder
+ * .setOutputFile("sample2.bcf")
+ * .build();
+ * VariantContextWriter sample3_writer = builder
+ * .setOutputFile("sample3.vcf.bgzf")
+ * .build();
+ *
+ * Example: Explicitly turn off buffering and explicitly set the file type
+ *
+ * VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
+ * .setReferenceDictionary(refDict)
+ * .setOption(Options.INDEX_ON_THE_FLY)
+ * .unsetBuffering();
+ *
+ * VariantContextWriter sample1_writer = builder
+ * .setOutputFile("sample1.custom_extension")
+ * .setOutputFileType(OutputType.VCF)
+ * .build();
+ * VariantContextWriter sample2_writer = builder
+ * .setOutputFile("sample2.custom_extension")
+ * .setOutputFileType(OutputType.BLOCK_COMPRESSED_VCF)
+ * .build();
+
+ */
+public class VariantContextWriterBuilder {
+ public static final EnumSet<Options> DEFAULT_OPTIONS = EnumSet.of(Options.INDEX_ON_THE_FLY);
+ public static final EnumSet<Options> NO_OPTIONS = EnumSet.noneOf(Options.class);
+
+ public enum OutputType {
+ UNSPECIFIED,
+ VCF,
+ BCF,
+ BLOCK_COMPRESSED_VCF,
+ VCF_STREAM,
+ BCF_STREAM
+ }
+
+ public static final EnumSet<OutputType> FILE_TYPES = EnumSet.of(OutputType.VCF, OutputType.BCF, OutputType.BLOCK_COMPRESSED_VCF);
+ public static final EnumSet<OutputType> STREAM_TYPES = EnumSet.of(OutputType.VCF_STREAM, OutputType.BCF_STREAM);
+
+ private SAMSequenceDictionary refDict = null;
+ private OutputType outType = OutputType.UNSPECIFIED;
+ private File outFile = null;
+ private OutputStream outStream = null;
+ private IndexCreator idxCreator = null;
+ private int bufferSize = Defaults.BUFFER_SIZE;
+ private boolean createMD5 = Defaults.CREATE_MD5;
+ private EnumSet<Options> options = DEFAULT_OPTIONS.clone();
+
+ /**
+ * Default constructor. Adds USE_ASYNC_IO to the Options if it is present in Defaults.
+ */
+ public VariantContextWriterBuilder() {
+ if (Defaults.USE_ASYNC_IO)
+ options.add(Options.USE_ASYNC_IO);
+ }
+
+ /**
+ * Set the reference dictionary to be used by VariantContextWriters created by this builder
+ *
+ * @param refDict the reference dictionary
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder setReferenceDictionary(final SAMSequenceDictionary refDict) {
+ this.refDict = refDict;
+ return this;
+ }
+
+ /**
+ * Set the output file for the next VariantContextWriter created by this builder
+ * Determines file type implicitly from the filename
+ *
+ * @param outFile the file the VariantContextWriter will write to
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder setOutputFile(final File outFile) {
+ this.outFile = outFile;
+ this.outStream = null;
+ determineOutputTypeFromFilename();
+ return this;
+ }
+
+ /**
+ * Set the output file for the next VariantContextWriter created by this builder
+ * Determines file type implicitly from the filename
+ *
+ * @param outFile the file the VariantContextWriter will write to
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder setOutputFile(final String outFile) {
+ this.outFile = new File(outFile);
+ this.outStream = null;
+ determineOutputTypeFromFilename();
+ return this;
+ }
+
+ /**
+ * Set the output file type for the next VariantContextWriter created by this builder
+ *
+ * @param outType the type of file the VariantContextWriter will write to
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder setOutputFileType(final OutputType outType) {
+ if (!FILE_TYPES.contains(outType))
+ throw new IllegalArgumentException("Must choose a file type, not other output types.");
+
+ if (this.outFile == null || this.outStream != null)
+ throw new IllegalArgumentException("Cannot set a file type if the output is not to a file.");
+
+ this.outType = outType;
+ return this;
+ }
+
+ /**
+ * Set the output VCF stream for the next VariantContextWriter created by this builder
+ * If buffered writing is desired, caller must provide some kind of buffered OutputStream.
+ *
+ * @param outStream the output stream to write to
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder setOutputVCFStream(final OutputStream outStream) {
+ this.outStream = outStream;
+ this.outFile = null;
+ this.outType = OutputType.VCF_STREAM;
+ return this;
+ }
+
+ /**
+ * Set the output BCF stream for the next VariantContextWriter created by this builder
+ * If buffered writing is desired, caller must provide some kind of buffered OutputStream.
+ *
+ * @param outStream the output stream to write to
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder setOutputBCFStream(final OutputStream outStream) {
+ this.outStream = outStream;
+ this.outFile = null;
+ this.outType = OutputType.BCF_STREAM;
+ return this;
+ }
+
+ /**
+ * Set the output stream (VCF, by default) for the next VariantContextWriter created by this builder
+ * If buffered writing is desired, caller must provide some kind of buffered OutputStream.
+ *
+ * @param outStream the output stream to write to
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder setOutputStream(final OutputStream outStream) {
+ return setOutputVCFStream(outStream);
+ }
+
+ /**
+ * Set an IndexCreator for the next VariantContextWriter created by this builder
+ *
+ * @param idxCreator the IndexCreator to use
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder setIndexCreator(final IndexCreator idxCreator) {
+ this.idxCreator = idxCreator;
+ return this;
+ }
+
+ /**
+ * Do not pass an IndexCreator to the next VariantContextWriter created by this builder
+ *
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder clearIndexCreator() {
+ this.idxCreator = null;
+ return this;
+ }
+
+ /**
+ * Set a buffer size for the file output stream passed to the next VariantContextWriter created by this builder
+ * Set to 0 for no buffering
+ * Does not affect OutputStreams passed directly to VariantContextWriterBuilder
+ *
+ * @param bufferSize the buffer size to use
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder setBuffer(final int bufferSize) {
+ this.bufferSize = bufferSize;
+ return this;
+ }
+
+ /**
+ * Do not use buffering in the next VariantContextWriter created by this builder
+ * Does not affect OutputStreams passed directly to VariantContextWriterBuilder
+ *
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder unsetBuffering() {
+ this.bufferSize = 0;
+ return this;
+ }
+
+ /**
+ * Choose whether to also create an MD5 digest file for the next VariantContextWriter created by this builder
+ *
+ * @param createMD5 boolean, true to create an MD5 digest
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder setCreateMD5(final boolean createMD5) {
+ this.createMD5 = createMD5;
+ return this;
+ }
+
+ /**
+ * Create an MD5 digest file for the next VariantContextWriter created by this builder
+ *
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder setCreateMD5() {
+ return setCreateMD5(true);
+ }
+
+ /**
+ * Don't create an MD5 digest file for the next VariantContextWriter created by this builder
+ *
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder unsetCreateMD5() {
+ return setCreateMD5(false);
+ }
+
+ /**
+ * Replace the set of Options for the VariantContextWriterBuilder with a new set
+ *
+ * @param options the complete set of options to use
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder setOptions(final EnumSet<Options> options) {
+ this.options = options;
+ return this;
+ }
+
+ /**
+ * Add one option to the set of Options for the VariantContextWriterBuilder, if it's not already present
+ *
+ * @param option the option to set
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder setOption(final Options option) {
+ this.options.add(option);
+ return this;
+ }
+
+ /**
+ * Remove one option from the set of Options for the VariantContextWriterBuilder, if it's present
+ *
+ * @param option the option to unset
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder unsetOption(final Options option) {
+ this.options.remove(option);
+ return this;
+ }
+
+ /**
+ * Remove all options from the set of Options for the VariantContextWriterBuilder
+ *
+ * @return this VariantContextWriterBuilder
+ */
+ public VariantContextWriterBuilder clearOptions() {
+ this.options = NO_OPTIONS;
+ return this;
+ }
+
+ /**
+ * Validate and build the VariantContextWriter
+ *
+ * @return the VariantContextWriter as specified by previous method calls
+ */
+ public VariantContextWriter build() {
+ VariantContextWriter writer = null;
+
+ // don't allow FORCE_BCF to modify the outType state
+ OutputType typeToBuild = this.outType;
+
+ if (this.options.contains(Options.FORCE_BCF)) {
+ if (FILE_TYPES.contains(this.outType))
+ typeToBuild = OutputType.BCF;
+ else if (STREAM_TYPES.contains(this.outType))
+ typeToBuild = OutputType.BCF_STREAM;
+ }
+
+ OutputStream outStreamFromFile = this.outStream;
+ if (FILE_TYPES.contains(this.outType)) {
+ try {
+ outStreamFromFile = IOUtil.maybeBufferOutputStream(new FileOutputStream(outFile), bufferSize);
+ } catch (final FileNotFoundException e) {
+ throw new RuntimeIOException("File not found: " + outFile, e);
+ }
+
+ if (createMD5)
+ outStreamFromFile = new Md5CalculatingOutputStream(outStreamFromFile, new File(outFile.getAbsolutePath() + ".md5"));
+ }
+
+ switch (typeToBuild) {
+ case UNSPECIFIED:
+ throw new IllegalArgumentException("Must specify file or stream output type.");
+ case VCF:
+ if ((refDict == null) && (options.contains(Options.INDEX_ON_THE_FLY)))
+ throw new IllegalArgumentException("A reference dictionary is required for creating Tribble indices on the fly");
+
+ writer = createVCFWriter(outFile, outStreamFromFile);
+ break;
+ case BLOCK_COMPRESSED_VCF:
+ if (refDict == null)
+ idxCreator = new TabixIndexCreator(TabixFormat.VCF);
+ else
+ idxCreator = new TabixIndexCreator(refDict, TabixFormat.VCF);
+
+ writer = createVCFWriter(outFile, new BlockCompressedOutputStream(outStreamFromFile, outFile));
+ break;
+ case BCF:
+ if ((refDict == null) && (options.contains(Options.INDEX_ON_THE_FLY)))
+ throw new IllegalArgumentException("A reference dictionary is required for creating Tribble indices on the fly");
+
+ writer = createBCFWriter(outFile, outStreamFromFile);
+ break;
+ case VCF_STREAM:
+ if (options.contains(Options.INDEX_ON_THE_FLY))
+ throw new IllegalArgumentException("VCF index creation not supported for stream output.");
+
+ writer = createVCFWriter(null, outStream);
+ break;
+ case BCF_STREAM:
+ if (options.contains(Options.INDEX_ON_THE_FLY))
+ throw new IllegalArgumentException("BCF index creation not supported for stream output.");
+
+ writer = createBCFWriter(null, outStream);
+ break;
+ }
+
+ if (this.options.contains(Options.USE_ASYNC_IO))
+ writer = new AsyncVariantContextWriter(writer, AsyncVariantContextWriter.DEFAULT_QUEUE_SIZE);
+
+ return writer;
+ }
+
+ private void determineOutputTypeFromFilename() {
+ if (isBCF(this.outFile)) {
+ this.outType = OutputType.BCF;
+ } else if (isCompressedVCF(this.outFile)) {
+ this.outType = OutputType.BLOCK_COMPRESSED_VCF;
+ } else if (isVCF(this.outFile)) {
+ this.outType = OutputType.VCF;
+ }
+ else {
+ this.outType = OutputType.UNSPECIFIED;
+ }
+ }
+
+ private boolean isVCF(final File outFile) {
+ return outFile != null && outFile.getName().endsWith(".vcf");
+ }
+
+ private boolean isBCF(final File outFile) {
+ return outFile != null && outFile.getName().endsWith(".bcf");
+ }
+
+ private boolean isCompressedVCF(final File outFile) {
+ if (outFile == null)
+ return false;
+
+ return AbstractFeatureReader.hasBlockCompressedExtension(outFile);
+ }
+
+ private VariantContextWriter createVCFWriter(final File writerFile, final OutputStream writerStream) {
+ if (idxCreator == null) {
+ return new VCFWriter(writerFile, writerStream, refDict,
+ options.contains(Options.INDEX_ON_THE_FLY),
+ options.contains(Options.DO_NOT_WRITE_GENOTYPES),
+ options.contains(Options.ALLOW_MISSING_FIELDS_IN_HEADER));
+ }
+ else {
+ return new VCFWriter(writerFile, writerStream, refDict, idxCreator,
+ options.contains(Options.INDEX_ON_THE_FLY),
+ options.contains(Options.DO_NOT_WRITE_GENOTYPES),
+ options.contains(Options.ALLOW_MISSING_FIELDS_IN_HEADER));
+ }
+ }
+
+ private VariantContextWriter createBCFWriter(final File writerFile, final OutputStream writerStream) {
+ if (idxCreator == null) {
+ return new BCF2Writer(writerFile, writerStream, refDict,
+ options.contains(Options.INDEX_ON_THE_FLY),
+ options.contains(Options.DO_NOT_WRITE_GENOTYPES));
+ }
+ else {
+ return new BCF2Writer(writerFile, writerStream, refDict, idxCreator,
+ options.contains(Options.INDEX_ON_THE_FLY),
+ options.contains(Options.DO_NOT_WRITE_GENOTYPES));
+ }
+ }
+}
diff --git a/src/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterFactory.java b/src/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterFactory.java
index 1ddfa8d..85a7f22 100644
--- a/src/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterFactory.java
+++ b/src/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterFactory.java
@@ -29,6 +29,7 @@ import net.sf.samtools.Defaults;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.util.BlockCompressedOutputStream;
import net.sf.samtools.util.IOUtil;
+import org.broad.tribble.AbstractFeatureReader;
import org.broad.tribble.index.IndexCreator;
import org.broad.tribble.index.tabix.TabixFormat;
import org.broad.tribble.index.tabix.TabixIndexCreator;
@@ -41,12 +42,14 @@ import java.util.EnumSet;
*
* @author depristo
* @since 5/12
+ *
+ * @deprecated Replaced by {@link org.broadinstitute.variant.variantcontext.writer.VariantContextWriterBuilder}
*/
+ at Deprecated
public class VariantContextWriterFactory {
public static final EnumSet<Options> DEFAULT_OPTIONS = EnumSet.of(Options.INDEX_ON_THE_FLY);
public static final EnumSet<Options> NO_OPTIONS = EnumSet.noneOf(Options.class);
- public static final String[] BLOCK_COMPRESSED_EXTENSIONS = {".gz", ".bgz", ".bgzf"};
static {
if (Defaults.USE_ASYNC_IO) {
@@ -242,11 +245,10 @@ public class VariantContextWriterFactory {
}
public static boolean isCompressedVcf(final File location) {
- if (location == null) return false;
- for (final String extension : BLOCK_COMPRESSED_EXTENSIONS) {
- if (location.getName().endsWith(extension)) return true;
- }
- return false;
+ if (location == null)
+ return false;
+
+ return AbstractFeatureReader.hasBlockCompressedExtension(location);
}
public static VariantContextWriter sortOnTheFly(final VariantContextWriter innerWriter, final int maxCachingStartDistance) {
diff --git a/src/java/org/broadinstitute/variant/vcf/AbstractVCFCodec.java b/src/java/org/broadinstitute/variant/vcf/AbstractVCFCodec.java
index 314a23f..32e9a8f 100644
--- a/src/java/org/broadinstitute/variant/vcf/AbstractVCFCodec.java
+++ b/src/java/org/broadinstitute/variant/vcf/AbstractVCFCodec.java
@@ -34,6 +34,7 @@ import org.broad.tribble.util.ParsingUtils;
import org.broadinstitute.variant.utils.GeneralUtils;
import org.broadinstitute.variant.variantcontext.*;
+import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
@@ -86,6 +87,12 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
*/
protected boolean doOnTheFlyModifications = true;
+ /**
+ * If non-null, we will replace the sample name read from the VCF header with this sample name. This feature works
+ * only for single-sample VCFs.
+ */
+ protected String remappedSampleName = null;
+
protected AbstractVCFCodec() {
super(VariantContext.class);
}
@@ -165,6 +172,20 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
if ( sawFormatTag && sampleNames.size() == 0 )
throw new TribbleException.InvalidHeader("The FORMAT field was provided but there is no genotype/sample data");
+ // If we're performing sample name remapping and there is exactly one sample specified in the header, replace
+ // it with the remappedSampleName. Throw an error if there are 0 or multiple samples and remapping was requested
+ // for this file.
+ if ( remappedSampleName != null ) {
+ // We currently only support on-the-fly sample name remapping for single-sample VCFs
+ if ( sampleNames.isEmpty() || sampleNames.size() > 1 ) {
+ throw new TribbleException(String.format("Cannot remap sample name to %s because %s samples are specified in the VCF header, and on-the-fly sample name remapping is only supported for single-sample VCFs",
+ remappedSampleName, sampleNames.isEmpty() ? "no" : "multiple"));
+ }
+
+ sampleNames.clear();
+ sampleNames.add(remappedSampleName);
+ }
+
} else {
if ( str.startsWith(VCFConstants.INFO_HEADER_START) ) {
final VCFInfoHeaderLine info = new VCFInfoHeaderLine(str.substring(7), version);
@@ -739,6 +760,16 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
doOnTheFlyModifications = false;
}
+ /**
+ * Replaces the sample name read from the VCF header with the remappedSampleName. Works
+ * only for single-sample VCFs -- attempting to perform sample name remapping for multi-sample
+ * VCFs will produce an Exception.
+ *
+ * @param remappedSampleName replacement sample name for the sample specified in the VCF header
+ */
+ public void setRemappedSampleName( final String remappedSampleName ) {
+ this.remappedSampleName = remappedSampleName;
+ }
protected void generateException(String message) {
throw new TribbleException(String.format("The provided VCF file is malformed at approximately line number %d: %s", lineNo, message));
diff --git a/src/java/org/broadinstitute/variant/vcf/VCFCompoundHeaderLine.java b/src/java/org/broadinstitute/variant/vcf/VCFCompoundHeaderLine.java
index 89adce6..12db895 100644
--- a/src/java/org/broadinstitute/variant/vcf/VCFCompoundHeaderLine.java
+++ b/src/java/org/broadinstitute/variant/vcf/VCFCompoundHeaderLine.java
@@ -32,6 +32,7 @@ import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.LinkedHashMap;
+import java.util.ArrayList;
import java.util.Map;
/**
@@ -150,7 +151,11 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
*/
protected VCFCompoundHeaderLine(String line, VCFHeaderVersion version, SupportedHeaderLineType lineType) {
super(lineType.toString(), "");
- Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Number","Type","Description"));
+
+ final ArrayList<String> expectedTags = new ArrayList(Arrays.asList("ID","Number","Type","Description"));
+ if ( version.isAtLeastAsRecentAs(VCFHeaderVersion.VCF4_2) )
+ expectedTags.add("Version");
+ final Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version, line, expectedTags);
name = mapping.get("ID");
count = -1;
final String numberStr = mapping.get("Number");
diff --git a/src/java/org/broadinstitute/variant/vcf/VCFEncoder.java b/src/java/org/broadinstitute/variant/vcf/VCFEncoder.java
index fdb5883..f50cac3 100644
--- a/src/java/org/broadinstitute/variant/vcf/VCFEncoder.java
+++ b/src/java/org/broadinstitute/variant/vcf/VCFEncoder.java
@@ -247,7 +247,7 @@ public class VCFEncoder {
/*
* Add the genotype data
*/
- private void addGenotypeData(final VariantContext vc, final Map<Allele, String> alleleMap, final List<String> genotypeFormatKeys, final StringBuilder builder) {
+ public void addGenotypeData(final VariantContext vc, final Map<Allele, String> alleleMap, final List<String> genotypeFormatKeys, final StringBuilder builder) {
final int ploidy = vc.getMaxPloidy(2);
for (final String sample : this.header.getGenotypeSamples()) {
@@ -360,7 +360,7 @@ public class VCFEncoder {
}
}
- private Map<Allele, String> buildAlleleStrings(final VariantContext vc) {
+ public Map<Allele, String> buildAlleleStrings(final VariantContext vc) {
final Map<Allele, String> alleleMap = new HashMap<Allele, String>(vc.getAlleles().size()+1);
alleleMap.put(Allele.NO_CALL, VCFConstants.EMPTY_ALLELE); // convenience for lookup
diff --git a/src/scripts/release_picard.sh b/src/scripts/release_picard.sh
index 340a0d2..1689299 100755
--- a/src/scripts/release_picard.sh
+++ b/src/scripts/release_picard.sh
@@ -32,7 +32,7 @@ function usage () {
}
function branch_exists() {
- if svn info $1 2>&1 | fgrep -q 'Not a valid URL'
+ if svn info $1 2>&1 | egrep -q '(Not a valid URL)|(non-existent in revision)'
then return 1
else return 0
fi
@@ -93,7 +93,8 @@ then echo "$TMPDIR/Picard-public already exists. Please remove or specify a dif
exit 1
fi
-svn --username $USERNAME copy -m "Release $RELEASE_ID" $SVNROOT/trunk $SVNROOT/branches/$RELEASE_ID
+# NB: do not copy the trunk to branches, as we already are copying it to tags.
+#svn --username $USERNAME copy -m "Release $RELEASE_ID" $SVNROOT/trunk $SVNROOT/branches/$RELEASE_ID
svn --username $USERNAME copy -m "Release $RELEASE_ID" $SVNROOT/trunk $SVNROOT/tags/$RELEASE_ID
cd $TMPDIR
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC.sam b/src/tests/java/net/sf/picard/fastq/.gitignore
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC.sam
rename to src/tests/java/net/sf/picard/fastq/.gitignore
diff --git a/src/tests/java/net/sf/picard/illumina/CheckIlluminaDirectoryTest.java b/src/tests/java/net/sf/picard/illumina/CheckIlluminaDirectoryTest.java
index 20b9404..bb9cef5 100644
--- a/src/tests/java/net/sf/picard/illumina/CheckIlluminaDirectoryTest.java
+++ b/src/tests/java/net/sf/picard/illumina/CheckIlluminaDirectoryTest.java
@@ -7,6 +7,7 @@ import net.sf.picard.illumina.parser.IlluminaFileUtil;
import net.sf.picard.illumina.parser.IlluminaFileUtilTest;
import net.sf.picard.io.IoUtil;
import net.sf.samtools.util.CloserUtil;
+import org.broad.tribble.index.Index;
import org.testng.Assert;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeMethod;
@@ -26,14 +27,9 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import static net.sf.picard.illumina.parser.IlluminaDataType.BaseCalls;
-import static net.sf.picard.illumina.parser.IlluminaDataType.Noise;
+import static net.sf.picard.illumina.parser.IlluminaDataType.*;
import static net.sf.picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat;
-import static net.sf.picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat.Bcl;
-import static net.sf.picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat.Filter;
-import static net.sf.picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat.Locs;
-import static net.sf.picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat.Pos;
-import static net.sf.picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat.Qseq;
+import static net.sf.picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat.*;
import static net.sf.samtools.util.CollectionUtil.makeList;
@@ -78,26 +74,27 @@ public class CheckIlluminaDirectoryTest {
public void makeFiles(final SupportedIlluminaFormat[] formats, final int lane, final List<Integer> tiles,
final int[] cycles) {
for (final IlluminaFileUtil.SupportedIlluminaFormat format : formats) {
- IlluminaFileUtilTest.makeFiles(format, intensityDir, lane, tiles, cycles, 0);
+ IlluminaFileUtilTest.makeFiles(format, intensityDir, lane, tiles, cycles);
}
}
public String[] makeCheckerArgs(final File basecallDir, final int lane, final String readStructure,
final IlluminaDataType[] dataTypes, final List<Integer> filterTiles,
- final boolean makeFakeFiles) {
- final String[] dataTypeArgs = new String[dataTypes.length + filterTiles.size() + 4];
+ final boolean makeFakeFiles, final boolean createSymLinks) {
+ final String[] dataTypeArgs = new String[dataTypes.length + filterTiles.size() + 5];
dataTypeArgs[0] = "B=" + basecallDir;
dataTypeArgs[1] = StandardOptionDefinitions.LANE_SHORT_NAME + "=" + lane;
dataTypeArgs[2] = "RS=" + readStructure;
dataTypeArgs[3] = "F=" + makeFakeFiles;
+ dataTypeArgs[4] = "X=" + createSymLinks;
for (int i = 0; i < dataTypes.length; i++) {
- dataTypeArgs[i + 4] = "DT=" + dataTypes[i];
+ dataTypeArgs[i + 5] = "DT=" + dataTypes[i];
}
if (filterTiles.size() > 0) {
- final int start = dataTypes.length + 4;
+ final int start = dataTypes.length + 5;
for (int i = start; i < dataTypeArgs.length; i++) {
dataTypeArgs[i] = "T=" + filterTiles.get(i - start);
}
@@ -177,7 +174,7 @@ public class CheckIlluminaDirectoryTest {
public Object[][] positiveTestData() {
return new Object[][]{
{
- new SupportedIlluminaFormat[]{Bcl, Locs, Pos, Filter, Qseq},
+ new SupportedIlluminaFormat[]{Bcl, Locs, Pos, Filter},
new IlluminaDataType[]{BaseCalls, IlluminaDataType.QualityScores, IlluminaDataType.Position,
IlluminaDataType.PF},
3, makeList(1101, 1201, 1301, 2101, 2201, 2301), IlluminaFileUtilTest.cycleRange(1, 50),
@@ -228,7 +225,7 @@ public class CheckIlluminaDirectoryTest {
writeTileMetricsOutFile(makeMap(makeList(lane - 1, lane + 1, lane),
makeList(makeList(1, 2, 3), tiles, tiles)));
- final String[] args = makeCheckerArgs(basecallDir, lane, readStructure, dataTypes, filterTiles, false);
+ final String[] args = makeCheckerArgs(basecallDir, lane, readStructure, dataTypes, filterTiles, false, false);
final int result = new CheckIlluminaDirectory().instanceMain(args);
Assert.assertEquals(result, 0);
}
@@ -239,13 +236,12 @@ public class CheckIlluminaDirectoryTest {
{ //Completely missing data types
new SupportedIlluminaFormat[]{Bcl, Filter},
new IlluminaDataType[]{BaseCalls, IlluminaDataType.QualityScores, IlluminaDataType.PF,
- IlluminaDataType.Position, IlluminaDataType.RawIntensities, IlluminaDataType.Barcodes,
- Noise},
+ IlluminaDataType.Position, IlluminaDataType.Barcodes},
new ArrayList<String>(),
new ArrayList<String>(),
2, makeList(1101, 1201, 1301, 2101, 2201, 2301), IlluminaFileUtilTest.cycleRange(1, 152),
"68T8B68T",
- 4, new ArrayList<Integer>(), true
+ 2, new ArrayList<Integer>(), true
},
{
new SupportedIlluminaFormat[]{Bcl, Filter},
@@ -293,7 +289,8 @@ public class CheckIlluminaDirectoryTest {
IlluminaFileUtilTest.emptyRelativeFiles(intensityDir, filesToEmpty);
writeTileMetricsOutFile(makeMap(makeList(lane - 1, lane + 1, lane), makeList(makeList(1, 2, 3), tiles, tiles)));
- final String[] args = makeCheckerArgs(basecallDir, lane, readStructure, dataTypes, filterTiles, makeFakeFiles);
+ final String[] args =
+ makeCheckerArgs(basecallDir, lane, readStructure, dataTypes, filterTiles, makeFakeFiles, false);
int result = new CheckIlluminaDirectory().instanceMain(args);
Assert.assertEquals(expectedNumErrors, result);
//if we previously faked files make sure CheckIlluminaDirectory returns with no failures
@@ -337,7 +334,8 @@ public class CheckIlluminaDirectoryTest {
final File cycleDir = new File(basecallDir, "L005/C9.1");
writeFileOfSize(new File(cycleDir, "s_5_3.bcl"), 222);
- final String[] args = makeCheckerArgs(basecallDir, lane, "50T", dataTypes, new ArrayList<Integer>(), false);
+ final String[] args =
+ makeCheckerArgs(basecallDir, lane, "50T", dataTypes, new ArrayList<Integer>(), false, false);
final int result = new CheckIlluminaDirectory().instanceMain(args);
Assert.assertEquals(1, result);
}
@@ -346,35 +344,45 @@ public class CheckIlluminaDirectoryTest {
public void basedirDoesntExistTest() {
final String[] args = makeCheckerArgs(new File("a_made_up_file/in_some_weird_location"), 1, "76T76T",
new IlluminaDataType[]{IlluminaDataType.Position},
- new ArrayList<Integer>(), false);
+ new ArrayList<Integer>(), false, false);
final int result = new CheckIlluminaDirectory().instanceMain(args);
}
@Test
- public void qseqTest() {
- final IlluminaDataType[] dataTypes =
- new IlluminaDataType[]{BaseCalls, IlluminaDataType.QualityScores, IlluminaDataType.PF,
- IlluminaDataType.Position};
- final int lane = 4;
- final List<Integer> tiles = makeList(1, 2, 3);
-
- IoUtil.copyDirectoryTree(new File("testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir"), basecallDir);
- writeTileMetricsOutFile(makeMap(makeList(lane), makeList(tiles)));
-
- String[] args = makeCheckerArgs(basecallDir, lane, "76T76T", dataTypes, new ArrayList<Integer>(),
- false);
+ public void symlinkLocsTest() {
+ final List<Integer> tileList = makeList(1101, 1102, 1103, 2101, 2102, 2103);
+ final int lane = 5;
+ makeFiles(new SupportedIlluminaFormat[]{Bcl}, lane, tileList, IlluminaFileUtilTest.cycleRange(1, 50));
+ String[] args =
+ makeCheckerArgs(basecallDir, lane, "50T", new IlluminaDataType[]{Position}, new ArrayList<Integer>(),
+ false,
+ true);
+ writeTileMetricsOutFile(makeMap(makeList(lane), makeList(tileList)));
+
+ createSingleLocsFile();
+ final File intensityLaneDir = new File(intensityDir, IlluminaFileUtil.longLaneStr(lane));
+ intensityLaneDir.mkdirs();
int result = new CheckIlluminaDirectory().instanceMain(args);
Assert.assertEquals(result, 0);
+ //now that we have created the loc files lets test to make sure they are there
+ args = makeCheckerArgs(basecallDir, lane, "50T", new IlluminaDataType[]{IlluminaDataType.Position},
+ new ArrayList<Integer>(), false,
+ true);
- args = makeCheckerArgs(basecallDir, lane, "76T77T", dataTypes, new ArrayList<Integer>(), false);
result = new CheckIlluminaDirectory().instanceMain(args);
- Assert.assertEquals(result, 1);
+ Assert.assertEquals(result, 0);
+ }
- IlluminaFileUtilTest.deleteRelativeFiles(basecallDir, makeList("s_4_1_0002_qseq.txt"));
+ private void createSingleLocsFile() {
+ try {
+ final File singleLocsFile = new File(intensityDir, "s.locs");
+ final FileWriter writer = new FileWriter(singleLocsFile);
+ writer.write("This is a test string.");
+ writer.close();
+ } catch (final IOException e) {
+ e.printStackTrace();
+ }
- args = makeCheckerArgs(basecallDir, lane, "76T76T", dataTypes, new ArrayList<Integer>(), false);
- result = new CheckIlluminaDirectory().instanceMain(args);
- Assert.assertEquals(result, 1);
}
}
diff --git a/src/tests/java/net/sf/picard/illumina/ExtractIlluminaBarcodesTest.java b/src/tests/java/net/sf/picard/illumina/ExtractIlluminaBarcodesTest.java
index d1bdcbd..dd71d57 100644
--- a/src/tests/java/net/sf/picard/illumina/ExtractIlluminaBarcodesTest.java
+++ b/src/tests/java/net/sf/picard/illumina/ExtractIlluminaBarcodesTest.java
@@ -45,19 +45,22 @@ import net.sf.picard.illumina.parser.*;
* @author alecw at broadinstitute.org
*/
public class ExtractIlluminaBarcodesTest {
- private static final File TEST_DATA_DIR = new File("testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes");
+ private static final File SINGLE_DATA_DIR = new File("testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls");
+ private static final File DUAL_DATA_DIR = new File("testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls");
private static final String[] BARCODES = {
- "ACAGTG",
- "ACAGTT", // This one is artificial -- one edit away from the first one
- "ACTTGA",
- "ATCACG",
- "CAGATC",
- "CGATGT",
- "CTTGTA",
- "GATCAG",
- "GCCAAT",
- "TAGCTT",
- "TGACCA"
+ "CAACTCTC",
+ "CAACTCTG", // This one is artificial -- one edit away from the first one
+ "ACAGGTAT",
+ "GACCGTTG",
+ "ATTATCAA",
+ "TGCTGCTG",
+ "AACAATGG",
+ "TGTAATCA",
+ "GCCGTCGA",
+ "GTCCACAG",
+ "TTGTCTAT",
+ "GTGGAGAC",
+ "TTGCAAAT"
};
private File basecallsDir;
@@ -69,33 +72,15 @@ public class ExtractIlluminaBarcodesTest {
basecallsDir = File.createTempFile("eib.", ".tmp");
Assert.assertTrue(basecallsDir.delete());
Assert.assertTrue(basecallsDir.mkdir());
- for (final File source : TEST_DATA_DIR.listFiles()) {
- if (!source.isFile()) {
- continue;
- }
- final File dest = new File(basecallsDir, source.getName());
- IoUtil.copyFile(source, dest);
- }
+ IoUtil.copyDirectoryTree(SINGLE_DATA_DIR, basecallsDir);
dual = File.createTempFile("eib_dual", ".tmp");
Assert.assertTrue(dual.delete());
Assert.assertTrue(dual.mkdir());
- for (final File source : new File(TEST_DATA_DIR, "dual").listFiles()) {
- if (!source.isFile()) {
- continue;
- }
- final File dest = new File(dual, source.getName());
- IoUtil.copyFile(source, dest);
- }
+ IoUtil.copyDirectoryTree(DUAL_DATA_DIR, dual);
qual = File.createTempFile("eib_qual", ".tmp");
Assert.assertTrue(qual.delete());
Assert.assertTrue(qual.mkdir());
- for (final File source : new File(TEST_DATA_DIR, "qual").listFiles()) {
- if (!source.isFile()) {
- continue;
- }
- final File dest = new File(qual, source.getName());
- IoUtil.copyFile(source, dest);
- }
+ IoUtil.copyDirectoryTree(DUAL_DATA_DIR, qual);
}
@AfterTest
@@ -107,50 +92,55 @@ public class ExtractIlluminaBarcodesTest {
@Test
public void testSingleEndWithBarcodeAtStart() throws Exception {
- final MetricsFile<ExtractIlluminaBarcodes.BarcodeMetric, Integer> metricsFile = runIt(1, "6B36T");
- Assert.assertEquals(metricsFile.getMetrics().get(0).PERFECT_MATCHES, 1);
+ final MetricsFile<ExtractIlluminaBarcodes.BarcodeMetric, Integer> metricsFile = runIt(1, "8B25T");
+ Assert.assertEquals(metricsFile.getMetrics().get(11).PERFECT_MATCHES, 1);
}
@Test
public void testSingleEndWithBarcodeAtEnd() throws Exception {
- final MetricsFile<ExtractIlluminaBarcodes.BarcodeMetric, Integer> metricsFile = runIt(2, "36T6B");
- Assert.assertEquals(metricsFile.getMetrics().get(0).PERFECT_MATCHES, 1);
+ final MetricsFile<ExtractIlluminaBarcodes.BarcodeMetric, Integer> metricsFile = runIt(1, "25T8B");
+ Assert.assertEquals(metricsFile.getMetrics().get(0).PERFECT_MATCHES, 5);
}
@Test
public void testPairedEndWithBarcodeOnFirstEnd() throws Exception {
- final MetricsFile<ExtractIlluminaBarcodes.BarcodeMetric, Integer> metricsFile = runIt(3, "36T6B36T");
- Assert.assertEquals(metricsFile.getMetrics().get(0).PERFECT_MATCHES, 1);
+ final MetricsFile<ExtractIlluminaBarcodes.BarcodeMetric, Integer> metricsFile = runIt(1, "25T8B25T");
+ Assert.assertEquals(metricsFile.getMetrics().get(0).PERFECT_MATCHES, 5);
}
@Test
public void testPairedEndWithBarcodeOnSecondEnd() throws Exception {
- final MetricsFile<ExtractIlluminaBarcodes.BarcodeMetric, Integer> metricsFile = runIt(4, "36T36T6B");
- Assert.assertEquals(metricsFile.getMetrics().get(0).PERFECT_MATCHES, 1);
+ final MetricsFile<ExtractIlluminaBarcodes.BarcodeMetric, Integer> metricsFile = runIt(1, "25T25T8B");
+ Assert.assertEquals(metricsFile.getMetrics().get(12).PERFECT_MATCHES, 1);
}
@Test
public void testNonWritableOutputFile() throws Exception {
- final File existingFile = new File(basecallsDir, "s_1_0001_barcode.txt.gz");
- existingFile.createNewFile();
- existingFile.setReadOnly();
- final String readStructure = "6B36T";
- final int lane = 1;
-
- final File metricsFile = File.createTempFile("eib.", ".metrics");
- metricsFile.deleteOnExit();
-
- final List<String> args = new ArrayList<String>(Arrays.asList(
- "BASECALLS_DIR=" + basecallsDir.getPath(),
- "LANE=" + lane,
- "READ_STRUCTURE=" + readStructure,
- "METRICS_FILE=" + metricsFile.getPath(),
- "COMPRESS_OUTPUTS=true"
- ));
- for (final String barcode : BARCODES) {
- args.add("BARCODE=" + barcode);
+ final File existingFile = new File(basecallsDir, "s_1_1101_barcode.txt.gz");
+ try {
+ existingFile.setReadOnly();
+ final String readStructure = "25T8B25T";
+ final int lane = 1;
+
+ final File metricsFile = File.createTempFile("eib.", ".metrics");
+ metricsFile.deleteOnExit();
+
+ final List<String> args = new ArrayList<String>(Arrays.asList(
+ "BASECALLS_DIR=" + basecallsDir.getPath(),
+ "LANE=" + lane,
+ "READ_STRUCTURE=" + readStructure,
+ "METRICS_FILE=" + metricsFile.getPath(),
+ "COMPRESS_OUTPUTS=true"
+ ));
+ for (final String barcode : BARCODES) {
+ args.add("BARCODE=" + barcode);
+ }
+ Assert.assertEquals(new ExtractIlluminaBarcodes().instanceMain(args.toArray(new String[args.size()])), 4);
}
- Assert.assertEquals(new ExtractIlluminaBarcodes().instanceMain(args.toArray(new String[args.size()])), 4);
+ finally {
+ existingFile.setWritable(true);
+ }
+
}
/**
@@ -163,40 +153,33 @@ public class ExtractIlluminaBarcodesTest {
*/
@Test
public void testBarcodeMatching() throws Exception {
- final int lane = 5;
- final int barcodePosition = 37;
- final MetricsFile<ExtractIlluminaBarcodes.BarcodeMetric, Integer> metricsFile = runIt(lane, "36T6B");
+ final int lane = 1;
+ final int barcodePosition = 26;
+ final MetricsFile<ExtractIlluminaBarcodes.BarcodeMetric, Integer> metricsFile = runIt(lane, "25T8B25T");
- ExtractIlluminaBarcodes.BarcodeMetric metricACAGTG = null;
- ExtractIlluminaBarcodes.BarcodeMetric metricTGACCA = null;
+ ExtractIlluminaBarcodes.BarcodeMetric metricOne = null;
+ ExtractIlluminaBarcodes.BarcodeMetric metricTwo = null;
ExtractIlluminaBarcodes.BarcodeMetric metricNoMatch = null;
for (final ExtractIlluminaBarcodes.BarcodeMetric metric : metricsFile.getMetrics()) {
- if (metric.BARCODE.equals("ACAGTG")) {
- metricACAGTG = metric;
- } else if (metric.BARCODE.equals("TGACCA")) {
- metricTGACCA = metric;
- } else if (metric.BARCODE.equals("NNNNNN")) {
+ if (metric.BARCODE.equals(BARCODES[0])) {
+ metricOne = metric;
+ } else if (metric.BARCODE.equals(BARCODES[2])) {
+ metricTwo = metric;
+ } else if (metric.BARCODE.equals("NNNNNNNN")) {
metricNoMatch = metric;
}
}
- Assert.assertEquals(metricACAGTG.PERFECT_MATCHES, 1);
- Assert.assertEquals(metricACAGTG.ONE_MISMATCH_MATCHES, 0);
- Assert.assertEquals(metricACAGTG.PF_READS, 1);
- Assert.assertEquals(metricACAGTG.READS, 1);
-
- for (final ExtractIlluminaBarcodes.BarcodeMetric metric : metricsFile.getMetrics()) {
- if (metric == metricACAGTG || metric == metricTGACCA || metric == metricNoMatch) {
- continue;
- }
- Assert.assertEquals(metric.READS, 0);
- }
+ Assert.assertEquals(metricOne.PERFECT_MATCHES, 5);
+ Assert.assertEquals(metricOne.ONE_MISMATCH_MATCHES, 0);
+ Assert.assertEquals(metricOne.PF_READS, 3);
+ Assert.assertEquals(metricOne.READS, 5);
// one inexact match
- Assert.assertEquals(metricTGACCA.READS, 1);
- Assert.assertEquals(metricTGACCA.ONE_MISMATCH_MATCHES, 1);
+ Assert.assertEquals(metricTwo.READS, 4);
+ Assert.assertEquals(metricTwo.ONE_MISMATCH_MATCHES, 0);
- Assert.assertEquals(metricNoMatch.READS, 2);
- Assert.assertEquals(metricNoMatch.PF_READS, 1);
+ Assert.assertEquals(metricNoMatch.READS, 140);
+ Assert.assertEquals(metricNoMatch.PF_READS, 112);
// Check the barcode files themselves
final File[] barcodeFiles = IoUtil.getFilesMatchingRegexp(basecallsDir, "s_" + lane + "_\\d{4}_barcode.txt");
@@ -207,69 +190,53 @@ public class ExtractIlluminaBarcodesTest {
// Exact match
String[] illuminaFields = barcodeParser.next();
Assert.assertEquals(illuminaFields[1], "Y");
- Assert.assertEquals(illuminaFields[2], "ACAGTG");
+ Assert.assertEquals(illuminaFields[2], "CAACTCTC");
// Inexact match
illuminaFields = barcodeParser.next();
Assert.assertEquals(illuminaFields[1], "Y");
- Assert.assertEquals(illuminaFields[2], "TGACCA");
+ Assert.assertEquals(illuminaFields[2], "ACAGGTAT");
// Too many mismatches
illuminaFields = barcodeParser.next();
Assert.assertEquals(illuminaFields[1], "N");
- // Next match too close
- illuminaFields = barcodeParser.next();
- Assert.assertEquals(illuminaFields[1], "N");
-
- Assert.assertFalse(barcodeParser.hasNext());
barcodeParser.close();
// Tack on test of barcode-informed Illumina Basecall parsing
- final ReadStructure rs = new ReadStructure("36T6B");
- final IlluminaDataProviderFactory factory = new IlluminaDataProviderFactory(basecallsDir, lane, rs,
+ final ReadStructure rs = new ReadStructure("25T8B25T");
+ final IlluminaDataProviderFactory factory = new IlluminaDataProviderFactory(basecallsDir, lane, rs,
new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY),
IlluminaDataType.BaseCalls, IlluminaDataType.QualityScores, IlluminaDataType.Barcodes);
- testParsing(factory, rs, metricACAGTG, barcodePosition);
+ testParsing(factory, rs, metricOne, barcodePosition);
}
- @Test(dataProvider = "dualBarcodeData")
- public void testDualBarcodes(final int lane, final String readStructure, final int perfectMatches, final int oneMismatchMatches,
- final String testName) throws Exception {
+ @Test
+ public void testDualBarcodes() throws Exception {
final File metricsFile = File.createTempFile("dual.", ".metrics");
metricsFile.deleteOnExit();
final List<String> args = new ArrayList<String>(Arrays.asList(
"BASECALLS_DIR=" + dual.getAbsolutePath(),
- "LANE=" + lane,
- "BARCODE_FILE=" + new File(dual, "barcodeData." + lane).getAbsolutePath(),
+ "LANE=" + 1,
"METRICS_FILE=" + metricsFile.getPath(),
- "READ_STRUCTURE=" + readStructure
+ "READ_STRUCTURE=" + "25T8B8B25T"
));
+ args.add("BARCODE=" + "CAATAGTCCGACTCTC");
+
Assert.assertEquals(new ExtractIlluminaBarcodes().instanceMain(args.toArray(new String[args.size()])), 0);
final MetricsFile<ExtractIlluminaBarcodes.BarcodeMetric,Integer> result = new MetricsFile<ExtractIlluminaBarcodes.BarcodeMetric,Integer>();
result.read(new FileReader(metricsFile));
- Assert.assertEquals(result.getMetrics().get(0).PERFECT_MATCHES, perfectMatches, "Got wrong number of perfect matches");
- Assert.assertEquals(result.getMetrics().get(0).ONE_MISMATCH_MATCHES, oneMismatchMatches, "Got wrong number of one-mismatch matches");
- }
-
- @DataProvider(name = "dualBarcodeData")
- public Object[][] getDualBarcodeTestData() {
- return new Object[][] {
- {4, "10T8B6B10T", 3, 2, "Two barcodes in the middle, but one read is shorter than the barcode in the file"},
- {5, "10T8B6B2S10T", 3, 2, "Two barcodes in the middle, but one is shorter than the read lengths"},
- {6, "10T8B8B10T", 1, 2, "Two barcodes in the middle"},
- {7, "8B10T10T8B", 1, 2, "Two barcodes on either end"},
- {8, "4B10T4B4B10T4B", 1, 2, "Four crazy barcodes, one on either end and two in the middle"}
- };
+ Assert.assertEquals(result.getMetrics().get(0).PERFECT_MATCHES, 1, "Got wrong number of perfect matches");
+ Assert.assertEquals(result.getMetrics().get(0).ONE_MISMATCH_MATCHES, 0, "Got wrong number of one-mismatch matches");
}
/**
* Testing the quality thresholding. Looking at a single barcode (ACAGTG) with a min quality of 25 and no mismatches
*/
@Test(dataProvider = "qualityBarcodeData")
- public void testQualityBarcodes(final int lane, final String readStructure, final String barcode, final int quality,
+ public void testQualityBarcodes(final int quality,
final int maxMismatches, final int perfectMatches, final int oneMismatch,
final String testName) throws Exception {
final File metricsFile = File.createTempFile("qual.", ".metrics");
@@ -277,12 +244,12 @@ public class ExtractIlluminaBarcodesTest {
final List<String> args = new ArrayList<String>(Arrays.asList(
"BASECALLS_DIR=" + qual.getPath(),
- "LANE=" + lane,
- "READ_STRUCTURE=" + readStructure,
+ "LANE=" + 1,
+ "READ_STRUCTURE=25T8B25T",
"METRICS_FILE=" + metricsFile.getPath(),
"MINIMUM_BASE_QUALITY=" + quality,
"MAX_MISMATCHES=" + maxMismatches,
- "BARCODE=" + barcode
+ "BARCODE=CAATAGTC"
));
Assert.assertEquals(new ExtractIlluminaBarcodes().instanceMain(args.toArray(new String[args.size()])), 0);
@@ -295,11 +262,8 @@ public class ExtractIlluminaBarcodesTest {
@DataProvider(name = "qualityBarcodeData")
public Object[][] getQualityTestData() {
return new Object[][] {
- {1, "6B36T", "ACAGTG", 25, 0, 1, 0, "Barcode has good quality, 1 match"},
- {2, "6B36T", "ACAGTG", 25, 0, 0, 0, "Barcode has quality failures, no matches"},
- {3, "6B36T", "ACAGTG", 25, 0, 0, 0, "Barcode has one low quality, no matches"},
- {4, "36T6B", "ACAGTG", 25, 0, 0, 0, "Barcode at end, quality failures, no matches"},
- {5, "6B36T", "ACAGTG", 25, 1, 0, 1, "Barcode has 1 low quality, 1 mismatch allowed, 1 match"}
+ {16, 0, 1, 0, "Barcode has good quality, 1 match"},
+ {25, 0, 0, 0, "Barcode has quality failures, no matches"}
};
}
@@ -319,6 +283,7 @@ public class ExtractIlluminaBarcodesTest {
Assert.assertEquals(cluster.getRead(readStructure.templates.getIndices()[0]).getBases().length, barcodePosition - 1);
}
Assert.assertEquals(numReads, metricACAGTG.READS);
+ dataProvider.close();
}
private MetricsFile<ExtractIlluminaBarcodes.BarcodeMetric, Integer> runIt(final int lane, final String readStructure)
diff --git a/src/tests/java/net/sf/picard/illumina/IlluminaBasecallsToFastqTest.java b/src/tests/java/net/sf/picard/illumina/IlluminaBasecallsToFastqTest.java
index d20c8ec..1ffe88c 100644
--- a/src/tests/java/net/sf/picard/illumina/IlluminaBasecallsToFastqTest.java
+++ b/src/tests/java/net/sf/picard/illumina/IlluminaBasecallsToFastqTest.java
@@ -40,8 +40,10 @@ import java.util.List;
public class IlluminaBasecallsToFastqTest {
- private static final File BASECALLS_DIR = new File("testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir");
- private static final File TEST_DATA_DIR = new File("testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest");
+ private static final File BASECALLS_DIR = new File("testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls");
+ private static final File DUAL_BASECALLS_DIR = new File("testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls");
+ private static final File TEST_DATA_DIR = new File("testdata/net/sf/picard/illumina/25T8B25T/fastq");
+ private static final File DUAL_TEST_DATA_DIR = new File("testdata/net/sf/picard/illumina/25T8B8B25T/fastq");
@Test
public void testNonBarcoded() throws Exception {
@@ -55,7 +57,7 @@ public class IlluminaBasecallsToFastqTest {
new IlluminaBasecallsToFastq().instanceMain(new String[]{
"BASECALLS_DIR=" + BASECALLS_DIR,
"LANE=" + lane,
- "READ_STRUCTURE=76T76T",
+ "READ_STRUCTURE=25T8B25T",
"OUTPUT_PREFIX=" + outputPrefix,
"RUN_BARCODE=HiMom",
"MACHINE_NAME=machine1",
@@ -67,20 +69,20 @@ public class IlluminaBasecallsToFastqTest {
@Test
public void testMultiplexWithIlluminaReadNameHeaders() throws Exception {
- final File outputDir = File.createTempFile("testMultiplex.", ".dir");
+ final File outputDir = File.createTempFile("testMultiplexRH.", ".dir");
try {
outputDir.delete();
outputDir.mkdir();
outputDir.deleteOnExit();
- final String filePrefix = "testMultiplex";
+ final String filePrefix = "testMultiplexRH";
final File outputPrefix = new File(outputDir, filePrefix);
new IlluminaBasecallsToFastq().instanceMain(new String[]{
"BASECALLS_DIR=" + BASECALLS_DIR,
- "LANE=" + 7,
+ "LANE=" + 1,
"RUN_BARCODE=HiMom",
- "READ_STRUCTURE=" + "30T8B",
+ "READ_STRUCTURE=" + "25T8B25T",
"OUTPUT_PREFIX=" + outputPrefix.getAbsolutePath(),
"MACHINE_NAME=machine1",
"FLOWCELL_BARCODE=abcdeACXX",
@@ -102,12 +104,12 @@ public class IlluminaBasecallsToFastqTest {
@Test
public void testDeMultiplexed() throws Exception {
- runStandardTest(7, "multiplexedBarcode.", "barcode.params", 1, "30T8B");
+ runStandardTest(1, "multiplexedBarcode.", "mp_barcode.params", 1, "25T8B25T", BASECALLS_DIR, TEST_DATA_DIR);
}
@Test
public void testDualBarcodes() throws Exception {
- runStandardTest(9, "dualBarcode.", "barcode_double.params", 2, "30T8B8B");
+ runStandardTest(1, "dualBarcode.", "barcode_double.params", 2, "25T8B8B25T", DUAL_BASECALLS_DIR, DUAL_TEST_DATA_DIR);
}
/**
@@ -121,7 +123,8 @@ public class IlluminaBasecallsToFastqTest {
* @throws Exception
*/
private void runStandardTest(final int lane, final String jobName, final String libraryParamsFile,
- final int concatNColumnFields, final String readStructureString) throws Exception {
+ final int concatNColumnFields, final String readStructureString, final File baseCallsDir,
+ final File testDataDir) throws Exception {
final File outputDir = File.createTempFile(jobName, ".dir");
try {
outputDir.delete();
@@ -131,7 +134,7 @@ public class IlluminaBasecallsToFastqTest {
final File libraryParams = new File(outputDir, libraryParamsFile);
libraryParams.deleteOnExit();
final List<File> outputPrefixes = new ArrayList<File>();
- final LineReader reader = new BufferedLineReader(new FileInputStream(new File(TEST_DATA_DIR, libraryParamsFile)));
+ final LineReader reader = new BufferedLineReader(new FileInputStream(new File(testDataDir, libraryParamsFile)));
final PrintWriter writer = new PrintWriter(libraryParams);
final String header = reader.readLine();
writer.println(header + "\tOUTPUT_PREFIX");
@@ -146,9 +149,10 @@ public class IlluminaBasecallsToFastqTest {
writer.println(line + "\t" + outputPrefix);
}
writer.close();
+ reader.close();
new IlluminaBasecallsToFastq().instanceMain(new String[]{
- "BASECALLS_DIR=" + BASECALLS_DIR,
+ "BASECALLS_DIR=" + baseCallsDir,
"LANE=" + lane,
"RUN_BARCODE=HiMom",
"READ_STRUCTURE=" + readStructureString,
@@ -161,11 +165,11 @@ public class IlluminaBasecallsToFastqTest {
for (final File outputSam : outputPrefixes) {
for (int i = 1; i <= readStructure.templates.length(); ++i) {
String filename = outputSam.getName() + "." + i + ".fastq";
- IoUtil.assertFilesEqual(new File(outputSam.getParentFile(), filename), new File(TEST_DATA_DIR, filename));
+ IoUtil.assertFilesEqual(new File(outputSam.getParentFile(), filename), new File(testDataDir, filename));
}
for (int i = 1; i <= readStructure.barcodes.length(); ++i) {
String filename = outputSam.getName() + ".barcode_" + i + ".fastq";
- IoUtil.assertFilesEqual(new File(outputSam.getParentFile(), filename), new File(TEST_DATA_DIR, filename));
+ IoUtil.assertFilesEqual(new File(outputSam.getParentFile(), filename), new File(testDataDir, filename));
}
}
} finally {
diff --git a/src/tests/java/net/sf/picard/illumina/IlluminaBasecallsToSamAdapterClippingTest.java b/src/tests/java/net/sf/picard/illumina/IlluminaBasecallsToSamAdapterClippingTest.java
index fdfa647..4c2a863 100644
--- a/src/tests/java/net/sf/picard/illumina/IlluminaBasecallsToSamAdapterClippingTest.java
+++ b/src/tests/java/net/sf/picard/illumina/IlluminaBasecallsToSamAdapterClippingTest.java
@@ -37,27 +37,25 @@ import java.io.File;
*/
public class IlluminaBasecallsToSamAdapterClippingTest {
- private static final File TEST_DATA_DIR = new File("testdata/net/sf/picard/illumina");
- //private static final File SEQUENCE_DICTIONARY = new File(TEST_DATA_DIR, "Homo_sapiens_assembly18.seqdict.sam");
+ private static final File TEST_DATA_DIR = new File("testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls");
private static final String ALIAS = "myalias";
private static final String RUN_BARCODE = "305PJAAXX080716";
- private static final String READ_GROUP_NAME = "0";
/**
* Run IlluminaBasecallsToSam on a few test cases, and verify that results agree with hand-checked expectation.
*/
@Test(dataProvider="data")
- public void testBasic(String LANE, String readStructure) throws Exception {
+ public void testBasic(final String LANE, final String readStructure) throws Exception {
// Create the SAM file from Gerald output
final File samFile = File.createTempFile("." + LANE + ".illuminaBasecallsToSam", ".sam");
samFile.deleteOnExit();
final String[] illuminaArgv = {
- "BASECALLS_DIR=" + TEST_DATA_DIR + "/IlluminaTests/BasecallsDir",
+ "BASECALLS_DIR=" + TEST_DATA_DIR,
"LANE=" + LANE,
"RUN_BARCODE=" + RUN_BARCODE,
"READ_STRUCTURE=" + readStructure,
"OUTPUT=" + samFile,
- "ALIAS=" + ALIAS,
+ "ALIAS=" + ALIAS
};
Assert.assertEquals(new IlluminaBasecallsToSam().instanceMain(illuminaArgv), 0);
@@ -68,32 +66,26 @@ public class IlluminaBasecallsToSamAdapterClippingTest {
// look for clipped adaptor attribute in lane 3 PE (2) and in lane 6 (1) non-PE
int count = 0; int matchCount = 0;
- for (SAMRecord record : samReader) {
+ for (final SAMRecord record : samReader) {
if (record.getIntegerAttribute(ReservedTagConstants.XT) != null) {
count ++;
- if ((count == 1 || count ==2) && LANE.equals("3")){
- Assert.assertEquals (65, (int)record.getIntegerAttribute(ReservedTagConstants.XT));
+ if ((count == 1 || count == 2) && LANE.equals("2")){
+ Assert.assertEquals (114, (int)record.getIntegerAttribute(ReservedTagConstants.XT));
matchCount++;
- } else if (count == 1 && LANE.equals("6")){
- Assert.assertEquals (141, (int)record.getIntegerAttribute(ReservedTagConstants.XT));
+ } else if (count == 1 || count == 2 && LANE.equals("1")) {
+ Assert.assertEquals(68, (int) record.getIntegerAttribute(ReservedTagConstants.XT));
matchCount++;
- } else {
- Assert.assertTrue(false, "Lane:" + LANE + " " + count +
- " Unexpected adapter trim " + record.getIntegerAttribute(ReservedTagConstants.XT) +
- " count=" + count + " matchCount=" + matchCount +
- " at record " + record);
}
}
}
+ samReader.close();
}
@DataProvider(name="data")
private Object[][] getIlluminaBasecallsToSamTestData(){
return new Object[][] {
- {"1", "76T76T"},
- {"2", "76T"},
- {"4", "76T76T"},
- {"5", "76T"},
+ {"1", "125T125T"},
+ {"2", "125T125T"},
};
}
diff --git a/src/tests/java/net/sf/picard/illumina/IlluminaBasecallsToSamTest.java b/src/tests/java/net/sf/picard/illumina/IlluminaBasecallsToSamTest.java
index 12e7180..b1d2c0f 100644
--- a/src/tests/java/net/sf/picard/illumina/IlluminaBasecallsToSamTest.java
+++ b/src/tests/java/net/sf/picard/illumina/IlluminaBasecallsToSamTest.java
@@ -44,9 +44,10 @@ import java.util.List;
*/
public class IlluminaBasecallsToSamTest {
- private static final File BASECALLS_DIR = new File("testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir");
- private static final File TEST_DATA_DIR = new File("testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest");
-
+ private static final File BASECALLS_DIR = new File("testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls");
+ private static final File DUAL_BASECALLS_DIR = new File("testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls");
+ private static final File TEST_DATA_DIR = new File("testdata/net/sf/picard/illumina/25T8B25T/sams");
+ private static final File DUAL_TEST_DATA_DIR = new File("testdata/net/sf/picard/illumina/25T8B8B25T/sams");
@Test
public void testTileNumberComparator() {
Assert.assertTrue(IlluminaBasecallsConverter.TILE_NUMBER_COMPARATOR.compare(100, 10) < 0, "");
@@ -54,6 +55,7 @@ public class IlluminaBasecallsToSamTest {
Assert.assertTrue(IlluminaBasecallsConverter.TILE_NUMBER_COMPARATOR.compare(10, 10) == 0, "");
}
+
@Test
public void testNonBarcoded() throws Exception {
final File outputBam = File.createTempFile("nonBarcoded.", ".sam");
@@ -62,7 +64,7 @@ public class IlluminaBasecallsToSamTest {
new IlluminaBasecallsToSam().instanceMain(new String[]{
"BASECALLS_DIR=" + BASECALLS_DIR,
"LANE=" + lane,
- "READ_STRUCTURE=76T76T",
+ "READ_STRUCTURE=25S8S25T",
"OUTPUT=" + outputBam,
"RUN_BARCODE=HiMom",
"SAMPLE_ALIAS=HiDad",
@@ -73,18 +75,18 @@ public class IlluminaBasecallsToSamTest {
@Test
public void testMultiplexed() throws Exception {
- runStandardTest(7, "multiplexedBarcode.", "barcode.params", 1, "30T8B");
+ runStandardTest(1, "multiplexedBarcode.", "barcode.params", 1, "25T8B25T", BASECALLS_DIR, TEST_DATA_DIR);
}
//Same as testMultiplexed except we use BARCODE_1 instead of BARCODE
@Test
public void testMultiplexedWithAlternateBarcodeName() throws Exception {
- runStandardTest(7, "singleBarcodeAltName.", "multiplexed_positive_rgtags.params", 1, "30T8B");
+ runStandardTest(1, "singleBarcodeAltName.", "multiplexed_positive_rgtags.params", 1, "25T8B25T", BASECALLS_DIR, TEST_DATA_DIR);
}
@Test
public void testDualBarcodes() throws Exception {
- runStandardTest(9, "dualBarcode.", "barcode_double.params", 2, "30T8B8B");
+ runStandardTest(1, "dualBarcode.", "barcode_double.params", 1, "25T8B8B25T", DUAL_BASECALLS_DIR, DUAL_TEST_DATA_DIR);
}
/**
@@ -97,7 +99,7 @@ public class IlluminaBasecallsToSamTest {
public void testCorruptDataReturnCode() throws Exception {
boolean exceptionThrown = false;
try {
- runStandardTest(9, "dualBarcode.", "negative_test.params", 2, "30T8B8B");
+ runStandardTest(9, "dualBarcode.", "negative_test.params", 2, "30T8B8B", BASECALLS_DIR, TEST_DATA_DIR);
} catch (Throwable e) {
exceptionThrown = true;
} finally {
@@ -115,7 +117,9 @@ public class IlluminaBasecallsToSamTest {
* @param readStructure
* @throws Exception
*/
- private void runStandardTest(final int lane, final String jobName, final String libraryParamsFile, final int concatNColumnFields, final String readStructure) throws Exception {
+ private void runStandardTest(final int lane, final String jobName, final String libraryParamsFile,
+ final int concatNColumnFields, final String readStructure,
+ final File baseCallsDir, final File testDataDir) throws Exception {
final File outputDir = File.createTempFile(jobName, ".dir");
outputDir.delete();
outputDir.mkdir();
@@ -124,7 +128,7 @@ public class IlluminaBasecallsToSamTest {
final File libraryParams = new File(outputDir, libraryParamsFile);
libraryParams.deleteOnExit();
final List<File> samFiles = new ArrayList<File>();
- final LineReader reader = new BufferedLineReader(new FileInputStream(new File(TEST_DATA_DIR, libraryParamsFile)));
+ final LineReader reader = new BufferedLineReader(new FileInputStream(new File(testDataDir, libraryParamsFile)));
final PrintWriter writer = new PrintWriter(libraryParams);
final String header = reader.readLine();
writer.println(header + "\tOUTPUT");
@@ -140,9 +144,10 @@ public class IlluminaBasecallsToSamTest {
writer.println(line + "\t" + outputSam);
}
writer.close();
+ reader.close();
new IlluminaBasecallsToSam().instanceMain(new String[]{
- "BASECALLS_DIR=" + BASECALLS_DIR,
+ "BASECALLS_DIR=" + baseCallsDir,
"LANE=" + lane,
"RUN_BARCODE=HiMom",
"READ_STRUCTURE=" + readStructure,
@@ -150,7 +155,7 @@ public class IlluminaBasecallsToSamTest {
});
for (final File outputSam : samFiles) {
- IoUtil.assertFilesEqual(outputSam, new File(TEST_DATA_DIR, outputSam.getName()));
+ IoUtil.assertFilesEqual(outputSam, new File(testDataDir, outputSam.getName()));
}
}
}
diff --git a/src/tests/java/net/sf/picard/illumina/parser/BclParserTest.java b/src/tests/java/net/sf/picard/illumina/parser/BclParserTest.java
index 77d594b..7894b8e 100644
--- a/src/tests/java/net/sf/picard/illumina/parser/BclParserTest.java
+++ b/src/tests/java/net/sf/picard/illumina/parser/BclParserTest.java
@@ -1,11 +1,5 @@
package net.sf.picard.illumina.parser;
-import static net.sf.picard.illumina.parser.BinTdUtil.A;
-import static net.sf.picard.illumina.parser.BinTdUtil.C;
-import static net.sf.picard.illumina.parser.BinTdUtil.G;
-import static net.sf.picard.illumina.parser.BinTdUtil.T;
-import static net.sf.picard.illumina.parser.BinTdUtil.P;
-
import net.sf.picard.PicardException;
import net.sf.picard.illumina.parser.readers.BclQualityEvaluationStrategy;
import net.sf.picard.io.IoUtil;
@@ -14,77 +8,140 @@ import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
+import java.util.ArrayList;
import java.util.Arrays;
+import java.util.List;
import java.util.Map;
+import static net.sf.picard.illumina.parser.BinTdUtil.*;
+
public class BclParserTest {
- public static final File TEST_DATA_DIR = new File("testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L003");
- public static final String READ_STRUCTURE = "25T8B25T";
+ public static final File TEST_DATA_DIR = new File("testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001");
+ public static final File MULTI_TILE_DATA_DIR = new File("/seq/tng/jcarey/testdata/NextSeq/Data/Intensities/BaseCalls/L001");
+ public static final String READ_STRUCTURE = "25T8B25T";
public static final String READ_STRUCTURE_WSKIPS = "25S8B25S";
public static final String READ_STRUCTURE_WSKIPS_PARTIAL = "10T5S10T8B5T20S";
- public static final String READ_STRUCTURE_WSKIPS_BAD = "10T5S10T2B4S2B5T20S";
- public static final int [] READ_LENGTHS = new int[]{25,8,25};
- public static final int LANE = 3;
- public static final IlluminaDataType DATA_TYPES [] = {IlluminaDataType.BaseCalls, IlluminaDataType.QualityScores};
- public static final int TILE_SIZES = 20;
-
+ public static final String READ_STRUCTURE_WSKIPS_BAD = "10T5S10T2B4S2B5T20S";
+ public static final int[] READ_LENGTHS = new int[]{25, 8, 25};
+ public static final int LANE = 1;
+ public static final IlluminaDataType DATA_TYPES[] = {IlluminaDataType.BaseCalls, IlluminaDataType.QualityScores};
+ public static final int TILE_SIZES = 60;
- public static CycleIlluminaFileMap makeCycleIlluminaFileMap(final File tdDir, final int [] tiles, final int [] outputCycles) {
- final CycleIlluminaFileMap fileMap = new CycleIlluminaFileMap();
-
- for(final Integer tile : tiles) {
- fileMap.put(tile, new CycleFilesIterator(tdDir, LANE, tile, outputCycles, ".bcl"));
- }
- return fileMap;
- }
-
- public static Integer [] boxArr(final int [] ints) {
- final Integer [] boxArr = new Integer[ints.length];
- for(int i = 0; i < boxArr.length; i++) {
+ public static Integer[] boxArr(final int[] ints) {
+ final Integer[] boxArr = new Integer[ints.length];
+ for (int i = 0; i < boxArr.length; i++) {
boxArr[i] = ints[i];
}
return boxArr;
}
- @DataProvider(name="tileMaps")
- public Object [][] getTileMaps() {
- return new Object[][] {
- //TILES, NUM_CLUSTER TO BE READ, SEEK AT THIS READ, INDEX TO TILETOSEEK, ORDERED TILE INDEX (FOR OUT OF ORDER TILES)
- {new int[]{1101, 1201, 2101}, 60, -1, -1, -1},
- {new int[]{1101, 2101, 1201}, 60, -1, -1, -1},
- {new int[]{2101, 1201}, 40, -1, -1, -1},
- {new int[]{1101, 2101}, 40, -1, -1, -1},
- {new int[]{1101}, 20, -1, -1, -1},
-
- //Cases with seeking
- {new int[]{1101, 1201, 2101}, 86, 25, 0, 0},
- {new int[]{1101, 2101, 1201}, 86, 25, 0, 0},
- {new int[]{2101, 1201}, 40, 19, 0, 1},
- {new int[]{1101, 2101}, 76, 35, 0, 0},
- {new int[]{1101}, 26, 5, 0, 0}
+ @DataProvider(name = "tileMaps")
+ public Object[][] getTileMaps() {
+ return new Object[][]{
+ //TILES, NUM_CLUSTER TO BE READ, SEEK AT THIS READ, INDEX TO TILETOSEEK, ORDERED TILE INDEX (FOR OUT OF ORDER TILES)
+ {new int[]{1101, 1201, 2101}, 180, -1, -1, -1},
+ {new int[]{1101, 2101, 1201}, 180, -1, -1, -1},
+ {new int[]{2101, 1201}, 120, -1, -1, -1},
+ {new int[]{1101, 2101}, 120, -1, -1, -1},
+ {new int[]{1101}, 60, -1, -1, -1},
+
+ //Cases with seeking
+ {new int[]{1101, 1201, 2101}, 206, 25, 0, 0},
+ {new int[]{1101, 2101, 1201}, 206, 25, 0, 0},
+ {new int[]{2101, 1201}, 80, 19, 0, 1},
+ {new int[]{1101, 2101}, 156, 35, 0, 0},
+ {new int[]{1101}, 66, 5, 0, 0}
};
}
- public void compareClusterToBclData(final ClusterData cluster, final BclData bclData, final int clusterNum, final int countNum) {
- final byte [][] bases = bclData.getBases();
- final byte [][] qualities = bclData.getQualities();
+ @DataProvider(name = "multiTileMaps")
+ public Object[][] getMultiTileMaps() {
+ return new Object[][]{
+ //TILES, NUM_CLUSTER TO BE READ, SEEK AT THIS READ, INDEX TO TILETOSEEK, ORDERED TILE INDEX (FOR OUT OF ORDER TILES)
+ {new int[]{11101, 11102, 11103}, 341292, -1, -1, -1}
+ };
+ }
- Assert.assertEquals(bases.length, cluster.getNumReads(), "At cluster num " + clusterNum);
- Assert.assertEquals(qualities.length, cluster.getNumReads(), "At cluster num " + clusterNum);
- for(int i = 0; i < cluster.getNumReads(); i++) {
- Assert.assertEquals(bases[i], cluster.getRead(i).getBases(), " Bases differ for read " + i + " at cluster num " + clusterNum + " at cluster count " + countNum);
+ public void compareClusterToBclData(final ClusterData cluster, final BclData bclData, final int clusterNum, final int countNum) {
+ final byte[][] bases = bclData.getBases();
+ final byte[][] qualities = bclData.getQualities();
+
+ Assert.assertEquals(bases.length, cluster.getNumReads(), "At cluster num " + clusterNum);
+ Assert.assertEquals(qualities.length, cluster.getNumReads(), "At cluster num " + clusterNum);
+
+ final StringBuilder baseBuilder = new StringBuilder();
+ final StringBuilder qualBuilder = new StringBuilder();
+ final StringBuilder barcode = new StringBuilder();
+ baseBuilder.append("new byte[]{");
+ for (int i = 0; i < bases.length; i++) {
+ final byte[] subBase = bases[i];
+ final byte[] subQual = qualities[i];
+ for (int j = 0; j < subBase.length; j++) {
+ if ((char) subBase[j] == '.') {
+ baseBuilder.append('P');
+ } else {
+ baseBuilder.append((char) subBase[j]);
+ }
+ baseBuilder.append(",");
+ qualBuilder.append(subQual[j]);
+ qualBuilder.append(",");
+ if (i == 1) {
+ if ((char) subBase[j] == '.') {
+ barcode.append('P');
+ } else {
+ barcode.append((char) subBase[j]);
+ }
+ }
+ }
+ }
+ baseBuilder.deleteCharAt(baseBuilder.length() - 1);
+ qualBuilder.deleteCharAt(qualBuilder.length() - 1);
+ baseBuilder.append("},\n new byte[]{");
+ baseBuilder.append(qualBuilder.toString());
+ baseBuilder.append("},\n \"");
+ baseBuilder.append(barcode.toString());
+ baseBuilder.append("\"");
+
+ for (int i = 0; i < cluster.getNumReads(); i++) {
+ if (!Arrays.equals(bases[i], cluster.getRead(i).getBases())) {
+ System.out.println(cluster.getLane() + " : " + cluster.getTile() + " : " + clusterNum);
+ System.out.println(baseBuilder.toString());
+ }
+ Assert.assertEquals(bases[i], cluster.getRead(i).getBases(), " Bases differ for read " + i + " at cluster num " + clusterNum + " at cluster count " + countNum);
Assert.assertEquals(qualities[i], cluster.getRead(i).getQualities(), " Qualities differ for read " + i + " at cluster num " + clusterNum + " at cluster count " + countNum);
}
}
- public void fullBclParserTestImpl(final File dir, final String readStructure, final int[] tiles, final int size, final int seekAfter, final int newTileIndex, final int orderedTileIndex) {
+ public void fullBclParserTestImpl(final File dir, final String readStructure, final int[] tiles, final int size, final int seekAfter, final int newTileIndex, final int orderedTileIndex,
+ final boolean multiTile) {
final ReadStructure rs = new ReadStructure(readStructure);
final OutputMapping outputMapping = new OutputMapping(rs);
+ final IlluminaFileUtil util = new IlluminaFileUtil(dir.getParentFile(), LANE);
+ final PerTilePerCycleFileUtil bclFileUtil = (PerTilePerCycleFileUtil) util.getUtil(IlluminaFileUtil.SupportedIlluminaFormat.Bcl);
+ final MultiTileBclFileUtil multiTileBclFileUtil = (MultiTileBclFileUtil) util.getUtil(IlluminaFileUtil.SupportedIlluminaFormat.MultiTileBcl);
+
+
+ final List<Integer> tileIntegers = new ArrayList<Integer>();
+ for (final int tile : tiles) {
+ tileIntegers.add(tile);
+ }
+
+ final BclParser bclParser;
+ if(multiTile){
+ final File bci = new File(MULTI_TILE_DATA_DIR, "s_" + LANE + ".bci");
+ bclParser = new MultiTileBclParser(dir, LANE, multiTileBclFileUtil.getFiles(tileIntegers, outputMapping.getOutputCycles()),
+ outputMapping, true, new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY),
+ new TileIndex(bci));
+ }
+ else{
+ bclParser = new BclParser(dir, LANE, bclFileUtil.getFiles(tileIntegers, outputMapping.getOutputCycles()),
+ outputMapping, new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY));
+ }
+
- final BclParser bclParser = new BclParser(dir, 3, makeCycleIlluminaFileMap(dir, tiles, outputMapping.getOutputCycles()), outputMapping, new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY));
final Map<Integer, ClusterData> testData = BinTdUtil.clusterData(LANE, Arrays.asList(boxArr(tiles)), readStructure, DATA_TYPES);
int count = 0;
@@ -104,18 +161,19 @@ public class BclParserTest {
count++;
}
Assert.assertEquals(count, size);
+ bclParser.close();
}
public static void deleteBclFiles(final File laneDirectory, final String readStructure) {
final ReadStructure rs = new ReadStructure(readStructure);
int index = 1;
- for(final ReadDescriptor rd : rs.descriptors) {
- if(rd.type == ReadType.S) {
- for(int i = index; i < index + rd.length; i++) {
+ for (final ReadDescriptor rd : rs.descriptors) {
+ if (rd.type == ReadType.S) {
+ for (int i = index; i < index + rd.length; i++) {
final File cycleDir = new File(laneDirectory, "C" + i + ".1");
- final File [] cycleFiles = cycleDir.listFiles();
- for(final File toDelete : cycleFiles) {
- if(!toDelete.delete()) {
+ final File[] cycleFiles = cycleDir.listFiles();
+ for (final File toDelete : cycleFiles) {
+ if (!toDelete.delete()) {
throw new RuntimeException("Couldn't delete file " + toDelete.getAbsolutePath());
}
}
@@ -128,13 +186,18 @@ public class BclParserTest {
@Test(dataProvider = "tileMaps")
public void fullBclParserTest(final int[] tiles, final int size, final int seekAfter, final int newTileIndex, final int orderedTileIndex) {
- fullBclParserTestImpl(TEST_DATA_DIR, READ_STRUCTURE, tiles, size, seekAfter, newTileIndex, orderedTileIndex);
+ fullBclParserTestImpl(TEST_DATA_DIR, READ_STRUCTURE, tiles, size, seekAfter, newTileIndex, orderedTileIndex, false);
+ }
+
+ //@Test(dataProvider = "multiTileMaps")
+ public void fullMTBclParserTest(final int[] tiles, final int size, final int seekAfter, final int newTileIndex, final int orderedTileIndex) {
+ fullBclParserTestImpl(MULTI_TILE_DATA_DIR, READ_STRUCTURE, tiles, size, seekAfter, newTileIndex, orderedTileIndex, true);
}
@Test(dataProvider = "tileMaps")
public void fullBclParserTestWSkips(final int[] tiles, final int size, final int seekAfter, final int newTileIndex, final int orderedTileIndex) {
- fullBclParserTestImpl(TEST_DATA_DIR, READ_STRUCTURE_WSKIPS, tiles, size, seekAfter, newTileIndex, orderedTileIndex);
+ fullBclParserTestImpl(TEST_DATA_DIR, READ_STRUCTURE_WSKIPS, tiles, size, seekAfter, newTileIndex, orderedTileIndex, false);
}
@Test(dataProvider = "tileMaps")
@@ -157,21 +220,21 @@ public class BclParserTest {
Exception exc = null;
try {
- final File l003 = new File(basecallDir, "L003");
- if(!l003.mkdir()) {
- throw new RuntimeException("Couldn't make lane dir " + l003.getAbsolutePath());
+ final File l001 = new File(basecallDir, "L001");
+ if (!l001.mkdir()) {
+ throw new RuntimeException("Couldn't make lane dir " + l001.getAbsolutePath());
}
- copyBcls(TEST_DATA_DIR, l003);
- deleteBclFiles(l003, readStructure);
- fullBclParserTestImpl(l003, READ_STRUCTURE_WSKIPS, tiles, size, seekAfter, newTileIndex, orderedTileIndex);
- } catch(Exception thrExc) {
+ copyBcls(TEST_DATA_DIR, l001);
+ deleteBclFiles(l001, readStructure);
+ fullBclParserTestImpl(l001, READ_STRUCTURE_WSKIPS, tiles, size, seekAfter, newTileIndex, orderedTileIndex, false);
+ } catch (final Exception thrExc) {
exc = thrExc;
} finally {
IoUtil.deleteDirectoryTree(basecallDir);
}
- if(exc != null) {
- if(exc.getClass() == PicardException.class) {
+ if (exc != null) {
+ if (exc.getClass() == PicardException.class) {
throw new PicardException(exc.getMessage());
}
throw new RuntimeException(exc);
@@ -180,17 +243,17 @@ public class BclParserTest {
//Custom copy function to avoid copying .svn files etc...
public static void copyBcls(final File srcLaneDir, final File dstDir) {
- final File [] listFiles = srcLaneDir.listFiles();
+ final File[] listFiles = srcLaneDir.listFiles();
- for(final File dir : listFiles) {
- if(dir.isDirectory()) {
+ for (final File dir : listFiles) {
+ if (dir.isDirectory()) {
File cycleDir = null;
- for(final File file : dir.listFiles()) {
- if(file.getName().endsWith(".bcl")) {
- if(cycleDir == null) {
+ for (final File file : dir.listFiles()) {
+ if (file.getName().endsWith(".bcl")) {
+ if (cycleDir == null) {
cycleDir = new File(dstDir, dir.getName());
- if(!cycleDir.mkdir()) {
+ if (!cycleDir.mkdir()) {
throw new RuntimeException("Couldn't make directory (" + cycleDir.getAbsolutePath() + ")");
}
}
@@ -203,12 +266,12 @@ public class BclParserTest {
}
-
//Helper byte [] tuple for EAMSS testing
class BasesAndQuals {
- public final byte [] bases;
- public final byte [] quals;
- public final byte [] maskedQuals;
+ public final byte[] bases;
+ public final byte[] quals;
+ public final byte[] maskedQuals;
+
public BasesAndQuals(final byte[] bases, final byte[] quals, final Integer maskStart) {
this.bases = bases;
this.quals = quals;
@@ -216,9 +279,9 @@ public class BclParserTest {
}
private byte[] qualsMaskedFrom(final Integer maskStart) {
- final byte [] maskedQuals = Arrays.copyOf(quals, quals.length);
- if(maskStart != null) {
- for(int i = maskStart; i < maskedQuals.length; i++) {
+ final byte[] maskedQuals = Arrays.copyOf(quals, quals.length);
+ if (maskStart != null) {
+ for (int i = maskStart; i < maskedQuals.length; i++) {
maskedQuals[i] = BclParser.MASKING_QUALITY;
}
}
@@ -231,8 +294,8 @@ public class BclParserTest {
public String basesToString() {
final StringBuilder sb = new StringBuilder(bases.length);
- for(final byte base : bases ) {
- switch(base) {
+ for (final byte base : bases) {
+ switch (base) {
case A:
sb.append("A ");
break;
@@ -255,12 +318,12 @@ public class BclParserTest {
}
return sb.toString();
- };
+ }
- public String qualsToString(final byte [] qualsToConvert) {
+ public String qualsToString(final byte[] qualsToConvert) {
final StringBuilder sb = new StringBuilder(bases.length);
- for(final byte qual : qualsToConvert ) {
+ for (final byte qual : qualsToConvert) {
sb.append(String.valueOf((int) qual));
sb.append(",");
}
@@ -272,111 +335,111 @@ public class BclParserTest {
@DataProvider(name = "eamssDataNo10GSeries")
public Object[][] eamssDataNo10GSeries() {
- return new Object[][]{
- //Non-masking cases
-
- //tally very negative, 9G's
- {new BasesAndQuals(new byte []{ G, G, G, G, G, G, G, G, G},
- new byte []{13, 7, 35, 32, 31, 33, 31, 26, 29},
- null)},
-
- //tally barely negative
- {new BasesAndQuals(new byte []{ G, G, G, G, G, G, G, G, G},
- new byte []{13, 7, 35, 26, 18, 19, 35, 8, 33},
- null)},
-
- //Reaches 0, A stretch of more than 10 other types of bases
- {new BasesAndQuals(new byte []{ A, C, C, C, C, C, C, C, C, C, C, C, T, G, G, C, T, A, A},
- new byte []{ 7, 8, 33, 7, 2, 33, 16, 17, 19, 7, 6, 5, 35, 2, 33, 22, 18, 16, 25},
- null)},
-
- //Stays at 0, Stretches of G's Separated
- {new BasesAndQuals(new byte []{ T, G, G, G, G, G, G, G, P, P, G, G, G, G, G, G, G, T, A, A, G, G, G},
- new byte []{ 7, 8, 33, 7, 2, 33, 16, 17, 2, 2, 6, 5, 35, 2, 33, 22, 18, 16, 25, 33, 32, 16, 18},
- null)},
-
- //shorter
- {new BasesAndQuals(new byte []{ T, A, C},
- new byte []{ 25, 16, 16},
- null)},
-
- //Longer
- {new BasesAndQuals(new byte []{ T, A, C, G, G, P, P, T, C, C, C, C, T, T, T, G, G, G, A, T, G, C, A, T, A, C, G, G, P, P, T, C, C, C, C, T, T, T, G, G, G, A, T, G, C, A},
- new byte []{ 25, 16, 16, 33, 22, 2, 2, 33, 35, 3, 31, 38, 22, 19, 25, 16, 16, 31, 30, 2, 2, 33, 26, 3, 31, 38, 22, 19, 2, 2, 30, 27, 28, 16, 2, 2, 30, 16, 19, 21, 22, 17, 19, 16, 16, 16},
- null)},
-
-
- //Masking-Cases
-
- //tally very positive, 9Gs X - Mask From here
- {new BasesAndQuals(new byte []{ G, G, G, G, G, G, G, G, G},
- new byte []{13, 7, 35, 32, 2, 16, 33, 14, 19},
- 7)},
-
- //tally barely negative X - Mask from here
- {new BasesAndQuals(new byte []{ G, G, G, G, G, G, G, G, G},
- new byte []{13, 7, 35, 33, 18, 2, 6, 8, 33},
- 4)},
- //Reaches 0, A stretch of more than 10 other types of bases X - Mask From here
- {new BasesAndQuals(new byte []{ A, C, C, C, C, C, C, C, C, C, C, C, T, G, G, C, T, A, A},
- new byte []{ 7, 8, 33, 7, 2, 33, 16, 17, 19, 32, 33, 5, 8, 2, 2, 2, 33, 16, 25},
- 11)},
- //Stays at 0, Stretches of G's Separated X- Mask from here
- {new BasesAndQuals(new byte []{ T, G, G, G, G, G, G, G, P, P, G, G, G, G, G, G, G, T, A, A, G, G, G},
- new byte []{ 7, 8, 33, 7, 2, 33, 16, 17, 2, 2, 6, 5, 35, 2, 33, 30, 13, 16, 7, 2, 2, 16, 18},
- 16)},
- //shorter X - Mask from here
- {new BasesAndQuals(new byte []{ T, A, C},
- new byte []{ 2, 11, 13},
- 0)},
- //Longer X- Mask from here
- {new BasesAndQuals(new byte []{ T, A, C, G, G, P, P, T, C, C, C, C, T, T, T, G, G, G, A, T, G, C, A, T, A, C, G, G, P, P, T, C, C, C, C, T, T, T, G, G, G, A, T, G, C, A},
- new byte []{ 25, 16, 16, 33, 22, 2, 2, 33, 35, 3, 31, 38, 22, 19, 25, 16, 16, 31, 30, 2, 2, 33, 26, 3, 31, 38, 22, 19, 2, 2, 30, 27, 28, 16, 2, 2, 30, 16, 19, 21, 22, 2, 19, 16, 2, 2},
- 26)}
+ return new Object[][]{
+ //Non-masking cases
+
+ //tally very negative, 9G's
+ {new BasesAndQuals(new byte[]{G, G, G, G, G, G, G, G, G},
+ new byte[]{13, 7, 35, 32, 31, 33, 31, 26, 29},
+ null)},
+
+ //tally barely negative
+ {new BasesAndQuals(new byte[]{G, G, G, G, G, G, G, G, G},
+ new byte[]{13, 7, 35, 26, 18, 19, 35, 8, 33},
+ null)},
+
+ //Reaches 0, A stretch of more than 10 other types of bases
+ {new BasesAndQuals(new byte[]{A, C, C, C, C, C, C, C, C, C, C, C, T, G, G, C, T, A, A},
+ new byte[]{7, 8, 33, 7, 2, 33, 16, 17, 19, 7, 6, 5, 35, 2, 33, 22, 18, 16, 25},
+ null)},
+
+ //Stays at 0, Stretches of G's Separated
+ {new BasesAndQuals(new byte[]{T, G, G, G, G, G, G, G, P, P, G, G, G, G, G, G, G, T, A, A, G, G, G},
+ new byte[]{7, 8, 33, 7, 2, 33, 16, 17, 2, 2, 6, 5, 35, 2, 33, 22, 18, 16, 25, 33, 32, 16, 18},
+ null)},
+
+ //shorter
+ {new BasesAndQuals(new byte[]{T, A, C},
+ new byte[]{25, 16, 16},
+ null)},
+
+ //Longer
+ {new BasesAndQuals(new byte[]{T, A, C, G, G, P, P, T, C, C, C, C, T, T, T, G, G, G, A, T, G, C, A, T, A, C, G, G, P, P, T, C, C, C, C, T, T, T, G, G, G, A, T, G, C, A},
+ new byte[]{25, 16, 16, 33, 22, 2, 2, 33, 35, 3, 31, 38, 22, 19, 25, 16, 16, 31, 30, 2, 2, 33, 26, 3, 31, 38, 22, 19, 2, 2, 30, 27, 28, 16, 2, 2, 30, 16, 19, 21, 22, 17, 19, 16, 16, 16},
+ null)},
+
+
+ //Masking-Cases
+
+ //tally very positive, 9Gs X - Mask From here
+ {new BasesAndQuals(new byte[]{G, G, G, G, G, G, G, G, G},
+ new byte[]{13, 7, 35, 32, 2, 16, 33, 14, 19},
+ 7)},
+
+ //tally barely negative X - Mask from here
+ {new BasesAndQuals(new byte[]{G, G, G, G, G, G, G, G, G},
+ new byte[]{13, 7, 35, 33, 18, 2, 6, 8, 33},
+ 4)},
+ //Reaches 0, A stretch of more than 10 other types of bases X - Mask From here
+ {new BasesAndQuals(new byte[]{A, C, C, C, C, C, C, C, C, C, C, C, T, G, G, C, T, A, A},
+ new byte[]{7, 8, 33, 7, 2, 33, 16, 17, 19, 32, 33, 5, 8, 2, 2, 2, 33, 16, 25},
+ 11)},
+ //Stays at 0, Stretches of G's Separated X- Mask from here
+ {new BasesAndQuals(new byte[]{T, G, G, G, G, G, G, G, P, P, G, G, G, G, G, G, G, T, A, A, G, G, G},
+ new byte[]{7, 8, 33, 7, 2, 33, 16, 17, 2, 2, 6, 5, 35, 2, 33, 30, 13, 16, 7, 2, 2, 16, 18},
+ 16)},
+ //shorter X - Mask from here
+ {new BasesAndQuals(new byte[]{T, A, C},
+ new byte[]{2, 11, 13},
+ 0)},
+ //Longer X- Mask from here
+ {new BasesAndQuals(new byte[]{T, A, C, G, G, P, P, T, C, C, C, C, T, T, T, G, G, G, A, T, G, C, A, T, A, C, G, G, P, P, T, C, C, C, C, T, T, T, G, G, G, A, T, G, C, A},
+ new byte[]{25, 16, 16, 33, 22, 2, 2, 33, 35, 3, 31, 38, 22, 19, 25, 16, 16, 31, 30, 2, 2, 33, 26, 3, 31, 38, 22, 19, 2, 2, 30, 27, 28, 16, 2, 2, 30, 16, 19, 21, 22, 2, 19, 16, 2, 2},
+ 26)}
};
}
- /** For more information on EAMSS check BclParser and the large comment above runEamssForReadInPlace **/
+ /** For more information on EAMSS check BclParser and the large comment above runEamssForReadInPlace * */
@DataProvider(name = "eamssDataWithGSeries")
- public Object [][] eamssTestDat() {
+ public Object[][] eamssTestDat() {
return new Object[][]{
- //9 G's followed by tally max X - Mask from here
- {new BasesAndQuals(new byte []{ A, C, G, G, T, G, G, G, G, G, G, G, G, G, A, C, T},
- new byte []{ 7, 8, 33, 7, 12, 33, 16, 17, 2, 2, 32, 35, 35, 35, 2, 15, 9},
- 5)},
- //9 G's surpassed by tally max X - Mask from here
- {new BasesAndQuals(new byte []{ A, C, G, G, T, G, G, G, G, G, G, G, G, G, A, C, T},
- new byte []{ 7, 8, 2, 7, 2, 2, 16, 17, 2, 2, 32, 35, 35, 35, 2, 15, 9},
- 0)},
- //10 G's ending before tally max X - Mask from here
- {new BasesAndQuals(new byte []{ A, C, G, G, T, G, G, G, G, G, G, G, G, G, A, C, T},
- new byte []{ 7, 8, 2, 7, 2, 2, 16, 17, 2, 2, 32, 35, 35, 35, 33, 15, 9},
- 15)},
- //10 G's ending on tally max X - Mask from here Is this wrong?
- {new BasesAndQuals(new byte []{ A, C, C, G, C, C, G, G, G, G, G, G, G, G, G, G, T, T, A},
- new byte []{ 33, 31, 29, 32, 28, 27, 30, 18, 18, 18, 18, 19, 19, 19, 33, 18, 9, 9, 19},
- 6)},
- //10 G's no masking
- {new BasesAndQuals(new byte []{ A, C, C, G, C, C, G, G, G, G, G, G, G, G, G, G, T, T, A},
- new byte []{ 33, 31, 29, 32, 28, 27, 30, 18, 18, 18, 18, 19, 19, 19, 33, 18, 33, 32, 34},
- null)},
- //10 G' with an exception X - Mask from here
- {new BasesAndQuals(new byte []{ A, C, C, G, C, C, G, G, G, G, A, G, G, G, G, G, T, T, A},
- new byte []{ 33, 31, 29, 32, 28, 27, 30, 18, 18, 18, 18, 19, 19, 19, 33, 18, 9, 9, 19},
- 6)},
- //longer than 10 G's X - Mask from here
- {new BasesAndQuals(new byte []{ A, C, G, G, G, C, G, G, G, G, G, G, G, G, G, G, T, T, A},
- new byte []{ 33, 31, 29, 32, 28, 16, 33, 18, 18, 18, 18, 19, 19, 19, 33, 18, 3, 9, 19},
- 2)},
- //longer than 10 G's X - Mask from here
- {new BasesAndQuals(new byte []{ A, C, G, G, C, C, G, G, G, G, G, G, G, G, G, G, G, G, G},
- new byte []{ 33, 31, 29, 32, 28, 16, 33, 18, 18, 18, 18, 19, 19, 19, 33, 34, 33, 33, 3},
- 6)},
- //longer than 10 G's
- {new BasesAndQuals(new byte []{ A, C, G, G, C, C, G, G, G, G, G, G, G, G, G, G, G, G, G, T, A, C, T, T, G, G, G, G, G, G, G, G, G, G, G, G, G},
- new byte []{ 33, 31, 29, 32, 28, 16, 33, 18, 18, 18, 18, 19, 19, 19, 33, 34, 33, 33, 3, 33, 34, 2, 4, 8, 33, 7, 35, 15, 16, 31, 30, 38, 16, 15, 22, 29, 25},
- null)}
+ //9 G's followed by tally max X - Mask from here
+ {new BasesAndQuals(new byte[]{A, C, G, G, T, G, G, G, G, G, G, G, G, G, A, C, T},
+ new byte[]{7, 8, 33, 7, 12, 33, 16, 17, 2, 2, 32, 35, 35, 35, 2, 15, 9},
+ 5)},
+ //9 G's surpassed by tally max X - Mask from here
+ {new BasesAndQuals(new byte[]{A, C, G, G, T, G, G, G, G, G, G, G, G, G, A, C, T},
+ new byte[]{7, 8, 2, 7, 2, 2, 16, 17, 2, 2, 32, 35, 35, 35, 2, 15, 9},
+ 0)},
+ //10 G's ending before tally max X - Mask from here
+ {new BasesAndQuals(new byte[]{A, C, G, G, T, G, G, G, G, G, G, G, G, G, A, C, T},
+ new byte[]{7, 8, 2, 7, 2, 2, 16, 17, 2, 2, 32, 35, 35, 35, 33, 15, 9},
+ 15)},
+ //10 G's ending on tally max X - Mask from here Is this wrong?
+ {new BasesAndQuals(new byte[]{A, C, C, G, C, C, G, G, G, G, G, G, G, G, G, G, T, T, A},
+ new byte[]{33, 31, 29, 32, 28, 27, 30, 18, 18, 18, 18, 19, 19, 19, 33, 18, 9, 9, 19},
+ 6)},
+ //10 G's no masking
+ {new BasesAndQuals(new byte[]{A, C, C, G, C, C, G, G, G, G, G, G, G, G, G, G, T, T, A},
+ new byte[]{33, 31, 29, 32, 28, 27, 30, 18, 18, 18, 18, 19, 19, 19, 33, 18, 33, 32, 34},
+ null)},
+ //10 G' with an exception X - Mask from here
+ {new BasesAndQuals(new byte[]{A, C, C, G, C, C, G, G, G, G, A, G, G, G, G, G, T, T, A},
+ new byte[]{33, 31, 29, 32, 28, 27, 30, 18, 18, 18, 18, 19, 19, 19, 33, 18, 9, 9, 19},
+ 6)},
+ //longer than 10 G's X - Mask from here
+ {new BasesAndQuals(new byte[]{A, C, G, G, G, C, G, G, G, G, G, G, G, G, G, G, T, T, A},
+ new byte[]{33, 31, 29, 32, 28, 16, 33, 18, 18, 18, 18, 19, 19, 19, 33, 18, 3, 9, 19},
+ 2)},
+ //longer than 10 G's X - Mask from here
+ {new BasesAndQuals(new byte[]{A, C, G, G, C, C, G, G, G, G, G, G, G, G, G, G, G, G, G},
+ new byte[]{33, 31, 29, 32, 28, 16, 33, 18, 18, 18, 18, 19, 19, 19, 33, 34, 33, 33, 3},
+ 6)},
+ //longer than 10 G's
+ {new BasesAndQuals(new byte[]{A, C, G, G, C, C, G, G, G, G, G, G, G, G, G, G, G, G, G, T, A, C, T, T, G, G, G, G, G, G, G, G, G, G, G, G, G},
+ new byte[]{33, 31, 29, 32, 28, 16, 33, 18, 18, 18, 18, 19, 19, 19, 33, 34, 33, 33, 3, 33, 34, 2, 4, 8, 33, 7, 35, 15, 16, 31, 30, 38, 16, 15, 22, 29, 25},
+ null)}
};
}
@@ -384,7 +447,7 @@ public class BclParserTest {
final byte[] bases = Arrays.copyOf(bq.bases, bq.bases.length);
final byte[] quals = Arrays.copyOf(bq.quals, bq.quals.length);
- TestBclParser.runEamssForReadInPlace(bases, quals);
+ BclParser.runEamssForReadInPlace(bases, quals);
Assert.assertEquals(bases, bq.bases);
Assert.assertEquals(quals, bq.maskedQuals);
}
@@ -399,9 +462,3 @@ public class BclParserTest {
testEamss(bq);
}
}
-
-class TestBclParser extends BclParser{
- public TestBclParser() {
- super(null, 1, null, new OutputMapping(new ReadStructure("1T")), new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY));
- }
-}
diff --git a/src/tests/java/net/sf/picard/illumina/parser/BinTdUtil.java b/src/tests/java/net/sf/picard/illumina/parser/BinTdUtil.java
index 20090ac..519b11d 100644
--- a/src/tests/java/net/sf/picard/illumina/parser/BinTdUtil.java
+++ b/src/tests/java/net/sf/picard/illumina/parser/BinTdUtil.java
@@ -1,10 +1,10 @@
package net.sf.picard.illumina.parser;
-import static net.sf.samtools.util.CollectionUtil.makeList;
-
import java.io.File;
import java.util.*;
+import static net.sf.samtools.util.CollectionUtil.makeList;
+
//Illumina Dir Test Data
public class BinTdUtil {
public static final File IntensitiesDir = new File("testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/");
@@ -14,305 +14,183 @@ public class BinTdUtil {
return "s_" + lane + "_" + tile;
}
- public static final byte A = (byte)65;
- public static final byte C = (byte)67;
- public static final byte G = (byte)71;
- public static final byte T = (byte)84;
- public static final byte P = (byte)46; //dot
- public static final Map<String, List<ClusterData>> goldData = new HashMap<String, List<ClusterData>>();
- public static final Map<String, List<Integer>> goldIndices = new HashMap<String, List<Integer>>();
- public static final Map<String, Integer> goldSizes = new HashMap<String, Integer>();
+ public static final byte A = (byte) 65;
+ public static final byte C = (byte) 67;
+ public static final byte G = (byte) 71;
+ public static final byte T = (byte) 84;
+ public static final byte P = (byte) 46; //dot
+ public static final Map<String, List<ClusterData>> goldData = new HashMap<String, List<ClusterData>>();
+ public static final Map<String, List<Integer>> goldIndices = new HashMap<String, List<Integer>>();
+ public static final Map<String, Integer> goldSizes = new HashMap<String, Integer>();
+
static {
int lane = 1;
int tile = 1101;
goldIndices.put(ltStr(lane, tile), makeList(0, 2, 10, 18, 19));
goldData.put(ltStr(lane, tile), makeList(
- makeCd(lane, tile, 1075, 1001, true,
- new byte[]{ P, G, T, G, T, G, A, A, G, T, T, C, A, A, G, A, A, G, C, A, G, A, C, A, A, P, G, G, T, C, G, C, A, A, A, C, T, G, A, P, P, A, A, A, A, A, C, A, C, T, C, C, A, A, A, T, A, A },
- new byte[]{ 2, 16, 25, 35, 35, 35, 35, 30, 33, 37, 37, 39, 37, 35, 38, 37, 39, 37, 39, 40, 36, 39, 29, 31, 27, 2, 16, 28, 33, 35, 37, 37, 37, 27, 31, 31, 35, 30, 33, 2, 2, 17, 17, 34, 37, 37, 27, 34, 35, 30, 36, 39, 38, 10, 17, 27, 27, 34 },
- "AGGTCGCA"),
- makeCd(lane, tile, 1184, 1010, true,
- new byte[]{ P, G, T, G, A, A, C, A, A, A, C, T, G, G, T, T, T, T, A, T, C, T, G, G, T, P, G, G, T, C, G, C, A, C, C, C, T, A, T, C, A, G, T, T, T, G, T, T, G, T, C, A, C, T, T, C, C, A },
- new byte[]{ 2, 16, 28, 35, 35, 35, 37, 37, 39, 39, 39, 39, 39, 41, 40, 41, 41, 41, 36, 39, 39, 40, 40, 41, 38, 2, 16, 28, 35, 35, 37, 37, 37, 33, 33, 34, 37, 32, 35, 35, 36, 39, 39, 39, 39, 39, 40, 41, 40, 41, 41, 41, 39, 39, 38, 39, 39, 41 },
- "AGGTCGCA"),
- makeCd(lane, tile, 1175, 1044, true,
- new byte[]{ C, G, G, T, C, A, G, C, A, A, A, G, G, C, T, A, T, T, C, T, C, A, T, C, T, P, G, G, T, C, G, C, A, G, T, C, C, C, A, G, G, G, A, G, G, A, G, T, C, C, C, T, G, T, G, G, G, A },
- new byte[]{ 34, 34, 34, 37, 37, 37, 37, 37, 39, 39, 39, 39, 39, 40, 41, 41, 40, 41, 41, 40, 40, 34, 39, 37, 39, 2, 16, 28, 32, 35, 37, 37, 37, 31, 33, 34, 35, 37, 35, 35, 37, 39, 35, 37, 37, 30, 37, 37, 38, 41, 41, 41, 41, 40, 40, 40, 40, 31 },
- "AGGTCGCA"),
- makeCd(1, 1101, 1006, 1090, false,
- new byte[]{ P, A, C, C, P, C, T, C, A, G, G, A, G, C, A, G, A, G, T, G, P, P, P, P, P, P, P, G, T, C, G, C, P, P, P, P, P, P, P, P, P, P, P, P, P, C, A, C, C, A, P, P, P, P, P, T, C, P },
- new byte[]{ 2, 7, 7, 17, 2, 17, 27, 12, 12, 27, 29, 30, 26, 30, 27, 30, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 19, 32, 35, 37, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 },
- null),
- makeCd(lane, tile, 1018, 1110, false,
- new byte[]{ P, G, A, G, G, T, T, T, T, C, T, C, C, A, G, C, A, C, C, C, A, P, P, P, C, P, G, G, T, C, G, C, A, C, P, P, P, P, G, P, P, G, C, C, A, G, A, C, C, A, G, G, T, A, G, T, T, C },
- new byte[]{ 2, 15, 15, 28, 31, 27, 30, 30, 30, 30, 30, 30, 30, 31, 30, 31, 30, 30, 31, 30, 30, 2, 2, 2, 2, 2, 16, 28, 33, 35, 35, 37, 35, 33, 2, 2, 2, 2, 17, 2, 2, 17, 17, 32, 37, 37, 38, 40, 41, 41, 38, 41, 33, 34, 38, 37, 39, 40 },
- "AGGTCGCA")
- ));
- goldSizes.put(ltStr(lane, tile), 20);
+ makeCd(lane, tile, 1140, 2120, true,
+ new byte[]{P, C, C, C, C, A, A, C, A, T, T, C, T, A, A, T, T, A, T, G, C, C, T, C, A, C, A, A, C, T, C, T, C, T, T, T, T, T, T, T, T, T, T, T, T, T, A, A, C, T, T, T, G, C, A, A, A, T},
+ new byte[]{2, 16, 25, 33, 35, 37, 37, 35, 39, 37, 37, 35, 37, 40, 41, 41, 41, 40, 40, 41, 40, 40, 40, 40, 40, 31, 31, 31, 35, 35, 37, 35, 37, 31, 31, 31, 35, 35, 35, 35, 35, 39, 39, 39, 39, 37, 33, 31, 24, 37, 39, 40, 31, 33, 37, 39, 31, 31},
+ "CAACTCTC"),
+ makeCd(lane, tile, 1047, 2122, false,
+ new byte[]{P,C,T,A,A,P,G,P,A,C,T,P,T,G,P,G,T,G,T,G,C,P,P,P,P,P,P,P,A,P,P,P,P,P,P,T,C,A,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{2,15,26,31,31,2,19,2,18,31,31,2,18,31,2,17,27,31,31,31,31,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null),
+ makeCd(lane, tile, 1069, 2159, true,
+ new byte[]{T,C,C,C,T,T,A,C,C,A,T,C,A,A,A,T,C,A,A,T,T,G,P,C,C,G,T,C,C,A,C,A,G,G,A,C,G,T,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{34,34,34,37,37,37,37,37,39,39,39,39,39,41,41,41,41,41,41,41,41,41,2,18,32,31,33,33,37,37,37,37,37,27,27,27,31,30,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ "GTCCACAG"),
+ makeCd(lane, tile, 1175, 2197, true,
+ new byte[]{C,C,C,C,T,G,A,G,G,A,C,A,C,C,A,T,C,C,C,A,C,T,C,C,A,C,C,A,A,C,A,T,T,A,A,G,A,G,C,T,G,G,G,G,A,A,C,A,T,C,C,A,G,A,A,A,G,G},
+ new byte[]{34,34,34,37,37,37,37,37,39,39,39,39,39,41,41,41,41,41,41,41,41,41,41,41,41,34,34,34,37,37,37,37,37,33,34,31,37,37,37,37,37,39,39,39,39,39,41,41,41,41,41,41,41,41,41,41,41,41},
+ "CCAACATT"),
+ makeCd(lane, tile, 1048, 2197, false,
+ new byte[]{P,C,T,C,C,P,G,P,T,C,A,P,C,A,P,G,T,G,G,A,G,P,P,P,P,P,P,P,C,P,P,P,P,P,P,G,T,G,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{2,15,26,30,31,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null)
+ )
+ );
+ goldSizes.put(ltStr(lane, tile), 60);
tile = 1201;
goldIndices.put(ltStr(lane, tile), makeList(0, 1, 18, 19));
goldData.put(ltStr(lane, tile), makeList(
- makeCd(lane, tile, 1134, 1002, true,
- new byte[]{ P, A, C, C, T, G, C, G, T, G, T, C, A, G, C, A, A, C, A, T, C, C, G, C, C, P, G, G, T, C, G, C, A, A, P, G, G, G, C, P, P, C, A, T, C, A, C, A, G, G, A, G, C, C, T, G, C, C },
- new byte[]{ 2, 16, 28, 32, 33, 35, 35, 35, 39, 39, 39, 37, 30, 37, 35, 27, 26, 32, 37, 38, 31, 36, 32, 39, 40, 2, 16, 28, 33, 35, 37, 37, 35, 31, 2, 16, 19, 32, 35, 2, 2, 18, 27, 34, 37, 37, 35, 39, 38, 39, 40, 40, 40, 38, 34, 32, 34, 38 },
- "AGGTCGCA"),
- makeCd(lane, tile, 1224, 1012, false,
- new byte[]{ P, A, T, A, A, T, G, A, C, C, T, G, G, G, G, C, T, A, C, T, G, A, A, T, C, P, G, G, T, C, G, C, A, G, C, C, T, T, T, A, C, T, T, A, T, G, A, T, C, A, C, A, G, T, T, T, A, T },
- new byte[]{ 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 28, 32, 35, 35, 37, 37, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 },
- "AGGTCGCA"),
- makeCd(lane, tile, 1136, 1112, true,
- new byte[]{ A, G, G, A, A, T, G, G, C, T, T, G, C, T, T, A, A, G, A, C, T, T, G, C, C, P, G, G, T, C, G, C, A, T, A, T, C, C, A, A, A, A, T, C, A, A, A, A, T, G, A, A, A, T, G, C, A, G },
- new byte[]{ 34, 34, 34, 37, 37, 37, 37, 37, 38, 39, 39, 16, 32, 36, 37, 36, 39, 35, 34, 38, 40, 39, 34, 37, 39, 2, 16, 28, 33, 35, 35, 37, 37, 31, 34, 34, 37, 37, 37, 37, 37, 39, 39, 39, 39, 39, 40, 41, 40, 40, 40, 41, 40, 41, 41, 40, 36, 39 },
- "AGGTCGCA"),
- makeCd(lane, tile, 1201, 1117, true,
- new byte[]{ C, C, T, C, A, G, T, T, T, C, G, G, G, A, G, A, T, C, A, T, C, C, A, C, A, P, G, G, T, C, G, C, A, C, T, C, A, A, T, A, C, T, A, A, A, T, C, T, C, A, A, G, A, T, T, G, A, T },
- new byte[]{ 27, 31, 31, 35, 33, 35, 35, 35, 39, 39, 39, 39, 35, 31, 30, 33, 35, 32, 34, 32, 39, 29, 27, 37, 24, 2, 16, 28, 33, 35, 35, 37, 37, 30, 31, 31, 37, 35, 35, 36, 29, 37, 35, 35, 39, 33, 31, 37, 38, 31, 25, 25, 10, 32, 40, 35, 33, 39 },
- "AGGTCGCA")
+ makeCd(lane, tile, 1187, 2100, true,
+ new byte[]{P,G,C,G,G,T,A,A,T,T,C,C,A,G,C,T,C,C,A,A,T,A,G,C,G,T,A,T,C,T,G,C,C,A,A,A,A,A,A,G,A,G,C,C,C,G,C,A,T,T,G,C,C,G,A,G,A,C},
+ new byte[]{2,16,25,33,33,17,31,35,39,39,37,39,39,40,40,40,40,39,39,40,40,38,39,38,38,34,34,34,37,37,37,37,37,28,27,28,26,32,32,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ "TATCTGCC"),
+ makeCd(lane, tile, 1045, 2105, false,
+ new byte[]{P,T,A,A,A,G,A,G,A,A,A,T,C,A,A,G,A,A,T,A,C,T,A,T,T,C,T,G,T,A,A,T,C,P,T,T,T,T,T,T,T,T,T,T,P,P,T,T,T,T,T,T,T,T,T,T,T,T},
+ new byte[]{2,12,19,31,30,7,31,8,31,31,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,16,16,16,17,31,32,2,2,2,15,26,31,31,31,31,31,31,31,30,2,2,15,25,30,30,30,30,30,30,30,30,28,27},
+ "CTGTAATC"),
+ makeCd(lane, tile, 1159, 2179, false,
+ new byte[]{G,T,T,A,G,C,A,C,A,G,A,T,A,T,T,G,G,A,T,G,A,G,T,G,A,A,A,A,A,A,A,A,A,T,T,T,T,T,T,T,T,T,A,T,T,T,T,T,C,T,A,A,A,T,A,C,T,T},
+ new byte[]{2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,28,28,28,32,32,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null),
+ makeCd(lane, tile, 1103, 2184, true,
+ new byte[]{G,T,A,A,G,A,A,C,T,A,C,C,C,T,G,G,G,T,C,C,C,C,G,T,G,T,T,G,T,C,T,A,T,A,G,A,A,G,T,T,T,C,A,G,A,A,T,T,G,T,G,G,C,C,C,C,A,T},
+ new byte[]{31,31,33,37,37,37,37,37,39,39,39,39,39,41,41,41,41,38,40,41,41,41,41,39,40,31,34,34,37,37,37,37,37,33,31,33,37,37,35,36,37,39,39,39,39,39,41,41,41,38,39,40,41,41,41,41,41,40},
+ "TTGTCTAT")
));
- goldSizes.put(ltStr(lane, tile), 20);
+ goldSizes.put(ltStr(lane, tile), 60);
tile = 2101;
goldIndices.put(ltStr(lane, tile), makeList(7, 15, 16, 19));
goldData.put(ltStr(lane, tile), makeList(
- makeCd(lane, tile, 1218, 1037, true,
- new byte[]{ C, C, G, G, A, C, C, C, T, G, G, G, C, T, C, A, G, C, C, C, T, G, A, T, G, P, G, G, T, C, G, C, A, T, G, C, T, G, G, A, C, T, G, T, T, T, G, T, G, C, A, G, G, C, G, G, C, A },
- new byte[]{ 31, 34, 34, 37, 37, 35, 37, 37, 39, 38, 39, 39, 39, 41, 41, 41, 41, 41, 40, 41, 40, 41, 38, 40, 40, 2, 16, 28, 33, 35, 35, 37, 37, 34, 31, 31, 37, 37, 37, 37, 37, 38, 39, 39, 37, 37, 40, 38, 40, 41, 40, 40, 40, 41, 40, 41, 39, 33 },
- "AGGTCGCA"),
- makeCd(lane, tile, 1069, 1101, false,
- new byte[]{ G, P, T, T, P, P, P, T, T, A, A, A, C, A, T, G, G, T, G, C, T, T, A, G, T, P, G, G, T, C, G, C, A, A, A, T, T, C, C, C, C, C, T, C, C, C, C, C, A, T, C, T, A, T, A, A, T, T },
- new byte[]{ 27, 2, 15, 28, 2, 2, 2, 17, 18, 25, 29, 30, 31, 30, 30, 31, 31, 31, 30, 31, 31, 30, 30, 31, 30, 2, 16, 28, 33, 35, 37, 37, 37, 31, 33, 31, 37, 35, 35, 36, 37, 37, 39, 39, 39, 39, 41, 41, 40, 40, 38, 40, 40, 38, 34, 33, 37, 40 },
- "AGGTCGCA"),
- makeCd(lane, tile, 1209, 1106, true,
- new byte[]{ C, A, A, A, T, C, T, G, A, T, T, G, C, A, T, T, A, T, T, C, A, C, C, T, G, P, G, G, T, C, G, C, A, A, G, C, T, T, G, T, T, T, G, G, G, G, G, T, C, T, G, C, T, G, T, A, G, T },
- new byte[]{ 34, 34, 34, 37, 37, 35, 37, 37, 39, 39, 39, 39, 39, 40, 40, 41, 40, 40, 41, 38, 40, 41, 40, 41, 41, 2, 16, 28, 33, 35, 37, 37, 37, 33, 33, 34, 37, 37, 37, 35, 37, 39, 39, 39, 39, 38, 41, 37, 39, 40, 41, 41, 41, 41, 39, 40, 40, 40 },
- "AGGTCGCA"),
- makeCd(lane, tile, 1103, 1112, false,
- new byte[]{ A, C, C, A, P, P, P, T, G, C, C, C, C, G, G, T, G, G, G, G, G, C, T, G, C, P, G, G, T, C, G, C, A, A, G, G, A, G, G, G, G, G, G, G, G, G, G, T, G, A, G, G, G, A, A, C, C, G },
- new byte[]{ 26, 27, 27, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 28, 33, 35, 37, 37, 37, 25, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 },
- "AGGTCGCA")
- ));
- goldSizes.put(ltStr(lane, tile), 20);
-
- lane = 2;
-
- tile = 1101;
- goldIndices.put(ltStr(lane, tile), makeList(0, 8, 9, 10));
- goldData.put(ltStr(lane, tile), makeList(
- makeCd(lane, tile, 1178, 1003, false,
- new byte[]{ P, C, A, A, P, P, P, C, A, C, C, T, C, C, C, A, G, A, G, T, C, G, T, G, G, A, G, G, T, C, G, C, A, A, G, P, G, A, C, C, A, G, A, A, G, C, T, C, T, C, T, G, A, G, T, T, A, G },
- new byte[]{ 2, 15, 26, 31, 2, 2, 2, 17, 17, 28, 28, 29, 30, 30, 31, 30, 30, 29, 30, 30, 30, 30, 31, 2, 2, 33, 33, 34, 37, 37, 37, 37, 35, 31, 33, 2, 19, 32, 35, 35, 37, 39, 39, 38, 39, 39, 40, 40, 41, 38, 40, 41, 34, 39, 39, 40, 40, 41 },
- null),
- makeCd(lane, tile, 1215, 1071, true,
- new byte[]{ A, G, G, G, A, T, T, T, C, A, G, T, T, G, G, T, G, G, T, G, G, G, G, C, A, A, G, G, T, C, G, C, A, G, A, A, C, A, T, A, T, T, T, G, T, C, T, C, A, G, A, G, A, G, A, C, T, T },
- new byte[]{ 30, 31, 31, 32, 35, 35, 35, 35, 32, 23, 35, 30, 34, 38, 36, 27, 32, 38, 27, 34, 37, 38, 36, 32, 37, 33, 31, 34, 37, 37, 37, 37, 37, 31, 31, 31, 35, 35, 35, 33, 25, 35, 30, 39, 37, 32, 34, 37, 37, 39, 40, 40, 29, 38, 28, 35, 31, 37 },
- null),
- makeCd(lane, tile, 1189, 1093, false,
- new byte[]{ C, C, A, C, C, G, T, G, A, G, A, A, T, G, C, G, C, C, A, T, C, T, G, C, A, A, G, G, T, C, G, C, A, A, A, A, A, C, A, G, A, A, C, C, C, A, G, T, T, A, G, C, A, G, T, A, T, G },
- new byte[]{ 28, 16, 22, 27, 16, 23, 32, 32, 10, 17, 28, 17, 17, 30, 19, 32, 21, 30, 8, 27, 10, 31, 27, 28, 31, 33, 33, 33, 37, 37, 37, 37, 37, 16, 23, 10, 32, 30, 10, 32, 32, 18, 10, 27, 34, 16, 10, 17, 27, 11, 11, 32, 34, 39, 2, 2, 2, 2 },
- null),
- makeCd(lane, tile, 1171, 1103, false,
- new byte[]{ G, T, P, G, P, P, P, G, G, A, G, A, T, G, T, A, C, T, G, G, T, G, A, A, A, A, G, G, T, C, G, C, A, T, C, T, T, T, G, G, C, T, T, G, C, T, A, A, A, T, T, T, T, A, T, T, T, A },
- new byte[]{ 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 31, 31, 34, 35, 35, 37, 37, 37, 16, 10, 25, 32, 10, 17, 10, 10, 32, 33, 31, 30, 30, 25, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 },
- null)
- ));
- goldSizes.put(ltStr(lane, tile), 20);
-
- tile = 1201;
- goldIndices.put(ltStr(lane, tile), makeList(1, 3, 4, 17));
- goldData.put(ltStr(lane, tile), makeList(
- makeCd(lane, tile, 1228, 1012, true,
- new byte[]{ P, T, G, G, T, C, A, T, C, T, G, C, A, G, G, T, T, T, C, T, G, A, G, A, T, P, G, G, T, C, G, C, A, T, T, T, C, T, T, A, T, A, G, A, A, A, C, A, T, C, T, T, T, T, A, T, T, T },
- new byte[]{ 2, 16, 25, 33, 35, 33, 19, 35, 35, 35, 37, 35, 37, 38, 37, 35, 35, 38, 36, 37, 40, 34, 39, 33, 37, 2, 16, 25, 28, 28, 33, 31, 23, 31, 33, 31, 35, 37, 37, 35, 35, 33, 37, 37, 39, 39, 41, 40, 41, 37, 39, 41, 40, 40, 37, 39, 39, 34 },
- null),
- makeCd(lane, tile, 1229, 1034, true,
- new byte[]{ C, C, T, G, T, T, G, T, A, C, G, T, C, C, C, A, G, T, A, T, G, G, A, G, C, P, G, G, T, C, G, C, A, C, T, C, T, A, T, C, C, C, A, G, A, C, C, C, T, T, C, T, C, A, G, G, C, A },
- new byte[]{ 34, 34, 34, 37, 37, 37, 37, 37, 38, 39, 39, 39, 39, 40, 38, 39, 39, 41, 40, 40, 41, 41, 24, 31, 34, 2, 16, 28, 32, 35, 35, 37, 37, 31, 31, 31, 35, 35, 37, 35, 35, 27, 34, 35, 39, 35, 39, 35, 37, 39, 38, 40, 36, 39, 38, 39, 39, 40 },
- null),
- makeCd(lane, tile, 1194, 1053, true,
- new byte[]{ A, G, A, T, C, T, C, A, T, A, T, C, G, T, C, G, C, T, C, G, T, C, A, T, G, P, A, T, T, A, G, A, T, T, G, T, C, G, A, T, T, A, T, C, G, C, A, C, T, G, G, T, G, C, G, A, A, T },
- new byte[]{ 31, 31, 31, 37, 37, 35, 35, 37, 35, 37, 39, 39, 39, 38, 40, 38, 40, 40, 41, 41, 41, 36, 34, 36, 36, 2, 16, 16, 33, 28, 35, 32, 33, 31, 31, 31, 37, 37, 35, 35, 37, 37, 39, 39, 37, 30, 39, 33, 36, 36, 39, 36, 39, 39, 38, 30, 30, 30 },
- null),
- makeCd(lane, tile, 1173, 1158, true,
- new byte[]{ A, C, G, C, P, G, G, C, A, A, T, G, A, T, G, G, C, G, T, C, T, C, G, C, A, P, G, G, T, C, G, C, A, T, G, C, A, T, C, G, A, C, T, G, C, C, C, T, A, T, T, T, T, G, T, C, T, A },
- new byte[]{ 31, 30, 31, 35, 2, 17, 32, 32, 37, 37, 37, 37, 37, 40, 40, 40, 40, 40, 40, 40, 40, 40, 38, 38, 34, 2, 16, 28, 35, 35, 37, 37, 37, 33, 31, 31, 30, 35, 35, 35, 35, 30, 37, 39, 37, 37, 38, 37, 38, 39, 38, 34, 29, 36, 38, 39, 41, 38 },
- null)
-
- ));
- goldSizes.put(ltStr(lane, tile), 20);
-
- tile = 2101;
- goldIndices.put(ltStr(lane, tile), makeList(0, 11, 13, 19));
- goldData.put(ltStr(lane, tile), makeList(
- makeCd(lane, tile, 1139, 1012, true,
- new byte[]{ P, G, T, A, T, C, A, T, T, T, T, G, T, T, A, A, A, A, G, T, C, C, T, A, C, P, G, G, T, C, G, C, A, C, A, A, A, A, T, P, A, T, G, C, T, C, A, A, G, A, G, T, G, C, C, C, A, G },
- new byte[]{ 2, 16, 16, 32, 33, 35, 26, 35, 37, 37, 35, 30, 34, 38, 37, 37, 37, 33, 37, 36, 39, 40, 37, 35, 31, 2, 16, 28, 35, 35, 37, 37, 37, 27, 30, 26, 35, 35, 35, 2, 17, 17, 32, 27, 30, 34, 38, 39, 33, 38, 38, 40, 39, 34, 29, 31, 37, 36 },
- null),
- makeCd(lane, tile, 1177, 1057, true,
- new byte[]{ A, A, G, A, G, A, A, C, A, C, G, T, T, A, T, A, G, G, A, C, A, T, T, T, T, P, G, G, T, C, G, C, A, A, G, G, C, C, A, A, G, T, G, C, C, C, C, T, C, T, T, G, G, T, G, T, C, T },
- new byte[]{ 31, 27, 30, 35, 35, 30, 35, 35, 35, 37, 39, 37, 37, 38, 39, 36, 39, 39, 34, 36, 38, 38, 39, 40, 40, 2, 16, 28, 35, 35, 37, 37, 37, 31, 31, 31, 35, 35, 32, 37, 35, 39, 39, 32, 37, 35, 30, 36, 38, 36, 38, 39, 41, 36, 38, 36, 24, 34 },
- null),
- makeCd(lane, tile, 1070, 1062, false,
- new byte[]{ A, P, T, A, P, P, P, C, A, G, G, G, A, T, A, A, C, T, C, A, A, P, P, G, C, P, G, G, T, C, G, C, A, A, A, C, T, C, A, G, A, C, T, A, C, A, G, G, T, G, C, A, G, A, A, A, A, C },
- new byte[]{ 27, 2, 15, 31, 2, 2, 2, 19, 17, 31, 30, 31, 30, 30, 30, 30, 30, 30, 30, 30, 30, 2, 2, 2, 2, 2, 19, 28, 35, 35, 37, 37, 35, 31, 31, 34, 35, 35, 33, 37, 37, 37, 39, 39, 39, 39, 41, 40, 37, 39, 38, 38, 38, 39, 36, 39, 38, 38 },
- null),
- makeCd(lane, tile, 1246, 1085, true,
- new byte[]{ T, C, T, T, C, C, C, A, T, G, A, G, G, G, C, A, C, A, G, T, T, T, G, A, C, P, G, G, T, C, G, C, A, A, G, T, C, G, A, A, T, T, G, T, A, A, T, T, C, C, A, T, T, T, G, C, C, C },
- new byte[]{ 34, 34, 34, 37, 37, 37, 37, 37, 39, 39, 39, 39, 39, 40, 39, 39, 40, 40, 39, 38, 39, 40, 41, 39, 40, 2, 16, 28, 33, 35, 35, 37, 37, 34, 34, 34, 37, 37, 37, 37, 37, 39, 39, 39, 39, 39, 40, 41, 41, 39, 40, 41, 41, 41, 41, 40, 41, 40 },
- null)
- ));
- goldSizes.put(ltStr(lane, tile), 20);
-
- lane = 3;
- tile = 1101;
- goldIndices.put(ltStr(lane, tile), makeList(0, 8, 9, 10));
- goldData.put(ltStr(lane, tile), makeList(
- makeCd(3, 1101, 1224, 1003, true,
- new byte[]{ P, C, C, A, A, T, T, A, C, A, T, T, T, T, C, T, C, T, C, T, A, T, C, A, C, A, G, G, T, C, G, C, A, T, T, T, T, C, T, T, G, G, T, T, G, G, G, T, C, T, C, G, G, G, C, T, T, G },
- new byte[]{ 2, 16, 25, 33, 35, 35, 37, 37, 39, 39, 39, 39, 39, 40, 38, 40, 39, 40, 40, 40, 39, 39, 40, 40, 40, 31, 33, 34, 35, 37, 37, 37, 37, 34, 34, 34, 37, 37, 37, 37, 37, 39, 39, 39, 39, 39, 40, 39, 40, 41, 41, 41, 41, 40, 38, 38, 36, 39 },
- null),
- makeCd(3, 1101, 1195, 1128, false,
- new byte[]{ T, C, P, T, P, P, C, T, C, T, G, C, G, C, T, C, C, C, T, C, T, C, G, C, T, A, G, G, T, C, G, C, A, A, C, C, A, G, G, A, G, G, A, A, A, G, T, G, T, G, G, G, G, C, C, A, G, A },
- new byte[]{ 27, 26, 2, 17, 2, 2, 17, 17, 31, 30, 24, 30, 28, 30, 30, 30, 27, 30, 30, 27, 31, 22, 28, 30, 30, 34, 34, 31, 37, 37, 37, 37, 37, 31, 30, 33, 33, 35, 35, 30, 35, 37, 34, 35, 37, 39, 40, 38, 33, 38, 38, 36, 38, 32, 30, 36, 34, 37 },
- null),
- makeCd(3, 1101, 1232, 1155, true,
- new byte[]{ A, A, A, C, C, C, A, A, T, G, A, T, C, A, G, G, T, A, T, G, T, A, C, C, C, A, G, G, T, C, G, C, A, C, T, T, A, C, C, T, A, G, T, T, T, C, C, A, G, C, A, G, T, C, T, G, C, T },
- new byte[]{ 34, 34, 34, 37, 37, 37, 37, 37, 39, 39, 33, 39, 37, 40, 40, 41, 36, 39, 38, 39, 39, 40, 41, 40, 40, 34, 34, 34, 35, 37, 37, 37, 37, 34, 34, 34, 37, 37, 37, 37, 35, 39, 39, 37, 39, 39, 41, 41, 40, 41, 40, 41, 41, 40, 41, 41, 34, 39 },
- null),
- makeCd(3, 1101, 1240, 1185, false,
- new byte[]{ C, C, A, G, C, A, G, G, C, G, G, G, G, G, C, A, G, G, G, G, G, G, C, A, G, A, G, G, T, C, G, C, A, A, C, A, G, T, A, G, G, C, A, C, T, C, A, C, T, A, C, A, T, G, C, G, G, C },
- new byte[]{ 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 31, 33, 34, 35, 37, 37, 37, 37, 33, 10, 10, 32, 33, 25, 35, 35, 30, 35, 26, 17, 32, 32, 36, 33, 30, 10, 27, 34, 19, 10, 27, 31, 37 },
- null)
+ makeCd(lane, tile, 1123, 2095, true,
+ new byte[]{P,T,G,G,A,C,A,A,C,A,T,G,T,T,C,G,A,G,A,G,C,T,A,C,A,C,A,G,C,G,G,T,A,T,C,C,G,C,C,T,C,C,A,G,C,T,T,C,A,G,C,T,T,C,T,C,C,T},
+ new byte[]{2,16,28,33,33,35,35,35,37,37,37,37,35,38,37,38,40,38,30,37,26,39,39,37,40,31,30,31,35,35,37,31,31,31,31,31,37,35,35,37,37,39,39,39,39,39,41,39,38,38,41,40,41,41,41,36,39,39},
+ "CAGCGGTA"),
+ makeCd(lane, tile, 1162, 2139, true,
+ new byte[]{A,G,A,G,G,T,G,A,A,A,T,T,C,T,T,G,G,A,C,C,G,G,C,G,C,T,G,C,T,G,C,T,G,A,T,C,G,T,T,T,A,T,G,G,T,C,G,G,A,A,C,T,A,C,G,A,C,G},
+ new byte[]{31,31,31,35,35,35,35,35,39,37,39,39,39,35,33,25,36,37,39,39,34,32,38,30,35,34,34,34,37,37,37,37,37,33,34,34,37,37,37,37,37,39,39,39,39,39,40,41,41,41,41,41,41,41,40,41,41,40},
+ "TGCTGCTG"),
+ makeCd(lane, tile, 1013, 2146, true,
+ new byte[]{P,A,C,A,C,T,G,C,T,G,C,A,G,A,T,G,A,C,A,A,G,C,A,G,C,C,T,A,T,G,C,G,T,P,P,P,P,C,G,C,T,A,G,A,A,C,C,A,A,C,T,T,A,T,T,C,A,T},
+ new byte[]{2,19,33,35,37,37,37,37,39,39,39,39,39,41,41,41,41,41,41,41,41,41,41,41,41,34,34,34,37,37,37,37,37,2,2,2,2,17,19,28,30,31,31,30,31,30,31,31,30,31,31,31,31,31,31,30,31,31},
+ "CTATGCGT"),
+ makeCd(lane, tile, 1245, 2154, true,
+ new byte[]{T,C,G,T,T,A,A,G,T,A,T,A,T,T,C,T,T,A,G,G,T,A,T,T,T,C,T,G,T,A,A,T,C,A,C,C,A,A,T,C,A,G,T,A,G,C,A,C,C,A,C,T,A,T,A,C,A,C},
+ new byte[]{34,34,34,37,37,35,37,37,37,39,37,39,39,40,40,41,41,41,41,41,37,41,41,41,40,31,34,34,37,37,37,37,37,34,34,34,37,37,37,37,37,39,39,39,39,39,41,41,41,41,41,41,40,41,41,41,41,41},
+ "CTGTAATC")
));
- goldSizes.put(ltStr(lane, tile), 20);
+ goldSizes.put(ltStr(lane, tile), 60);
- tile = 1201;
- goldIndices.put(ltStr(lane, tile), makeList(2, 16, 17, 19));
- goldData.put(ltStr(lane, tile), makeList(
- makeCd(3, 1201, 1208, 1031, true,
- new byte[]{ C, T, G, C, P, C, A, G, G, C, A, T, T, C, A, C, A, A, T, G, G, A, G, G, C, P, G, G, T, C, G, C, A, T, G, C, T, G, G, G, A, T, T, A, C, A, G, G, C, G, T, G, G, G, G, A, C, T },
- new byte[]{ 31, 31, 31, 35, 2, 17, 28, 32, 37, 33, 30, 37, 37, 27, 34, 36, 27, 25, 34, 39, 36, 32, 37, 38, 27, 2, 16, 28, 32, 35, 35, 37, 35, 33, 31, 30, 35, 37, 32, 37, 30, 37, 39, 30, 35, 33, 36, 38, 33, 37, 39, 30, 2, 2, 2, 2, 2, 2 },
- null),
- makeCd(3, 1201, 1242, 1201, true,
- new byte[]{ A, T, C, T, G, C, C, G, C, A, C, C, T, C, T, G, A, C, T, T, T, G, T, A, C, P, G, G, T, C, G, C, A, G, G, A, A, A, G, G, G, T, A, A, T, A, A, G, T, A, T, G, A, C, T, T, G, A },
- new byte[]{ 31, 31, 27, 35, 35, 35, 35, 35, 32, 32, 37, 37, 37, 33, 18, 30, 27, 36, 37, 34, 39, 27, 34, 27, 24, 2, 19, 28, 33, 35, 37, 37, 35, 26, 30, 30, 35, 32, 35, 23, 35, 10, 32, 33, 37, 35, 39, 40, 19, 34, 37, 41, 39, 40, 38, 39, 39, 39 },
- null),
- makeCd(3, 1201, 1220, 1217, true,
- new byte[]{ A, G, A, C, C, G, G, C, G, G, A, G, A, T, G, T, G, A, A, C, G, T, G, G, G, P, G, G, T, C, G, C, A, T, G, G, G, A, A, G, T, G, C, T, G, C, A, G, G, C, T, C, A, C, T, G, C, G },
- new byte[]{ 30, 30, 30, 35, 35, 35, 35, 35, 35, 35, 25, 35, 30, 26, 33, 30, 35, 19, 33, 23, 35, 14, 33, 34, 2, 2, 16, 28, 33, 35, 35, 37, 37, 31, 34, 34, 37, 37, 37, 37, 35, 37, 39, 38, 35, 39, 40, 39, 40, 38, 40, 41, 38, 38, 38, 39, 40, 40 },
- null),
- makeCd(3, 1201, 1364, 1001, false,
- new byte[]{ P, T, T, T, A, A, A, C, C, C, C, A, A, C, A, A, T, T, A, A, T, T, T, T, A, P, G, G, T, C, G, C, A, T, G, P, P, G, A, A, G, T, G, C, A, G, T, T, A, G, A, T, C, C, T, T, C, A },
- new byte[]{ 2, 10, 16, 22, 32, 32, 32, 31, 32, 10, 30, 28, 32, 34, 27, 32, 32, 32, 34, 22, 22, 31, 33, 30, 30, 2, 16, 28, 33, 35, 37, 37, 37, 28, 33, 2, 2, 19, 10, 28, 32, 17, 32, 10, 17, 17, 27, 19, 34, 37, 10, 18, 32, 32, 34, 19, 10, 32 },
- null)
- ));
- goldSizes.put(ltStr(lane, tile), 20);
-
- tile = 2101;
- goldIndices.put(ltStr(lane, tile), makeList(0, 1, 2, 3));
- goldData.put(ltStr(lane, tile), makeList(
- makeCd(3, 2101, 1125, 1003, true,
- new byte[]{ P, G, T, C, T, G, G, C, C, T, T, G, C, T, G, C, T, G, T, C, C, C, T, G, G, A, G, G, T, C, G, C, A, C, C, C, A, G, A, T, T, T, T, T, T, A, T, C, A, C, A, G, A, G, T, T, G, A },
- new byte[]{ 2, 16, 28, 35, 35, 35, 37, 37, 39, 39, 39, 39, 39, 41, 41, 38, 40, 40, 40, 40, 41, 40, 40, 41, 41, 31, 34, 34, 35, 37, 37, 37, 37, 31, 31, 31, 37, 37, 35, 36, 37, 39, 39, 39, 39, 37, 40, 39, 38, 40, 38, 39, 38, 40, 39, 39, 40, 39 },
- null),
- makeCd(3, 2101, 1099, 1006, true,
- new byte[]{ P, T, G, C, T, G, T, T, T, C, A, C, A, G, C, C, T, C, T, T, C, A, A, T, C, A, G, G, T, C, G, C, A, A, T, T, T, T, A, C, T, A, T, T, C, T, T, T, C, A, G, G, C, T, T, T, C, A },
- new byte[]{ 2, 16, 28, 35, 35, 37, 35, 35, 39, 37, 39, 39, 38, 41, 40, 40, 40, 40, 40, 41, 40, 39, 40, 40, 40, 34, 34, 34, 37, 37, 37, 37, 37, 31, 31, 31, 37, 37, 36, 35, 37, 37, 39, 39, 39, 39, 41, 41, 41, 41, 41, 40, 40, 41, 40, 41, 39, 37 },
- null),
- makeCd(3, 2101, 1198, 1014, true,
- new byte[]{ P, C, C, A, G, A, T, G, T, T, A, C, A, T, G, G, T, G, A, G, C, C, A, G, A, A, G, G, T, C, G, C, A, T, C, A, G, T, C, T, C, T, C, A, C, T, G, T, G, C, T, G, T, G, T, C, C, T },
- new byte[]{ 2, 16, 28, 35, 35, 35, 37, 37, 39, 39, 39, 39, 39, 41, 41, 41, 38, 40, 39, 40, 40, 41, 40, 39, 39, 34, 34, 34, 37, 37, 37, 37, 37, 34, 34, 34, 37, 37, 37, 37, 37, 39, 37, 39, 39, 39, 41, 41, 41, 41, 41, 41, 40, 41, 41, 41, 41, 41 },
- null),
- makeCd(3, 2101, 1078, 1021, true,
- new byte[]{ G, C, A, A, A, P, G, A, T, G, A, G, A, T, C, G, C, T, G, G, G, C, C, T, G, A, G, G, T, C, G, C, A, G, C, A, C, T, C, G, G, C, C, T, C, G, A, G, T, A, T, C, C, T, T, T, A, G },
- new byte[]{ 34, 34, 34, 37, 37, 2, 17, 32, 37, 39, 39, 39, 39, 38, 37, 40, 40, 40, 40, 40, 40, 39, 40, 40, 40, 31, 33, 34, 35, 37, 37, 37, 37, 34, 34, 34, 37, 37, 37, 37, 37, 39, 37, 39, 38, 39, 40, 41, 41, 40, 38, 40, 41, 39, 40, 40, 29, 37 },
- null)
- ));
- goldSizes.put(ltStr(lane, tile), 20);
-
- //Using the same data as Lane 2 except breaking it up differently, this will cause the EAMSS filtering to mess with the data a little, rather than 25T8B25T it will become 19T8B8B19T
- lane = 4;
- tile = 1101;
- goldIndices.put(ltStr(lane, tile), makeList(0, 8, 9, 10));
+ tile = 11101;
+ goldIndices.put(ltStr(lane, tile), makeList(0, 2, 10, 18, 19));
goldData.put(ltStr(lane, tile), makeList(
- makeCd(lane, tile, 1178, 1003, false,
- new byte[]{ P, C, A, A, P, P, P, C, A, C, C, T, C, C, C, A, G, A, G, T, C, G, T, G, G, A, G, G, T, C, G, C, A, A, G, P, G, A, C, C, A, G, A, A, G, C, T, C, T, C, T, G, A, G, T, T, A, G },
- new byte[]{ 2, 15, 26, 31, 2, 2, 2, 17, 17, 28, 28, 29, 30, 30, 31, 30, 30, 29, 30, 30, 30, 30, 31, 7, 7, 33, 33, 34, 37, 37, 37, 37, 35, 31, 33, 2, 19, 32, 35, 35, 37, 39, 39, 38, 39, 39, 40, 40, 41, 38, 40, 41, 34, 39, 39, 40, 40, 41 },
- null),
- makeCd(lane, tile, 1215, 1071, true,
- new byte[]{ A, G, G, G, A, T, T, T, C, A, G, T, T, G, G, T, G, G, T, G, G, G, G, C, A, A, G, G, T, C, G, C, A, G, A, A, C, A, T, A, T, T, T, G, T, C, T, C, A, G, A, G, A, G, A, C, T, T },
- new byte[]{ 30, 31, 31, 32, 35, 35, 35, 35, 32, 23, 35, 30, 34, 38, 36, 27, 32, 38, 27, 34, 37, 38, 36, 32, 37, 33, 31, 34, 37, 37, 37, 37, 37, 31, 31, 31, 35, 35, 35, 33, 25, 35, 30, 39, 37, 32, 34, 37, 37, 39, 40, 40, 29, 38, 28, 35, 31, 37 },
- null),
- makeCd(lane, tile, 1189, 1093, false,
- new byte[]{ C, C, A, C, C, G, T, G, A, G, A, A, T, G, C, G, C, C, A, T, C, T, G, C, A, A, G, G, T, C, G, C, A, A, A, A, A, C, A, G, A, A, C, C, C, A, G, T, T, A, G, C, A, G, T, A, T, G },
- new byte[]{ 28, 16, 22, 27, 16, 23, 32, 32, 10, 17, 28, 17, 17, 30, 19, 32, 21, 30, 2, 27, 10, 31, 27, 28, 31, 33, 33, 33, 37, 37, 37, 37, 37, 16, 23, 10, 32, 30, 2, 32, 32, 18, 10, 27, 34, 16, 10, 17, 27, 11, 11, 32, 34, 39, 2, 2, 2, 2 },
- null),
- makeCd(lane, tile, 1171, 1103, false,
- new byte[]{ G, T, P, G, P, P, P, G, G, A, G, A, T, G, T, A, C, T, G, G, T, G, A, A, A, A, G, G, T, C, G, C, A, T, C, T, T, T, G, G, C, T, T, G, C, T, A, A, A, T, T, T, T, A, T, T, T, A },
- new byte[]{ 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 27, 8, 8, 13, 21, 31, 31, 34, 35, 35, 37, 37, 37, 16, 10, 25, 32, 2, 2, 10, 10, 32, 33, 31, 30, 30, 25, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 },
- null)
- ));
- goldSizes.put(ltStr(lane, tile), 20);
-
- tile = 1201;
- goldIndices.put(ltStr(lane, tile), makeList(1, 3, 4, 17));
+ makeCd(lane, tile, 1140, 2120, true,
+ new byte[]{P,A,A,C,T,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{2,32,32,32,32,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null),
+ makeCd(lane, tile, 1047, 2122, false,
+ new byte[]{P,A,A,G,A,C,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{2,32,32,32,27,37,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null),
+ makeCd(lane, tile, 1069, 2159, true,
+ new byte[]{P,C,T,T,G,T,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{2,32,32,32,32,37,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null),
+ makeCd(lane, tile, 1175, 2197, true,
+ new byte[]{P,A,A,A,T,T,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null),
+ makeCd(lane, tile, 1048, 2197, false,
+ new byte[]{P,A,A,G,A,C,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{2,27,22,32,32,37,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null)
+ )
+ );
+ goldSizes.put(ltStr(lane, tile), 341292);
+
+ tile = 11102;
+ goldIndices.put(ltStr(lane, tile), makeList(0, 2, 10, 18, 19));
goldData.put(ltStr(lane, tile), makeList(
- makeCd(lane, tile, 1228, 1012, true,
- new byte[]{ P, T, G, G, T, C, A, T, C, T, G, C, A, G, G, T, T, T, C, T, G, A, G, A, T, P, G, G, T, C, G, C, A, T, T, T, C, T, T, A, T, A, G, A, A, A, C, A, T, C, T, T, T, T, A, T, T, T },
- new byte[]{ 2, 16, 25, 33, 35, 33, 19, 35, 35, 35, 37, 35, 37, 38, 37, 35, 35, 38, 36, 37, 40, 34, 39, 33, 37, 2, 2, 2, 2, 28, 33, 31, 23, 31, 33, 31, 35, 37, 37, 35, 35, 33, 37, 37, 39, 39, 41, 40, 41, 37, 39, 41, 40, 40, 37, 39, 39, 34 },
- null),
- makeCd(lane, tile, 1229, 1034, true,
- new byte[]{ C, C, T, G, T, T, G, T, A, C, G, T, C, C, C, A, G, T, A, T, G, G, A, G, C, P, G, G, T, C, G, C, A, C, T, C, T, A, T, C, C, C, A, G, A, C, C, C, T, T, C, T, C, A, G, G, C, A },
- new byte[]{ 34, 34, 34, 37, 37, 37, 37, 37, 38, 39, 39, 39, 39, 40, 38, 39, 39, 41, 40, 40, 41, 41, 24, 31, 34, 2, 16, 28, 32, 35, 35, 37, 37, 31, 31, 31, 35, 35, 37, 35, 35, 27, 34, 35, 39, 35, 39, 35, 37, 39, 38, 40, 36, 39, 38, 39, 39, 40 },
- null),
- makeCd(lane, tile, 1194, 1053, true,
- new byte[]{ A, G, A, T, C, T, C, A, T, A, T, C, G, T, C, G, C, T, C, G, T, C, A, T, G, P, A, T, T, A, G, A, T, T, G, T, C, G, A, T, T, A, T, C, G, C, A, C, T, G, G, T, G, C, G, A, A, T },
- new byte[]{ 31, 31, 31, 37, 37, 35, 35, 37, 35, 37, 39, 39, 39, 38, 40, 38, 40, 40, 41, 41, 41, 36, 34, 36, 36, 2, 16, 16, 33, 28, 35, 32, 33, 31, 31, 31, 37, 37, 35, 35, 37, 37, 39, 39, 37, 30, 39, 33, 36, 36, 39, 36, 39, 39, 38, 30, 30, 30 },
- null),
- makeCd(lane, tile, 1173, 1158, true,
- new byte[]{ A, C, G, C, P, G, G, C, A, A, T, G, A, T, G, G, C, G, T, C, T, C, G, C, A, P, G, G, T, C, G, C, A, T, G, C, A, T, C, G, A, C, T, G, C, C, C, T, A, T, T, T, T, G, T, C, T, A },
- new byte[]{ 31, 30, 31, 35, 2, 17, 32, 32, 37, 37, 37, 37, 37, 40, 40, 40, 40, 40, 40, 40, 40, 40, 38, 38, 34, 2, 16, 28, 35, 35, 37, 37, 37, 33, 31, 31, 30, 35, 35, 35, 35, 30, 37, 39, 37, 37, 38, 37, 38, 39, 38, 34, 29, 36, 38, 39, 41, 38 },
- null)
-
- ));
- goldSizes.put(ltStr(lane, tile), 20);
-
- tile = 2101;
- goldIndices.put(ltStr(lane, tile), makeList(0, 11, 13, 19));
+ makeCd(lane, tile, 1140, 2120, true,
+ new byte[]{P,A,A,G,A,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{2,32,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null),
+ makeCd(lane, tile, 1047, 2122, false,
+ new byte[]{P,G,C,T,T,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{2,32,32,32,32,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null),
+ makeCd(lane, tile, 1069, 2159, true,
+ new byte[]{P,G,C,T,T,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{2,32,32,32,32,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null),
+ makeCd(lane, tile, 1175, 2197, true,
+ new byte[]{P,G,C,T,T,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{2,32,32,32,32,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null),
+ makeCd(lane, tile, 1048, 2197, false,
+ new byte[]{P,G,C,T,T,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{2,32,32,32,32,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null)
+ )
+ );
+ goldSizes.put(ltStr(lane, tile), 366884);
+
+ tile = 11103;
+ goldIndices.put(ltStr(lane, tile), makeList(0, 2, 10, 18, 19));
goldData.put(ltStr(lane, tile), makeList(
- makeCd(lane, tile, 1139, 1012, true,
- new byte[]{ P, G, T, A, T, C, A, T, T, T, T, G, T, T, A, A, A, A, G, T, C, C, T, A, C, P, G, G, T, C, G, C, A, C, A, A, A, A, T, P, A, T, G, C, T, C, A, A, G, A, G, T, G, C, C, C, A, G },
- new byte[]{ 2, 16, 16, 32, 33, 35, 26, 35, 37, 37, 35, 30, 34, 38, 37, 37, 37, 33, 37, 36, 39, 40, 37, 35, 31, 2, 16, 28, 35, 35, 37, 37, 37, 27, 30, 26, 35, 35, 35, 2, 17, 17, 32, 27, 30, 34, 38, 39, 33, 38, 38, 40, 39, 34, 29, 31, 37, 36 },
- null),
- makeCd(lane, tile, 1177, 1057, true,
- new byte[]{ A, A, G, A, G, A, A, C, A, C, G, T, T, A, T, A, G, G, A, C, A, T, T, T, T, P, G, G, T, C, G, C, A, A, G, G, C, C, A, A, G, T, G, C, C, C, C, T, C, T, T, G, G, T, G, T, C, T },
- new byte[]{ 31, 27, 30, 35, 35, 30, 35, 35, 35, 37, 39, 37, 37, 38, 39, 36, 39, 39, 34, 36, 38, 38, 39, 40, 40, 2, 16, 28, 35, 35, 37, 37, 37, 31, 31, 31, 35, 35, 32, 37, 35, 39, 39, 32, 37, 35, 30, 36, 38, 36, 38, 39, 41, 36, 38, 36, 24, 34 },
- null),
- makeCd(lane, tile, 1070, 1062, false,
- new byte[]{ A, P, T, A, P, P, P, C, A, G, G, G, A, T, A, A, C, T, C, A, A, P, P, G, C, P, G, G, T, C, G, C, A, A, A, C, T, C, A, G, A, C, T, A, C, A, G, G, T, G, C, A, G, A, A, A, A, C },
- new byte[]{ 27, 2, 15, 31, 2, 2, 2, 19, 17, 31, 30, 31, 30, 30, 30, 30, 30, 30, 30, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2, 35, 37, 37, 35, 31, 31, 34, 35, 35, 33, 37, 37, 37, 39, 39, 39, 39, 41, 40, 37, 39, 38, 38, 38, 39, 36, 39, 38, 38 },
- null),
- makeCd(lane, tile, 1246, 1085, true,
- new byte[]{ T, C, T, T, C, C, C, A, T, G, A, G, G, G, C, A, C, A, G, T, T, T, G, A, C, P, G, G, T, C, G, C, A, A, G, T, C, G, A, A, T, T, G, T, A, A, T, T, C, C, A, T, T, T, G, C, C, C },
- new byte[]{ 34, 34, 34, 37, 37, 37, 37, 37, 39, 39, 39, 39, 39, 40, 39, 39, 40, 40, 39, 38, 39, 40, 41, 39, 40, 2, 16, 28, 33, 35, 35, 37, 37, 34, 34, 34, 37, 37, 37, 37, 37, 39, 39, 39, 39, 39, 40, 41, 41, 39, 40, 41, 41, 41, 41, 40, 41, 40 },
- null)
- ));
- goldSizes.put(ltStr(lane, tile), 20);
+ makeCd(lane, tile, 1140, 2120, true,
+ new byte[]{P,G,C,T,T,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{2,32,32,32,32,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null),
+ makeCd(lane, tile, 1047, 2122, false,
+ new byte[]{P,G,C,T,T,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{2,32,32,32,32,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null),
+ makeCd(lane, tile, 1069, 2159, true,
+ new byte[]{P,G,C,T,T,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{2,32,32,32,32,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null),
+ makeCd(lane, tile, 1175, 2197, true,
+ new byte[]{P,G,C,T,T,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{2,32,32,32,32,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null),
+ makeCd(lane, tile, 1048, 2197, false,
+ new byte[]{P,G,C,T,T,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P},
+ new byte[]{2,32,32,32,32,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2},
+ null)
+ )
+ );
+ goldSizes.put(ltStr(lane, tile), 336434);
}
- public static Map<Integer, ClusterData> clusterData(final int lane, final List<Integer> tiles, final String readStructure, final IlluminaDataType ... dataTypes) {
+ public static Map<Integer, ClusterData> clusterData(final int lane, final List<Integer> tiles, final String readStructure, final IlluminaDataType... dataTypes) {
final List<Integer> sortedTiles = new ArrayList<Integer>(tiles);
Collections.sort(sortedTiles);
final Map<Integer, ClusterData> data = new HashMap<Integer, ClusterData>();
int offset = 0;
- for(final int tile : sortedTiles) {
- final String key = ltStr(lane,tile);
+ for (final int tile : sortedTiles) {
+ final String key = ltStr(lane, tile);
final List<ClusterData> cds = goldData.get(key);
final List<Integer> readNos = goldIndices.get(key);
final int size = goldSizes.get(key);
-
- for(int i = 0; i < cds.size(); i++) {
+
+ for (int i = 0; i < cds.size(); i++) {
data.put(offset + readNos.get(i), selectiveCopyCd(cds.get(i), readStructure, dataTypes));
}
@@ -321,14 +199,12 @@ public class BinTdUtil {
return data;
}
- public static ReadData [] copyReadData(final ReadStructure rs, final IlluminaDataType [] dts, final ClusterData toCopy) {
+ public static ReadData[] copyReadData(final ReadStructure rs, final IlluminaDataType[] dts, final ClusterData toCopy) {
boolean doBases = false;
boolean doQuals = false;
- boolean doInts = false;
- boolean doNoise = false;
- for(final IlluminaDataType dt : dts) {
- switch(dt) {
+ for (final IlluminaDataType dt : dts) {
+ switch (dt) {
case BaseCalls:
doBases = true;
break;
@@ -336,49 +212,32 @@ public class BinTdUtil {
case QualityScores:
doQuals = true;
break;
-
- case RawIntensities:
- doInts = true;
- break;
-
- case Noise:
- doNoise = true;
- break;
}
}
- if(!doBases && !doQuals && !doInts && !doNoise)
+ if (!doBases && !doQuals)
return null;
final ReadData rdToCopy = toCopy.getRead(0); //Only gonna be one read in this
- final ReadData [] rds = new ReadData[rs.nonSkips.length()];
+ final ReadData[] rds = new ReadData[rs.nonSkips.length()];
int index = 0;
int baseIndex = 0;
- for(int i = 0; i < rs.descriptors.size(); i++) {
+ for (int i = 0; i < rs.descriptors.size(); i++) {
final ReadDescriptor readDesc = rs.descriptors.get(i);
- if(readDesc.type != ReadType.S) {
+ if (readDesc.type != ReadType.S) {
final ReadData curRead = new ReadData(readDesc.type);
- if(doBases) {
- final byte [] bases = Arrays.copyOfRange(rdToCopy.getBases(), baseIndex, baseIndex + readDesc.length);
+ if (doBases) {
+ final byte[] bases = Arrays.copyOfRange(rdToCopy.getBases(), baseIndex, baseIndex + readDesc.length);
curRead.setBases(bases);
}
- if(doQuals) {
- final byte [] quals = Arrays.copyOfRange(rdToCopy.getQualities(), baseIndex, baseIndex + readDesc.length);
+ if (doQuals) {
+ final byte[] quals = Arrays.copyOfRange(rdToCopy.getQualities(), baseIndex, baseIndex + readDesc.length);
curRead.setQualities(quals);
}
- if(doInts) {
- final FourChannelIntensityData fcid = copyIntensities(rdToCopy.getRawIntensities(), baseIndex, readDesc.length);
- curRead.setRawIntensities(fcid);
- }
-
- if(doNoise) {
- final FourChannelIntensityData fcid = copyIntensities(rdToCopy.getNoise(), baseIndex, readDesc.length);
- curRead.setNoise(fcid);
- }
rds[index++] = curRead;
}
@@ -398,15 +257,15 @@ public class BinTdUtil {
return fcid;
}
- public static ClusterData selectiveCopyCd(final ClusterData toCopy, final String readStructure, final IlluminaDataType ... dataTypes) {
+ public static ClusterData selectiveCopyCd(final ClusterData toCopy, final String readStructure, final IlluminaDataType... dataTypes) {
final ReadStructure rs = new ReadStructure(readStructure);
- final ReadData [] rd = copyReadData(rs, dataTypes, toCopy);
+ final ReadData[] rd = copyReadData(rs, dataTypes, toCopy);
final ClusterData cd = new ClusterData(rd);
cd.setTile(toCopy.getTile());
cd.setLane(toCopy.getLane());
- for(final IlluminaDataType idt : dataTypes) {
- switch(idt) {
+ for (final IlluminaDataType idt : dataTypes) {
+ switch (idt) {
case Position:
cd.setX(toCopy.getX());
cd.setY(toCopy.getY());
@@ -428,7 +287,7 @@ public class BinTdUtil {
return cd;
}
- public static ClusterData makeCd(final int lane, final int tile, final int xCoord, final int yCoord, final boolean pf, final byte [] bases, final byte[] qualities, final String matchedBarcode) {
+ public static ClusterData makeCd(final int lane, final int tile, final int xCoord, final int yCoord, final boolean pf, final byte[] bases, final byte[] qualities, final String matchedBarcode) {
final ReadData rd = new ReadData();
rd.setBases(Arrays.copyOf(bases, bases.length));
rd.setQualities(Arrays.copyOf(qualities, bases.length));
diff --git a/src/tests/java/net/sf/picard/illumina/parser/ClusterIntensityFileReaderTest.java b/src/tests/java/net/sf/picard/illumina/parser/ClusterIntensityFileReaderTest.java
deleted file mode 100644
index ab80eee..0000000
--- a/src/tests/java/net/sf/picard/illumina/parser/ClusterIntensityFileReaderTest.java
+++ /dev/null
@@ -1,102 +0,0 @@
-/*
- * The MIT License
- *
- * Copyright (c) 2009 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
-package net.sf.picard.illumina.parser;
-
-import org.testng.annotations.Test;
-import org.testng.annotations.DataProvider;
-import org.testng.Assert;
-
-import java.io.File;
-
-/**
- * @author alecw at broadinstitute.org
- */
-public class ClusterIntensityFileReaderTest {
- private static final File TEST_DATA_DIR = new File("testdata/net/sf/picard/illumina/IlluminaTests/");
- private static final File INTENSITY_FILES_DIR = new File(TEST_DATA_DIR, "L001/C1.1");
-
- private static final int NUM_BASES = 2;
- private static final int NUM_CLUSTERS = 153010;
- private static enum DATA_FIELDS {CLUSTER_INDEX, A_CHANNEL, C_CHANNEL, G_CHANNEL, T_CHANNEL}
-
- //Cluster#, Expected A,C,G,T
- private static final int[][] CNF_DATA = new int[][]{
- //cluster A C G T
- new int[]{0, 0, 9, 0, 0},
- new int[]{1, 0, 15, 0, 0},
- new int[]{2, 0, 15, 0, 11},
- new int[]{51, 9, 23, 0, 9},
- new int[]{10001, 8, 22, 7, 11},
- new int[]{10002, 10, 9, 7, 9},
- new int[]{80000, 13, 55, 12, 76},
- new int[]{80001, 10, 54, 12, 73},
- new int[]{100001, 12, 33, 9, 45},
- new int[]{100010, 11, 52, 11, 70},
- new int[]{153009, 0, 0, 0, 0}
- };
-
- //Cluster#, Expected A,C,G,T
- private static final int[][] CIF_DATA = new int[][]{
- //cluster A C G T
- new int[]{0, 0, 0, 0, 0},
- new int[]{1, 0, 0, 0, 0},
- new int[]{2, 0, 0, 0, 0},
- new int[]{20001, 436, 333, -164, -63},
- new int[]{20002, 476, 354, -31, -61},
- new int[]{90001, 59, 332, -14, -240},
- new int[]{90002, -91, -29, -330, 1090},
- new int[]{153008, 0, 0, 0, 0},
- new int[]{153009, 0, 0, 0, 0}
- };
-
- @Test(dataProvider="data")
- public void testBasic(final File cifFile, final int [][] goldData) throws Exception {
- final ClusterIntensityFileReader cifr = new ClusterIntensityFileReader(cifFile);
- System.out.println("File: " + cifr.getFile() + "; First cycle: " + cifr.getFirstCycle() +
- "; Num cycles: " + cifr.getNumCycles() + "; Num clusters: " + cifr.getNumClusters());
-
- for (int [] goldRow : goldData) {
- final int cluster = goldRow[DATA_FIELDS.CLUSTER_INDEX.ordinal()];
- Assert.assertEquals(1, cifr.getNumCycles(), "Expected only 1 cycle, cluster: " + cluster);
-
- final int cycle = cifr.getFirstCycle();
- final String msg = "Cycle: " + cycle + "; Cluster: " + cluster;
- Assert.assertEquals(cifr.getValue(cluster, IntensityChannel.A, cycle), goldRow[DATA_FIELDS.A_CHANNEL.ordinal()], msg);
- Assert.assertEquals(cifr.getValue(cluster, IntensityChannel.C, cycle), goldRow[DATA_FIELDS.C_CHANNEL.ordinal()], msg);
- Assert.assertEquals(cifr.getValue(cluster, IntensityChannel.G, cycle), goldRow[DATA_FIELDS.G_CHANNEL.ordinal()], msg);
- Assert.assertEquals(cifr.getValue(cluster, IntensityChannel.T, cycle), goldRow[DATA_FIELDS.T_CHANNEL.ordinal()], msg);
- }
-
- Assert.assertEquals(NUM_CLUSTERS, cifr.getNumClusters());
- }
-
- @DataProvider(name = "data")
- private Object[][] getTestData()
- {
- return new Object[][]{
- {new File(INTENSITY_FILES_DIR, "s_1_1.cnf"), CNF_DATA},
- {new File(INTENSITY_FILES_DIR, "s_1_1.cif"), CIF_DATA},
- };
- }
-}
diff --git a/src/tests/java/net/sf/picard/illumina/parser/CycleIlluminaFileMapTest.java b/src/tests/java/net/sf/picard/illumina/parser/CycleIlluminaFileMapTest.java
index 8c5b887..eb775dd 100644
--- a/src/tests/java/net/sf/picard/illumina/parser/CycleIlluminaFileMapTest.java
+++ b/src/tests/java/net/sf/picard/illumina/parser/CycleIlluminaFileMapTest.java
@@ -40,8 +40,8 @@ import static net.sf.samtools.util.CollectionUtil.makeList;
*/
public class CycleIlluminaFileMapTest {
//TODO: REVAMP THIS
- private static final File TEST_DATA_DIR = new File("testdata/net/sf/picard/illumina/IlluminaTests/L001");
- private static final File ZERO_LENGTH_TEST_DATA_DIR = new File("testdata/net/sf/picard/illumina/IlluminaTests/L002");
+ private static final File TEST_DATA_DIR = new File("testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001");
+ private static final File ZERO_LENGTH_TEST_DATA_DIR = new File("testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L002");
private static final int [] ALL_CYCLES = {1,2,3,4};
private static String laneToDir(int lane) {
@@ -60,36 +60,28 @@ public class CycleIlluminaFileMapTest {
public Object [][] iteratorTestData() {
return new Object[][] {
new Object[] {
- TEST_DATA_DIR, 1, 1, ".cif",
- makeList(new File(TEST_DATA_DIR + "/C1.1", "s_1_1.cif"),
- new File(TEST_DATA_DIR + "/C2.1", "s_1_1.cif"),
- new File(TEST_DATA_DIR + "/C3.1", "s_1_1.cif"),
- new File(TEST_DATA_DIR + "/C4.1", "s_1_1.cif")),
+ TEST_DATA_DIR, 1, 1101, ".bcl",
+ makeList(new File(TEST_DATA_DIR + "/C1.1", "s_1_1101.bcl"),
+ new File(TEST_DATA_DIR + "/C2.1", "s_1_1101.bcl"),
+ new File(TEST_DATA_DIR + "/C3.1", "s_1_1101.bcl"),
+ new File(TEST_DATA_DIR + "/C4.1", "s_1_1101.bcl")),
ALL_CYCLES
},
new Object[] {
- TEST_DATA_DIR, 1, 2, ".cnf",
- makeList(new File(TEST_DATA_DIR + "/C1.1", "s_1_2.cnf"),
- new File(TEST_DATA_DIR + "/C2.1", "s_1_2.cnf"),
- new File(TEST_DATA_DIR + "/C3.1", "s_1_2.cnf"),
- new File(TEST_DATA_DIR + "/C4.1", "s_1_2.cnf")),
- ALL_CYCLES
- },
- new Object[] {
- ZERO_LENGTH_TEST_DATA_DIR, 1, 1, ".cif", new ArrayList<File>(), new int[]{},
+ ZERO_LENGTH_TEST_DATA_DIR, 1, 1101, ".bcl", new ArrayList<File>(), new int[]{},
},
new Object[] {
- TEST_DATA_DIR, 1, 3, ".cnf", new ArrayList<File>(), new int[]{}
+ TEST_DATA_DIR, 1, 1201, ".bcl", new ArrayList<File>(), new int[]{}
},
new Object[] {
- TEST_DATA_DIR, 2, 1, ".cnf", new ArrayList<File>(), new int[]{}
+ TEST_DATA_DIR, 2, 1101, ".bcl", new ArrayList<File>(), new int[]{}
},
};
}
- @Test(dataProvider = "iteratorTestData")
+ /* @Test(dataProvider = "iteratorTestData")
public void cycledFilesIteratorTest(final File parentDir, final int lane, final int tile, final String fileType, final List<File> expectedFiles, final int [] cycles) {
final CycleFilesIterator toTest = new CycleFilesIterator(parentDir, lane, tile, cycles, fileType);
Iterator<File> expectedIter = expectedFiles.iterator();
@@ -105,25 +97,25 @@ public class CycleIlluminaFileMapTest {
@Test
public void passingAssertCycledIlluminaFileMapTest() {
final CycleIlluminaFileMap fileMap = new CycleIlluminaFileMap();
- fileMap.put(1, new CycleFilesIterator(TEST_DATA_DIR, 1, 1, ALL_CYCLES, ".cif"));
- fileMap.put(2, new CycleFilesIterator(TEST_DATA_DIR, 1, 2, ALL_CYCLES, ".cif"));
- fileMap.assertValid(makeList(1,2), ALL_CYCLES);
+ fileMap.put(1101, new CycleFilesIterator(TEST_DATA_DIR, 1, 1101, ALL_CYCLES, ".bcl"));
+ fileMap.put(1201, new CycleFilesIterator(TEST_DATA_DIR, 1, 1201, ALL_CYCLES, ".bcl"));
+ fileMap.assertValid(makeList(1101,1201), ALL_CYCLES);
}
@Test(expectedExceptions = PicardException.class)
public void tileFailingAssertCycledIlluminaFileMapTest() {
final CycleIlluminaFileMap fileMap = new CycleIlluminaFileMap();
- fileMap.put(1, new CycleFilesIterator(TEST_DATA_DIR, 1, 1, ALL_CYCLES, ".cif"));
- fileMap.put(2, new CycleFilesIterator(TEST_DATA_DIR, 1, 2, ALL_CYCLES, ".cif"));
+ fileMap.put(1, new CycleFilesIterator(TEST_DATA_DIR, 1, 1, ALL_CYCLES, ".bcl"));
+ fileMap.put(2, new CycleFilesIterator(TEST_DATA_DIR, 1, 2, ALL_CYCLES, ".bcl"));
fileMap.assertValid(makeList(1,2,3), ALL_CYCLES);
}
@Test(expectedExceptions = PicardException.class)
public void cycleFailingAssertCycledIlluminaFileMapTest() {
final CycleIlluminaFileMap fileMap = new CycleIlluminaFileMap();
- fileMap.put(1, new CycleFilesIterator(TEST_DATA_DIR, 1, 1, ALL_CYCLES, ".cif"));
- fileMap.put(2, new CycleFilesIterator(TEST_DATA_DIR, 1, 2, ALL_CYCLES, ".cif"));
+ fileMap.put(1, new CycleFilesIterator(TEST_DATA_DIR, 1, 1, ALL_CYCLES, ".bcl"));
+ fileMap.put(2, new CycleFilesIterator(TEST_DATA_DIR, 1, 2, ALL_CYCLES, ".bcl"));
fileMap.assertValid(makeList(1,2), new int[]{1,2,3,4,5});
- }
+ }*/
}
diff --git a/src/tests/java/net/sf/picard/illumina/parser/FilterParserTest.java b/src/tests/java/net/sf/picard/illumina/parser/FilterParserTest.java
index 5d5f98a..1a256e1 100644
--- a/src/tests/java/net/sf/picard/illumina/parser/FilterParserTest.java
+++ b/src/tests/java/net/sf/picard/illumina/parser/FilterParserTest.java
@@ -8,89 +8,91 @@ import org.testng.annotations.Test;
import java.io.File;
import java.lang.reflect.Array;
import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
import java.util.List;
public class FilterParserTest {
- private static final File TestDataDir = new File("testdata/net/sf/picard/illumina/parserTests");
+ private static final File TestDataDir = new File("testdata/net/sf/picard/illumina/parserTests");
private static final File BaseCallsDir = new File(TestDataDir, "filterParser");
private static final boolean F = false;
private static final boolean T = true;
- public static final Boolean [] s_1_0001_filter = {F,F,T,F, T,T,F,F, T,F,T,T, F,T,T};
- public static final Boolean [] s_1_0002_filter = {F,F,F,F, F,T,T,F, F,F,F,T, F,F,F,T, T,T,T,T};
- public static final Boolean [] s_1_0003_filter = {T,F,F,F, T,T,F,F};
- public static final Boolean [] s_1_0004_filter = {T, F, F, F, F, T, F, F, F, F, T, F, F, F, F, T, T, F, F, T,
- T, F, T, F, T, T, F, F, T, T, F, T, T, T, T, F, T, T, T, T,
- F, T, F, F, F, T, F, T, F, T, T, F, F, T, T, T, F, F, T, T};
-
- public static final Boolean [] tileToValue(int tile) {
- switch(tile) {
- case 1: return s_1_0001_filter;
- case 2: return s_1_0002_filter;
- case 3: return s_1_0003_filter;
- case 4: return s_1_0004_filter;
+ public static final Boolean[] s_1_0001_filter = {F, F, T, F, T, T, F, F, T, F, T, T, F, T, T};
+ public static final Boolean[] s_1_0002_filter = {F, F, F, F, F, T, T, F, F, F, F, T, F, F, F, T, T, T, T, T};
+ public static final Boolean[] s_1_0003_filter = {T, F, F, F, T, T, F, F};
+ public static final Boolean[] s_1_0004_filter = {T, F, F, F, F, T, F, F, F, F, T, F, F, F, F, T, T, F, F, T,
+ T, F, T, F, T, T, F, F, T, T, F, T, T, T, T, F, T, T, T, T,
+ F, T, F, F, F, T, F, T, F, T, T, F, F, T, T, T, F, F, T, T};
+
+ public static final Boolean[] tileToValue(int tile) {
+ switch (tile) {
+ case 1:
+ return s_1_0001_filter;
+ case 2:
+ return s_1_0002_filter;
+ case 3:
+ return s_1_0003_filter;
+ case 4:
+ return s_1_0004_filter;
}
throw new RuntimeException("You shouldn't reach this statement!");
}
- public static final Boolean [] allTilesToValues(Integer [] tiles) {
- Boolean [][] values = new Boolean[tiles.length][];
- for(int i = 0; i < tiles.length; i++) {
+ public static final Boolean[] allTilesToValues(Integer[] tiles) {
+ Boolean[][] values = new Boolean[tiles.length][];
+ for (int i = 0; i < tiles.length; i++) {
values[i] = tileToValue(tiles[i]);
}
return arrayFlatten(values);
}
- public static final List<Integer> arrayToList(final Integer [] array) {
+ public static final List<Integer> arrayToList(final Integer[] array) {
final List<Integer> list = new ArrayList<Integer>();
- for(int item : array) {
+ for (int item : array) {
list.add(item);
}
return list;
}
- public static final <T> T[] arrayFlatten(final T [][] arrays) {
+ public static final <T> T[] arrayFlatten(final T[][] arrays) {
int total = 0;
- for(T [] arr : arrays) {
+ for (T[] arr : arrays) {
total += arr.length;
}
int resultIndex = 0;
- final T [] result = (T[]) Array.newInstance(arrays[0][0].getClass(), total);
- for(int i = 0; i < arrays.length; i++) {
+ final T[] result = (T[]) Array.newInstance(arrays[0][0].getClass(), total);
+ for (int i = 0; i < arrays.length; i++) {
System.arraycopy(arrays[i], 0, result, resultIndex, arrays[i].length);
resultIndex += arrays[i].length;
}
return result;
}
- @DataProvider(name="passingTiles")
- public Object [][] passingTiles() {
- return new Object[][] {
- {new Integer[]{1}},
- {new Integer[]{2}},
- {new Integer[]{4}},
- {new Integer[]{1,4}},
- {new Integer[]{2,3}},
- {new Integer[]{1,2,3,4}}
+ @DataProvider(name = "passingTiles")
+ public Object[][] passingTiles() {
+ return new Object[][]{
+ {new Integer[]{1}},
+ {new Integer[]{2}},
+ {new Integer[]{4}},
+ {new Integer[]{1, 4}},
+ {new Integer[]{2, 3}},
+ {new Integer[]{1, 2, 3, 4}}
};
}
- @Test(dataProvider = "passingTiles" )
- public void passingParserTest(Integer [] tiles) {
+ @Test(dataProvider = "passingTiles")
+ public void passingParserTest(Integer[] tiles) {
final IlluminaFileUtil fUtil = new IlluminaFileUtil(BaseCallsDir, 1);
- final Boolean [] values = allTilesToValues(tiles);
+ final Boolean[] values = allTilesToValues(tiles);
final List<Integer> tileList = arrayToList(tiles);
- final FilterParser fp = new FilterParser(fUtil.filter().getFiles(tileList));
+ final FilterParser fp = new FilterParser(((PerTileFileUtil) fUtil.getUtil(IlluminaFileUtil.SupportedIlluminaFormat.Filter)).getFiles(tileList));
fp.verifyData(tileList, null); //filter parser doesn't care about cycle
- for(final boolean expectedValue : values) {
+ for (final boolean expectedValue : values) {
Assert.assertTrue(fp.hasNext());
Assert.assertEquals(fp.next().isPf(), expectedValue);
}
@@ -99,37 +101,38 @@ public class FilterParserTest {
//seek back to the beginning and do it again!
fp.seekToTile(tiles[0]);
- for(final boolean expectedValue : values) {
+ for (final boolean expectedValue : values) {
Assert.assertTrue(fp.hasNext());
Assert.assertEquals(fp.next().isPf(), expectedValue);
}
Assert.assertFalse(fp.hasNext());
+ fp.close();
}
- @DataProvider(name="seekToTile")
- public Object [][] seekToTile() {
- return new Object[][] {
- //seek after how many, tiles to load, expected values
- {0, 2, new Integer[]{2}, new Boolean[][]{s_1_0002_filter}},
- {4, 4, new Integer[]{1,4}, new Boolean[][]{new Boolean[]{F,F,T,F}, s_1_0004_filter}},
- {0, 3, new Integer[]{2,3}, new Boolean[][]{s_1_0003_filter}},
- {15, 3, new Integer[]{1,2,3,4}, new Boolean[][]{s_1_0001_filter, s_1_0003_filter, s_1_0004_filter}}
+ @DataProvider(name = "seekToTile")
+ public Object[][] seekToTile() {
+ return new Object[][]{
+ //seek after how many, tiles to load, expected values
+ {0, 2, new Integer[]{2}, new Boolean[][]{s_1_0002_filter}},
+ {4, 4, new Integer[]{1, 4}, new Boolean[][]{new Boolean[]{F, F, T, F}, s_1_0004_filter}},
+ {0, 3, new Integer[]{2, 3}, new Boolean[][]{s_1_0003_filter}},
+ {15, 3, new Integer[]{1, 2, 3, 4}, new Boolean[][]{s_1_0001_filter, s_1_0003_filter, s_1_0004_filter}}
};
}
- @Test(dataProvider = "seekToTile" )
- public void passingSeekingParserTest(int skipBefore, int tileToSkipTo, Integer [] tiles, Boolean [][] expectedValues) {
+ @Test(dataProvider = "seekToTile")
+ public void passingSeekingParserTest(int skipBefore, int tileToSkipTo, Integer[] tiles, Boolean[][] expectedValues) {
final IlluminaFileUtil fUtil = new IlluminaFileUtil(BaseCallsDir, 1);
- final Boolean [] values = arrayFlatten(expectedValues);
+ final Boolean[] values = arrayFlatten(expectedValues);
final List<Integer> tileList = arrayToList(tiles);
- final FilterParser fp = new FilterParser(fUtil.filter().getFiles(tileList));
+ final FilterParser fp = new FilterParser(((PerTileFileUtil) fUtil.getUtil(IlluminaFileUtil.SupportedIlluminaFormat.Filter)).getFiles(tileList));
int read = 0;
- for(final boolean expectedValue : values) {
- if(read == skipBefore) {
+ for (final boolean expectedValue : values) {
+ if (read == skipBefore) {
fp.seekToTile(tileToSkipTo);
}
@@ -139,28 +142,30 @@ public class FilterParserTest {
}
Assert.assertFalse(fp.hasNext());
+ fp.close();
}
- @DataProvider(name="failingVerifyTiles")
- public Object [][] failingVerifyTiles() {
- return new Object[][] {
- {new Integer[]{1}, new Integer[]{2}},
- {new Integer[]{2}, new Integer[]{1}},
- {new Integer[]{4}, new Integer[]{5}},
- {new Integer[]{1,4}, new Integer[]{1,3,4}},
- {new Integer[]{2,3}, new Integer[]{2,3,4}},
- {new Integer[]{1,2,3,4}, new Integer[]{1,2,3,4,5}},
- {new Integer[]{2,3,4}, new Integer[]{1,2,3,4}}
+ @DataProvider(name = "failingVerifyTiles")
+ public Object[][] failingVerifyTiles() {
+ return new Object[][]{
+ {new Integer[]{1}, new Integer[]{2}},
+ {new Integer[]{2}, new Integer[]{1}},
+ {new Integer[]{4}, new Integer[]{5}},
+ {new Integer[]{1, 4}, new Integer[]{1, 3, 4}},
+ {new Integer[]{2, 3}, new Integer[]{2, 3, 4}},
+ {new Integer[]{1, 2, 3, 4}, new Integer[]{1, 2, 3, 4, 5}},
+ {new Integer[]{2, 3, 4}, new Integer[]{1, 2, 3, 4}}
};
}
- @Test(dataProvider = "failingVerifyTiles", expectedExceptions = PicardException.class)
- public void verifyDataTest(final Integer[] initTiles, final Integer[] verifyTiles) {
+ @Test(dataProvider = "failingVerifyTiles", expectedExceptions = PicardException.class)
+ public void verifyDataTest(final Integer[] initTiles, final Integer[] verifyTiles) {
final IlluminaFileUtil fUtil = new IlluminaFileUtil(BaseCallsDir, 1);
final List<Integer> initTileList = arrayToList(initTiles);
final List<Integer> verifyTileList = arrayToList(verifyTiles);
- final FilterParser fp = new FilterParser(fUtil.filter().getFiles(initTileList));
+ final FilterParser fp = new FilterParser(((PerTileFileUtil) fUtil.getUtil(IlluminaFileUtil.SupportedIlluminaFormat.Filter)).getFiles(initTileList));
fp.verifyData(verifyTileList, null); //filter parser doesn't care about cycle values
- }
+ fp.close();
+ }
}
diff --git a/src/tests/java/net/sf/picard/illumina/parser/IlluminaDataProviderTest.java b/src/tests/java/net/sf/picard/illumina/parser/IlluminaDataProviderTest.java
index 15c1c0b..5724d91 100644
--- a/src/tests/java/net/sf/picard/illumina/parser/IlluminaDataProviderTest.java
+++ b/src/tests/java/net/sf/picard/illumina/parser/IlluminaDataProviderTest.java
@@ -33,43 +33,24 @@ import java.io.File;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
-import static net.sf.picard.illumina.parser.QSeqTdUtil.*;
-import static net.sf.picard.illumina.parser.QSeqTdUtil.getTiledReadData;
-import static net.sf.samtools.util.CollectionUtil.*;
+
+import static net.sf.samtools.util.CollectionUtil.makeList;
+//import static net.sf.samtools.util.CollectionUtil.*;
/**
-* @author jburke at broadinstitute.org
-*/
+ * @author jburke at broadinstitute.org
+ */
public class IlluminaDataProviderTest {
public static final BclQualityEvaluationStrategy bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY);
- public static final File PARSING_TEST_BASECALLS_DIR = new File("testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls");
- public static final File TEST_DATA_LOCATION = new File("testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir");
- public static final File BINARY_TD_LOCATION = new File("testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls");
- private static final IlluminaDataType [] DEFAULT_DATA_TYPES = new IlluminaDataType[]{
+ public static final File BINARY_TD_LOCATION = new File("testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls");
+ private static final IlluminaDataType[] DEFAULT_DATA_TYPES = new IlluminaDataType[]{
IlluminaDataType.Position, IlluminaDataType.BaseCalls, IlluminaDataType.QualityScores, IlluminaDataType.PF
};
- @Test(dataProvider="data")
- public void testIlluminaDataProviderQSeqMethod(
- final String testName, final int lane, final int size,
- final Map<Integer, ClusterData> readNoToClusterData,
- final IlluminaDataType[] extraDataTypes,
- final String illuminaConfigStr,
- final int seekAfterFirstRead, final int seekTestDataReadOffset,
- final File basecallsDirectory)
- throws Exception {
-
- final IlluminaDataType [] dts = getDataTypes(extraDataTypes);
- final IlluminaDataProviderFactory factory = new IlluminaDataProviderFactory(basecallsDirectory, lane, new ReadStructure(illuminaConfigStr), bclQualityEvaluationStrategy, dts);
- final IlluminaDataProvider dataProvider = factory.makeDataProvider();
-
- runTest(testName, size, readNoToClusterData, seekAfterFirstRead, seekTestDataReadOffset, dataProvider);
- }
-
private void runTest(
- final String testName, final int size,
+ final String testName, final int size,
final Map<Integer, ClusterData> readNoToClusterData,
final int seekAfterFirstRead, final int seekTestDataReadOffset,
final IlluminaDataProvider dataProvider)
@@ -92,12 +73,13 @@ public class IlluminaDataProviderTest {
count++;
}
Assert.assertEquals(count, size, testName);
+ dataProvider.close();
}
- private IlluminaDataType [] getDataTypes(IlluminaDataType [] extraDataTypes) {
- final IlluminaDataType [] dts;
+ private IlluminaDataType[] getDataTypes(final IlluminaDataType[] extraDataTypes) {
+ final IlluminaDataType[] dts;
- if(extraDataTypes == null) {
+ if (extraDataTypes == null) {
dts = DEFAULT_DATA_TYPES;
} else {
dts = Arrays.copyOf(DEFAULT_DATA_TYPES, DEFAULT_DATA_TYPES.length + extraDataTypes.length);
@@ -108,226 +90,100 @@ public class IlluminaDataProviderTest {
private void compareBasesAndQuals(final ReadData rd1, final ReadData rd2, final String testName) {
- Assert.assertEquals(rd1.getBases(), rd2.getBases(), testName);
+ Assert.assertEquals(rd1.getBases(), rd2.getBases(), testName);
Assert.assertEquals(rd1.getQualities(), rd2.getQualities(), testName);
- Assert.assertEquals(rd1.getReadType(), rd2.getReadType());
+ Assert.assertEquals(rd1.getReadType(), rd2.getReadType());
}
private void comparePositionalData(final ClusterData cd1, final ClusterData cd2, final String testName) {
Assert.assertEquals(cd1.getLane(), cd2.getLane(), testName);
Assert.assertEquals(cd1.getTile(), cd2.getTile(), testName);
- Assert.assertEquals(cd1.getX(), cd2.getX(), testName);
- Assert.assertEquals(cd1.getY(), cd2.getY(), testName);
+ Assert.assertEquals(cd1.getX(), cd2.getX(), testName);
+ Assert.assertEquals(cd1.getY(), cd2.getY(), testName);
}
//Doesn't compare intensities right now -- Do we want too?
private void compareReadData(final ClusterData cd1, final ClusterData cd2, final String testName) {
- comparePositionalData(cd1, cd2, testName);
+ comparePositionalData(cd1, cd2, testName);
Assert.assertEquals(cd1.getNumReads(), cd2.getNumReads());
- for(int i = 0; i < cd1.getNumReads(); i++) {
+ for (int i = 0; i < cd1.getNumReads(); i++) {
compareBasesAndQuals(cd1.getRead(i), cd2.getRead(i), testName);
}
- Assert.assertEquals(cd1.getMatchedBarcode(), cd2.getMatchedBarcode(), testName);
- Assert.assertEquals(cd1.isPf().booleanValue(), cd2.isPf().booleanValue(), testName);
- }
-
- /**
- * Data for one PE lane and one non-PE lane. The data are truncated versions of the qseq and sig2 files
- * for actual lanes.
- */
- @DataProvider(name = "data")
- private Object[][] getBasecallsTestData()
- {
- return new Object[][]{
- {
- "PE Bustard Parsing Test", 1, 60,
- qseqDataToClusterMap(makeList(getTiledReadData(s_1_1, makeList(1, 2, 3)), getTiledReadData(s_1_2, makeList(1,2,3))), makeOutputMapping("76T76T"), DEFAULT_DATA_TYPES),
- new IlluminaDataType[]{},
- "76T76T",
- 0, 0,
- TEST_DATA_LOCATION
- },
-
- {"PE with Barcode Bustard Parsing Test", 1, 60,
- qseqDataToClusterMap(makeList(getTiledReadData(s_1_1, makeList(1, 2, 3)), getTiledReadData(s_1_2, makeList(1,2,3))), makeOutputMapping("76T6B70T"), DEFAULT_DATA_TYPES),
- new IlluminaDataType[]{},
- "76T6B70T",
- 0, 0,
- TEST_DATA_LOCATION
- },
-
- {"PE Bustard Parsing Test with Noise/Intensity", 8, 20,
- qseqDataToClusterMap(makeList(getReadData(s_8_1_0001), getReadData(s_8_2_0001)), makeOutputMapping("4T4T"), DEFAULT_DATA_TYPES),
- new IlluminaDataType[]{IlluminaDataType.RawIntensities, IlluminaDataType.Noise},
- "4T4T",
- 0, 0,
- TEST_DATA_LOCATION
- },
-
- {"PE Bustard Parsing Test with Noise/Intensity", 8, 20,
- qseqDataToClusterMap(makeList(getReadData(s_8_1_0001), getReadData(s_8_2_0001)), makeOutputMapping("4T2B2T"), DEFAULT_DATA_TYPES),
- new IlluminaDataType[]{IlluminaDataType.RawIntensities, IlluminaDataType.Noise},
- "4T2B2T",
- 0, 0,
- TEST_DATA_LOCATION
- },
-
- {"PE, Barcode, seek Bustard Parsing Test", 1, 21,
- qseqDataToClusterMap(makeList(getTiledReadData(s_1_1, makeList(1, 2, 3)), getTiledReadData(s_1_2, makeList(1,2,3))), makeOutputMapping("76T6B70T"), DEFAULT_DATA_TYPES),
- new IlluminaDataType[]{},
- "76T6B70T",
- 3, getFileSize(s_1_1_0001) + getFileSize(s_1_2_0001) - 1,
- TEST_DATA_LOCATION
- },
-
- {"PE, Barcode, end with skip test", 1, 21,
- qseqDataToClusterMap(makeList(getTiledReadData(s_1_1, makeList(1, 2, 3)), getTiledReadData(s_1_2, makeList(1,2,3))), makeOutputMapping("76T6B1S"), DEFAULT_DATA_TYPES),
- new IlluminaDataType[]{},
- "76T6B1S",
- 3, getFileSize(s_1_1_0001) + getFileSize(s_1_2_0001) - 1,
- TEST_DATA_LOCATION
- },
-
- {"Non-PE Bustard Parsing Test", 5, 20,
- qseqDataToClusterMap(makeList(getReadData(s_5_1_0001)), makeOutputMapping("76T"), DEFAULT_DATA_TYPES),
- new IlluminaDataType[]{},
- "76T",
- 0, 0,
- TEST_DATA_LOCATION
- },
-
- {"Non-PE Bustard Parsing Test", 5, 20,
- qseqDataToClusterMap(makeList(getReadData(s_5_1_0001)), makeOutputMapping("70T6B"), DEFAULT_DATA_TYPES),
- new IlluminaDataType[]{},
- "70T6B",
- 0, 0,
- TEST_DATA_LOCATION
- },
-
- {"Barcode-aware PE Bustard Parsing Test", 6, 10,
- qseqDataToClusterMap(makeList(getReadData(s_6_1_0001), getReadData(s_6_2_0001), getReadData(s_6_3_0001)), makeOutputMapping("68T8B68T"), DEFAULT_DATA_TYPES),
- new IlluminaDataType[]{},
- "68T8B68T",
- 0, 0,
- TEST_DATA_LOCATION
- }
- };
- }
-
- private static OutputMapping makeOutputMapping(String readStructure) {
- return new OutputMapping(new ReadStructure(readStructure));
+ Assert.assertEquals(cd1.getMatchedBarcode(), cd2.getMatchedBarcode(), testName);
+ Assert.assertEquals(cd1.isPf().booleanValue(), cd2.isPf().booleanValue(), testName);
}
public void runBarcodeParsingTest(final IlluminaDataProviderFactory factory) {
-
- final IlluminaDataProvider dateProvider = factory.makeDataProvider();
- for (int i = 0; dateProvider.hasNext(); ++i) {
- final ClusterData cluster = dateProvider.next();
+ int total = 0;
+ final IlluminaDataProvider dataProvider = factory.makeDataProvider();
+ while (dataProvider.hasNext()) {
+ final ClusterData cluster = dataProvider.next();
final String matchedBarcode = cluster.getMatchedBarcode();
- if (i % 2 == 0) {
- // The barcode are not actual sequence in the test data, just 0-padded numbers
- Assert.assertNotNull(matchedBarcode);
- final int barcodeAsInt = Integer.parseInt(matchedBarcode);
- Assert.assertEquals(barcodeAsInt, i+1);
- } else {
- Assert.assertNull(matchedBarcode);
+ if (matchedBarcode != null) {
+ Assert.assertEquals(matchedBarcode, new String(cluster.getRead(1).getBases()));
+ }
+ if(total > 10){
+ break;
}
+ total++;
}
+ dataProvider.close();
}
@Test
public void barcodeParsingTest() {
- runBarcodeParsingTest(new IlluminaDataProviderFactory(PARSING_TEST_BASECALLS_DIR, 6, new ReadStructure("76T76T6B"), bclQualityEvaluationStrategy, IlluminaDataType.Barcodes));
+ runBarcodeParsingTest(new IlluminaDataProviderFactory(BINARY_TD_LOCATION, 1, new ReadStructure("25T8B25T"), bclQualityEvaluationStrategy, IlluminaDataType.BaseCalls,
+ IlluminaDataType.Barcodes));
}
- @DataProvider(name="binaryData")
+ @DataProvider(name = "binaryData")
public Object[][] binaryData() {
- return new Object[][] {
- {
- "Bustard Parsing Test(25T8B25T) w/Clocs", 1, 60,
- makeList(1101, 1201, 2101),
- new IlluminaDataType[]{IlluminaDataType.Barcodes},
- "25T8B25T",
- 0, 0,
- BINARY_TD_LOCATION
- },
- {
- "Bustard Parsing Test(25T8S25T) w/Clocs", 1, 60,
- makeList(1101, 1201, 2101),
- new IlluminaDataType[]{IlluminaDataType.Barcodes},
- "25T8S25T",
- 0, 0,
- BINARY_TD_LOCATION
- },
- {
- "Bustard Parsing Test(25T8S25T) w/Clocs with ending skip", 1, 60,
- makeList(1101, 1201, 2101),
- new IlluminaDataType[]{IlluminaDataType.Barcodes},
- "25T8B1S",
- 0, 0,
- BINARY_TD_LOCATION
- },
- {
- "Bustard Parsing Test(25S8S25T) w/Clocs", 1, 60,
- makeList(1101, 1201, 2101),
- new IlluminaDataType[]{IlluminaDataType.Barcodes},
- "25S8S25T",
- 0, 0,
- BINARY_TD_LOCATION
- },
- {
- "Bustard Parsing Test(25T8B25T) w/Clocs And Seeking", 1, 21,
- makeList(1101, 1201, 2101),
- new IlluminaDataType[]{IlluminaDataType.Barcodes},
- "25T8B25T",
- 2101, 39,
- BINARY_TD_LOCATION
- },
- {
- "Bustard Parsing Test(25T8B25T) w/Pos", 2, 60,
- makeList(1101, 1201, 2101),
- new IlluminaDataType[]{},
- "25T8B25T",
- 0, 0,
- BINARY_TD_LOCATION
- },
- {
- "Bustard Parsing Test(25T8B25T) w/Pos and Seeking", 2, 41,
- makeList(1101, 1201, 2101),
- new IlluminaDataType[]{},
- "25T8B25T",
- 1201, 19,
- BINARY_TD_LOCATION
- },
- {
- "Bustard Parsing Test(19T10B10B19T) w/Pos.gz", 4, 60,
- makeList(1101, 1201, 2101),
- new IlluminaDataType[]{},
- "19T10B10B19T",
- 0, 0,
- BINARY_TD_LOCATION
- },
- {
- "Bustard Parsing Test(19T10B10B19T) w/Pos.gz and Seeking", 4, 41,
- makeList(1101, 1201, 2101),
- new IlluminaDataType[]{},
- "19T10B10B19T",
- 1201, 19,
- BINARY_TD_LOCATION
- },
- {
- "Bustard Parsing Test(17T2S10B10B17T2S) w/Pos.gz and Seeking", 4, 41,
- makeList(1101, 1201, 2101),
- new IlluminaDataType[]{},
- "17T2S10B10B17T2S",
- 1201, 19,
- BINARY_TD_LOCATION
- }
+ return new Object[][]{
+ {
+ "Bustard Parsing Test(25T8B25T) w/Clocs", 1, 180,
+ makeList(1101, 1201, 2101),
+ new IlluminaDataType[]{IlluminaDataType.Barcodes},
+ "25T8B25T",
+ 0, 0,
+ BINARY_TD_LOCATION
+ },
+ {
+ "Bustard Parsing Test(25T8S25T) w/Clocs", 1, 180,
+ makeList(1101, 1201, 2101),
+ new IlluminaDataType[]{IlluminaDataType.Barcodes},
+ "25T8S25T",
+ 0, 0,
+ BINARY_TD_LOCATION
+ },
+ {
+ "Bustard Parsing Test(25T8S25T) w/Clocs with ending skip", 1, 180,
+ makeList(1101, 1201, 2101),
+ new IlluminaDataType[]{IlluminaDataType.Barcodes},
+ "25T8B1S",
+ 0, 0,
+ BINARY_TD_LOCATION
+ },
+ {
+ "Bustard Parsing Test(25S8S25T) w/Clocs", 1, 180,
+ makeList(1101, 1201, 2101),
+ new IlluminaDataType[]{IlluminaDataType.Barcodes},
+ "25S8S25T",
+ 0, 0,
+ BINARY_TD_LOCATION
+ },
+ {
+ "Bustard Parsing Test(25T8B25T) w/Clocs And Seeking", 1, 61,
+ makeList(1101, 1201, 2101),
+ new IlluminaDataType[]{IlluminaDataType.Barcodes},
+ "25T8B25T",
+ 2101, 4631,
+ BINARY_TD_LOCATION
+ }
};
}
- @Test(dataProvider="binaryData")
+ @Test(dataProvider = "binaryData")
public void testIlluminaDataProviderBclMethod(
final String testName, final int lane, final int size,
final List<Integer> tiles,
@@ -337,80 +193,78 @@ public class IlluminaDataProviderTest {
final File basecallsDirectory)
throws Exception {
- final IlluminaDataType [] dts = getDataTypes(extraDataTypes);
+ final IlluminaDataType[] dts = getDataTypes(extraDataTypes);
- Map<Integer, ClusterData> readNoToClusterData = BinTdUtil.clusterData(lane, tiles, illuminaConfigStr, dts);
+ final Map<Integer, ClusterData> readNoToClusterData = BinTdUtil.clusterData(lane, tiles, illuminaConfigStr, dts);
final IlluminaDataProviderFactory factory = new IlluminaDataProviderFactory(basecallsDirectory, lane, new ReadStructure(illuminaConfigStr), bclQualityEvaluationStrategy, dts);
- final IlluminaDataProvider dataProvider = factory.makeDataProvider();
+ final IlluminaDataProvider dataProvider = factory.makeDataProvider();
runTest(testName, size, readNoToClusterData, seekAfterFirstRead, seekTestDataReadOffset, dataProvider);
}
- //Unlike above, the data types here do not have DEFAULT_DATA_TYPES added before createing the dataProvider
- @DataProvider(name="badData")
+ //Unlike above, the data types here do not have DEFAULT_DATA_TYPES added before creating the dataProvider
+ @DataProvider(name = "badData")
public Object[][] badData() {
- return new Object[][] {
- {
- "Bad Lane(5)", 5, 60,
- makeList(1101, 1201, 2101),
- new IlluminaDataType[]{IlluminaDataType.Barcodes},
- "25T8B25T",
- BINARY_TD_LOCATION
- },
- {
- "Bad Read Structure(25TB25T)", 4, 60,
- makeList(1101, 1201, 2101),
- DEFAULT_DATA_TYPES,
- "25TB25T",
- BINARY_TD_LOCATION
- },
- {
- "Bad Read Structure(25T0B25T)", 4, 60,
- makeList(1101, 1201, 2101),
- DEFAULT_DATA_TYPES,
- "25T0B25T",
- BINARY_TD_LOCATION
- },
- {
- "Bad Read Structure(-225T0B25T)", 4, 60,
- makeList(1101, 1201, 2101),
- DEFAULT_DATA_TYPES,
- "-25T0B25T",
- BINARY_TD_LOCATION
- },
- {
- "Missing Barcodes File", 9, 60,
- makeList(1101, 1201, 2101),
- new IlluminaDataType[]{IlluminaDataType.Position, IlluminaDataType.Barcodes},
- "25T8B25T",
- BINARY_TD_LOCATION
- },
- {
- "Missing Cycle File", 9, 60,
- makeList(1101, 1201, 2101),
- new IlluminaDataType[]{IlluminaDataType.BaseCalls},
- "25T8B25T",
- BINARY_TD_LOCATION
- },
- {
- "Missing Filter File", 9, 60,
- makeList(1101, 1201, 2101),
- new IlluminaDataType[]{IlluminaDataType.PF, IlluminaDataType.BaseCalls, IlluminaDataType.QualityScores},
- "25T8B24T",
- BINARY_TD_LOCATION
- }
+ return new Object[][]{
+ {
+ "Bad Lane(5)", 5, 60,
+ makeList(1101, 1201, 2101),
+ new IlluminaDataType[]{IlluminaDataType.Barcodes},
+ "25T8B25T",
+ BINARY_TD_LOCATION
+ },
+ {
+ "Bad Read Structure(25TB25T)", 4, 60,
+ makeList(1101, 1201, 2101),
+ DEFAULT_DATA_TYPES,
+ "25TB25T",
+ BINARY_TD_LOCATION
+ },
+ {
+ "Bad Read Structure(25T0B25T)", 4, 60,
+ makeList(1101, 1201, 2101),
+ DEFAULT_DATA_TYPES,
+ "25T0B25T",
+ BINARY_TD_LOCATION
+ },
+ {
+ "Bad Read Structure(-225T0B25T)", 4, 60,
+ makeList(1101, 1201, 2101),
+ DEFAULT_DATA_TYPES,
+ "-25T0B25T",
+ BINARY_TD_LOCATION
+ },
+ {
+ "Missing Barcodes File", 9, 60,
+ makeList(1101, 1201, 2101),
+ new IlluminaDataType[]{IlluminaDataType.Position, IlluminaDataType.Barcodes},
+ "25T8B25T",
+ BINARY_TD_LOCATION
+ },
+ {
+ "Missing Cycle File", 9, 60,
+ makeList(1101, 1201, 2101),
+ new IlluminaDataType[]{IlluminaDataType.BaseCalls},
+ "25T8B25T",
+ BINARY_TD_LOCATION
+ },
+ {
+ "Missing Filter File", 9, 60,
+ makeList(1101, 1201, 2101),
+ new IlluminaDataType[]{IlluminaDataType.PF, IlluminaDataType.BaseCalls, IlluminaDataType.QualityScores},
+ "25T8B24T",
+ BINARY_TD_LOCATION
+ }
};
}
- @Test(dataProvider="badData", expectedExceptions = {PicardException.class, IllegalArgumentException.class})
- public void testIlluminaDataProviderMissingDatas(
- final String testName, final int lane, final int size,
- final List<Integer> tiles,
- final IlluminaDataType[] actualDts,
- final String illuminaConfigStr,
- final File basecallsDirectory)
+ @Test(dataProvider = "badData", expectedExceptions = {PicardException.class, IllegalArgumentException.class})
+ public void testIlluminaDataProviderMissingDatas(final int lane,
+ final IlluminaDataType[] actualDts,
+ final String illuminaConfigStr,
+ final File basecallsDirectory)
throws Exception {
final IlluminaDataProviderFactory factory = new IlluminaDataProviderFactory(basecallsDirectory, lane, new ReadStructure(illuminaConfigStr), bclQualityEvaluationStrategy, actualDts);
- final IlluminaDataProvider dataProvider = factory.makeDataProvider();
+ factory.makeDataProvider();
}
}
diff --git a/src/tests/java/net/sf/picard/illumina/parser/IlluminaFileUtilTest.java b/src/tests/java/net/sf/picard/illumina/parser/IlluminaFileUtilTest.java
index e7b0492..10ef89b 100644
--- a/src/tests/java/net/sf/picard/illumina/parser/IlluminaFileUtilTest.java
+++ b/src/tests/java/net/sf/picard/illumina/parser/IlluminaFileUtilTest.java
@@ -1,34 +1,42 @@
package net.sf.picard.illumina.parser;
import net.sf.picard.PicardException;
+import net.sf.picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat;
import net.sf.picard.io.IoUtil;
-import static net.sf.samtools.util.CollectionUtil.makeList;
import org.testng.Assert;
-import org.testng.annotations.*;
-
-import net.sf.picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+import java.io.DataOutputStream;
import java.io.File;
+import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
-import java.util.*;
+import java.io.OutputStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
import java.util.regex.Matcher;
import java.util.regex.Pattern;
+import static net.sf.samtools.util.CollectionUtil.makeList;
+
public class IlluminaFileUtilTest {
- private static final int DEFAULT_LANE = 7;
- private static final List<Integer> DEFAULT_TILES = makeList(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12);
+ private static final int DEFAULT_LANE = 7;
+ private static final List<Integer> DEFAULT_TILES = makeList(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12);
private static final List<Integer> DEFAULT_TILE_TEST_SUBSET = makeList(1, 4, 5, 6, 9, 10);
- private static final int DEFAULT_NUM_ENDS = 4;
- private static final int [] DEFAULT_ENDS = {1,2,3,4};
- private static final int [] DEFAULT_CYCLES = {1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20};
- private static final int DEFAULT_LAST_CYCLE = 20;
+ private static final int[] DEFAULT_CYCLES = {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20};
+ private static final int DEFAULT_LAST_CYCLE = 20;
// We have data for these that should agree
private static final List<SupportedIlluminaFormat> FORMATS_TO_TEST = Arrays.asList(
SupportedIlluminaFormat.Bcl,
- SupportedIlluminaFormat.Cif,
- SupportedIlluminaFormat.Cnf,
SupportedIlluminaFormat.Locs,
SupportedIlluminaFormat.Clocs,
SupportedIlluminaFormat.Pos,
@@ -43,7 +51,7 @@ public class IlluminaFileUtilTest {
private void setUp() throws Exception {
intensityDir = IoUtil.createTempDir("ift_test", "Intensities");
basecallDir = new File(intensityDir, "BaseCalls");
- if(!basecallDir.mkdir()) {
+ if (!basecallDir.mkdir()) {
throw new RuntimeException("Couldn't make basecalls dir " + basecallDir.getAbsolutePath());
}
}
@@ -53,104 +61,83 @@ public class IlluminaFileUtilTest {
IoUtil.deleteDirectoryTree(intensityDir);
}
- @DataProvider(name="validLanes")
+ @DataProvider(name = "validLanes")
public Object[][] validLanes() {
- return new Object[][] {
- {0, "s_0_1111", "s_0_1_1111_qseq.txt"},
- {1, "s_1_23", "s_1_9_0023_qseq.txt.gz"},
- {10, "s_10_1", "s_10_7_0001_qseq.txt.bz2"}
+ return new Object[][]{
+ {0, "s_0_1111.test"},
+ {1, "s_1_23.test"},
+ {10, "s_10_1.test"}
};
}
+
public void regexMatches(final String regex, final String toMatch) {
regexMatches(regex, toMatch, true);
}
- public void regexMatches(final String regex, final String toMatch, boolean expectedResult) {
+ public void regexMatches(final String regex, final String toMatch, final boolean expectedResult) {
final Pattern pt = Pattern.compile(regex);
final Matcher ma = pt.matcher(toMatch);
Assert.assertEquals(ma.matches(), expectedResult);
}
- @Test(dataProvider="validLanes")
- public void regexTests(final int lane, final String ltExample, final String qseqExample) {
- regexMatches(IlluminaFileUtil.makeParameterizedLaneAndTileRegex(lane), ltExample);
- regexMatches(IlluminaFileUtil.makeParameterizedQseqRegex(lane), qseqExample);
+ @Test(dataProvider = "validLanes")
+ public void regexTests(final int lane, final String ltExample) {
+ regexMatches(ParameterizedFileUtil.makeLaneTileRegex(".test", lane), ltExample);
}
- @DataProvider(name="validLanesInvalidRegexes")
+ @DataProvider(name = "validLanesInvalidRegexes")
public Object[][] validLanesInvalidRegexes() {
- return new Object[][] {
- {0, "s_-0_111", " s_-1_1_1111_qseq.txt"},
- {1, "s_1_A3", "s_1_9_0C23_qseq.txt.gz"},
- {10, "s_-100_1", "s_10_20_0001_qseq.txt.bz2"},
- {20, "s_21_1", "s_20_7_0001_qseq.txt.bz3"}
+ return new Object[][]{
+ {0, "s_-0_111"},
+ {1, "s_1_A3"},
+ {10, "s_-100_1"},
+ {20, "s_21_1"}
};
}
- @Test(dataProvider="validLanesInvalidRegexes")
- public void notMatchingRegexTest(final int lane, final String ltExample, final String qseqExample) {
- regexMatches(IlluminaFileUtil.makeParameterizedLaneAndTileRegex(lane), ltExample, false);
- regexMatches(IlluminaFileUtil.makeParameterizedQseqRegex(lane), qseqExample, false);
+
+ @Test(dataProvider = "validLanesInvalidRegexes")
+ public void notMatchingRegexTest(final int lane, final String ltExample) {
+ regexMatches(ParameterizedFileUtil.makeLaneTileRegex(".test", lane) , ltExample, false);
}
- @DataProvider(name="invalidLanes")
+ @DataProvider(name = "invalidLanes")
public Object[][] invalidLanes() {
- return new Object[][] {
+ return new Object[][]{
{-1000},
{-10},
{-1}
};
}
- @Test(dataProvider="invalidLanes", expectedExceptions = PicardException.class)
+ @Test(dataProvider = "invalidLanes", expectedExceptions = PicardException.class)
public void invalidLaneForLTRegex(final int lane) {
- IlluminaFileUtil.makeParameterizedLaneAndTileRegex(lane);
- }
-
- @Test(dataProvider="invalidLanes", expectedExceptions = PicardException.class)
- public void invalidLaneForQseqRegex(final int lane) {
- IlluminaFileUtil.makeParameterizedQseqRegex(lane);
+ ParameterizedFileUtil.makeLaneTileRegex(".test", lane);
}
public void assertDefaults(final IlluminaFileUtil fileUtil, final Integer lane, final List<SupportedIlluminaFormat> formatsToTest) {
- if(lane == null) {
+ if (lane == null) {
Assert.assertEquals(fileUtil.getLane(), DEFAULT_LANE);
} else {
Assert.assertEquals(new Integer(fileUtil.getLane()), lane);
}
- Assert.assertEquals(fileUtil.barcode(), fileUtil.getUtil(SupportedIlluminaFormat.Barcode));
- Assert.assertEquals(fileUtil.barcode().getTiles(), DEFAULT_TILES);
-
- Assert.assertEquals(fileUtil.bcl(), fileUtil.getUtil(SupportedIlluminaFormat.Bcl));
- Assert.assertEquals(fileUtil.bcl().getTiles(), DEFAULT_TILES);
-
- Assert.assertEquals(fileUtil.cif(), fileUtil.getUtil(SupportedIlluminaFormat.Cif));
- Assert.assertEquals(fileUtil.cif().getTiles(), DEFAULT_TILES);
-
- Assert.assertEquals(fileUtil.cnf(), fileUtil.getUtil(SupportedIlluminaFormat.Cnf));
- Assert.assertEquals(fileUtil.cnf().getTiles(), DEFAULT_TILES);
-
- Assert.assertEquals(fileUtil.pos(), fileUtil.getUtil(SupportedIlluminaFormat.Pos));
- Assert.assertEquals(fileUtil.pos().getTiles(), DEFAULT_TILES);
+ Assert.assertEquals(fileUtil.getUtil(SupportedIlluminaFormat.Barcode).getTiles(), DEFAULT_TILES);
- Assert.assertEquals(fileUtil.locs(), fileUtil.getUtil(SupportedIlluminaFormat.Locs));
- Assert.assertEquals(fileUtil.locs().getTiles(), DEFAULT_TILES);
+ Assert.assertEquals(fileUtil.getUtil(SupportedIlluminaFormat.Bcl).getTiles(), DEFAULT_TILES);
- Assert.assertEquals(fileUtil.clocs(), fileUtil.getUtil(SupportedIlluminaFormat.Clocs));
- Assert.assertEquals(fileUtil.clocs().getTiles(), DEFAULT_TILES);
+ Assert.assertEquals(fileUtil.getUtil(SupportedIlluminaFormat.Pos).getTiles(), DEFAULT_TILES);
- Assert.assertEquals(fileUtil.filter(), fileUtil.getUtil(SupportedIlluminaFormat.Filter));
- Assert.assertEquals(fileUtil.filter().getTiles(), DEFAULT_TILES);
+ Assert.assertEquals(fileUtil.getUtil(SupportedIlluminaFormat.Locs).getTiles(), DEFAULT_TILES);
- Assert.assertEquals(fileUtil.qseq(), fileUtil.getUtil(SupportedIlluminaFormat.Qseq));
- Assert.assertEquals(fileUtil.qseq().getTiles(), DEFAULT_TILES);
+ Assert.assertEquals(fileUtil.getUtil(SupportedIlluminaFormat.Clocs).getTiles(), DEFAULT_TILES);
- Assert.assertEquals(fileUtil.qseq().numberOfEnds(), DEFAULT_NUM_ENDS);
+ Assert.assertEquals(fileUtil.getUtil(SupportedIlluminaFormat.Filter).getTiles(), DEFAULT_TILES);
- final int [] detectedCycles = fileUtil.bcl().getDetectedCycles();
- Assert.assertEquals(detectedCycles.length, DEFAULT_CYCLES.length);
- for(int i = 0; i < DEFAULT_CYCLES.length; i++) {
- Assert.assertEquals(detectedCycles[i], DEFAULT_CYCLES[i], "Elements differ at index " + i);
+ final Set<Integer> detectedCycles = ((PerTilePerCycleFileUtil) fileUtil.getUtil(SupportedIlluminaFormat.Bcl)).getDetectedCycles();
+ Assert.assertEquals(detectedCycles.size(), DEFAULT_CYCLES.length);
+ int i = 0;
+ for(final Integer cycle : detectedCycles){
+ Assert.assertEquals(cycle.intValue(), DEFAULT_CYCLES[i++], "Elements differ at index " + i);
}
Assert.assertEquals(fileUtil.getActualTiles(formatsToTest), DEFAULT_TILES);
@@ -158,10 +145,10 @@ public class IlluminaFileUtilTest {
@Test
public void passNewUtilTest() {
- for(final SupportedIlluminaFormat format : SupportedIlluminaFormat.values()) {
- makeFiles(format, intensityDir, DEFAULT_LANE, DEFAULT_TILES, DEFAULT_CYCLES, DEFAULT_NUM_ENDS);
- makeFiles(format, intensityDir, DEFAULT_LANE+1, DEFAULT_TILES, DEFAULT_CYCLES, DEFAULT_NUM_ENDS, ".gz");
- makeFiles(format, intensityDir, DEFAULT_LANE+2, DEFAULT_TILES, DEFAULT_CYCLES, DEFAULT_NUM_ENDS, ".bz2");
+ for (final SupportedIlluminaFormat format : SupportedIlluminaFormat.values()) {
+ makeFiles(format, intensityDir, DEFAULT_LANE, DEFAULT_TILES, DEFAULT_CYCLES);
+ makeFiles(format, intensityDir, DEFAULT_LANE + 1, DEFAULT_TILES, DEFAULT_CYCLES, ".gz");
+ makeFiles(format, intensityDir, DEFAULT_LANE + 2, DEFAULT_TILES, DEFAULT_CYCLES, ".bz2");
}
final Set<SupportedIlluminaFormat> formatsToTest = new HashSet<SupportedIlluminaFormat>();
@@ -170,203 +157,113 @@ public class IlluminaFileUtilTest {
formatsToTest.remove(SupportedIlluminaFormat.MultiTileBcl);
formatsToTest.remove(SupportedIlluminaFormat.MultiTileFilter);
formatsToTest.remove(SupportedIlluminaFormat.MultiTileLocs);
- ArrayList<SupportedIlluminaFormat> formatsList = new ArrayList<SupportedIlluminaFormat>(formatsToTest);
+ final ArrayList<SupportedIlluminaFormat> formatsList = new ArrayList<SupportedIlluminaFormat>(formatsToTest);
- for(int i = 0; i < 3; i++) {
+ for (int i = 0; i < 3; i++) {
final IlluminaFileUtil fileUtil = new IlluminaFileUtil(new File(intensityDir, "BaseCalls"), DEFAULT_LANE + i);
Assert.assertEquals(fileUtil.getActualTiles(formatsList), DEFAULT_TILES);
- assertDefaults(fileUtil, DEFAULT_LANE+i, formatsList);
+ assertDefaults(fileUtil, DEFAULT_LANE + i, formatsList);
}
}
@Test
- public void passingVerifyTest_noQseq() {
- for(final SupportedIlluminaFormat format : SupportedIlluminaFormat.values()) {
- makeFiles(format, intensityDir, DEFAULT_LANE, DEFAULT_TILES, DEFAULT_CYCLES, DEFAULT_NUM_ENDS);
- makeFiles(format, intensityDir, DEFAULT_LANE+1, DEFAULT_TILES, DEFAULT_CYCLES, DEFAULT_NUM_ENDS, ".gz");
- makeFiles(format, intensityDir, DEFAULT_LANE+2, DEFAULT_TILES, DEFAULT_CYCLES, DEFAULT_NUM_ENDS, ".bz2");
+ public void passingVerifyTest() {
+ for (final SupportedIlluminaFormat format : SupportedIlluminaFormat.values()) {
+ makeFiles(format, intensityDir, DEFAULT_LANE, DEFAULT_TILES, DEFAULT_CYCLES);
+ makeFiles(format, intensityDir, DEFAULT_LANE + 1, DEFAULT_TILES, DEFAULT_CYCLES, ".gz");
+ makeFiles(format, intensityDir, DEFAULT_LANE + 2, DEFAULT_TILES, DEFAULT_CYCLES, ".bz2");
}
- for(int i = 0; i < 3; i++) {
+ for (int i = 0; i < 3; i++) {
final IlluminaFileUtil fileUtil = new IlluminaFileUtil(new File(intensityDir, "BaseCalls"), DEFAULT_LANE + i);
- for(final SupportedIlluminaFormat format : FORMATS_TO_TEST) {
- if(format != SupportedIlluminaFormat.Qseq) {
- Assert.assertEquals(new ArrayList<String>(), fileUtil.getUtil(format).verify(DEFAULT_TILES, DEFAULT_CYCLES));
- }
- }
- }
- }
-
- @DataProvider(name="passingQseqVerifyTestData")
- public Object[][] passingQseqVerifyTestData() {
- return new Object[][] {
- {4, makeList(1,2,3), cycleRange(1, 152)},
- {6, makeList(1), cycleRange(1, 144)},
- {6, makeList(1), cycleRange(100, 110)},
- };
- }
-
- @Test(dataProvider="passingQseqVerifyTestData")
- public void passingVerifyTest_qseq(final int lane, List<Integer> tiles, final int [] cycles) {
- final IlluminaFileUtil fileUtil = new IlluminaFileUtil(new File("testdata/net/sf/picard/illumina/IlluminaTests/", "BasecallsDir"), lane);
- Assert.assertEquals(new ArrayList<String>(), fileUtil.qseq().verify(tiles, cycles));
- }
-
- //Need one where the cycle range asked for is greater than that available
- //Need one where the various reads are missing
-
- @DataProvider(name="failingQseqVerifyTestData")
- public Object[][] failingQseqVerifyTestData() {
- return new Object[][] {
- {4, makeList(1,2,3), cycleRange(1, 153), new ArrayList<String>(), 1},
- {4, makeList(1,2,3), cycleRange(1, 152), makeList("BaseCalls/s_4_2_0002_qseq.txt"), 1},
- {4, makeList(1,2,3), cycleRange(1, 10), makeList("BaseCalls/s_4_1_0002_qseq.txt"), 1},
- {4, makeList(1,2,3), cycleRange(1, 10), makeList("BaseCalls/s_4_2_0002_qseq.txt"), 1},
- {6, makeList(1), cycleRange(1, 146), makeList("BaseCalls/s_6_2_0001_qseq.txt"), 78},
- {6, makeList(1), cycleRange(100, 110), makeList("BaseCalls/s_6_3_0001_qseq.txt"), 11},
- };
- }
- @Test(dataProvider="failingQseqVerifyTestData")
- public void failingVerifyTest_qseq(final int lane, List<Integer> tiles, final int [] cycles, final List<String> toDelete, int numErrors) {
- IoUtil.copyDirectoryTree(new File("testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir"), basecallDir);
-
- deleteRelativeFiles(toDelete);
-
- final IlluminaFileUtil fileUtil = new IlluminaFileUtil(basecallDir, lane);
- Assert.assertEquals(numErrors, fileUtil.qseq().verify(tiles, cycles).size());
- }
-
- @DataProvider(name="failingVerifyNoQSeq")
- public Object[][] failingVerify_noQseq() {
- return new Object[][] {
- { makeList("BaseCalls/L007/C4.1/s_7_9.bcl"), 1},
- { makeList("BaseCalls/L007/C20.1/s_7_11.bcl", "BaseCalls/L007/C20.1/s_7_12.bcl"), 2},
- { makeList("BaseCalls/L007/C10.1/"), 1},
- { makeList("L007/C1.1/s_7_1.cif", "L007/C20.1/s_7_12.cnf"), 2},
-
- { makeList("L007/s_7_2.locs", "L007/s_7_3.locs", "L007/s_7_4.locs"), 3},
- { makeList("BaseCalls/L007/C20.1/s_7_11.bcl", "BaseCalls/L007/C20.1/s_7_12.bcl", "L007/s_7_4.locs"), 3},
- { makeList("BaseCalls/L007/s_7_0005.filter", "BaseCalls/L007/s_7_0011.filter", "BaseCalls/s_7_0002_barcode.txt"), 3},
- };
- }
-
- @Test(dataProvider="failingVerifyNoQSeq")
- public void failingVerifyTest_noQseq(final List<String> filesToDelete, final int expectedNumDifferences) {
- for(final SupportedIlluminaFormat format : SupportedIlluminaFormat.values()) {
- makeFiles(format, intensityDir, DEFAULT_LANE, DEFAULT_TILES, DEFAULT_CYCLES, DEFAULT_NUM_ENDS);
- }
-
- deleteRelativeFiles(filesToDelete);
-
- final IlluminaFileUtil fileUtil = new IlluminaFileUtil(new File(intensityDir, "BaseCalls"), DEFAULT_LANE);
-
- int totalDifferences = 0;
- List<String> differences = new ArrayList<String>();
- for(final SupportedIlluminaFormat format : FORMATS_TO_TEST) {
- if(format != SupportedIlluminaFormat.Qseq) {
- final List<String> curDiffs = fileUtil.getUtil(format).verify(DEFAULT_TILES, DEFAULT_CYCLES);
- differences.addAll(curDiffs);
-
- totalDifferences += curDiffs.size();
+ for (final SupportedIlluminaFormat format : FORMATS_TO_TEST) {
+ Assert.assertEquals(new ArrayList<String>(), fileUtil.getUtil(format).verify(DEFAULT_TILES, DEFAULT_CYCLES));
}
}
-
- Assert.assertEquals(expectedNumDifferences, totalDifferences);
-
}
- @DataProvider(name="missingTileFormats")
+ @DataProvider(name = "missingTileFormats")
public Object[][] missingTileFormats() {
return new Object[][]{
- {
- 1,
- makeList(SupportedIlluminaFormat.Bcl, SupportedIlluminaFormat.Barcode),
- makeList(SupportedIlluminaFormat.Bcl, SupportedIlluminaFormat.Barcode),
- makeList("BaseCalls/s_1_0007_barcode.txt.gz"),
- ".gz"
- },
-
- {
- 2,
- Arrays.asList(SupportedIlluminaFormat.values()),
- Arrays.asList(SupportedIlluminaFormat.values()),
- makeCycleFileList(new File("BaseCalls"), ".bcl", 2, DEFAULT_CYCLES, 2),
- ".gz"
- },
- {
- 3,
- Arrays.asList(SupportedIlluminaFormat.values()),
- Arrays.asList(SupportedIlluminaFormat.values()),
- makeList("BaseCalls/L003/C1.1/s_3_2.bcl"),
- ".bz2"
- },
- {
- 4,
- Arrays.asList(SupportedIlluminaFormat.values()),
- Arrays.asList(SupportedIlluminaFormat.Pos, SupportedIlluminaFormat.Locs),
- makeList("s_4_10_pos.txt", "L004/s_4_2.locs"),
- null
- },
- {
- 5,
- makeList(SupportedIlluminaFormat.Cif, SupportedIlluminaFormat.Cnf, SupportedIlluminaFormat.Qseq),
- makeList(SupportedIlluminaFormat.Cif, SupportedIlluminaFormat.Qseq),
- makeList("BaseCalls/s_5_1_0003_qseq.txt.gz", "BaseCalls/s_5_2_0003_qseq.txt.gz",
- "BaseCalls/s_5_3_0003_qseq.txt.gz", "BaseCalls/s_5_4_0003_qseq.txt.gz",
- "BaseCalls/s_5_1_0004_qseq.txt.gz", "BaseCalls/s_5_2_0004_qseq.txt.gz",
- "BaseCalls/s_5_3_0004_qseq.txt.gz", "BaseCalls/s_5_4_0004_qseq.txt.gz"),
- ".gz"
- }
+ {
+ 1,
+ makeList(SupportedIlluminaFormat.Bcl, SupportedIlluminaFormat.Barcode),
+ makeList(SupportedIlluminaFormat.Bcl, SupportedIlluminaFormat.Barcode),
+ makeList("BaseCalls/s_1_0007_barcode.txt.gz"),
+ ".gz"
+ },
+
+ {
+ 2,
+ Arrays.asList(SupportedIlluminaFormat.values()),
+ Arrays.asList(SupportedIlluminaFormat.values()),
+ makeCycleFileList(new File("BaseCalls"), ".bcl", 2, DEFAULT_CYCLES, 2),
+ ".gz"
+ },
+ {
+ 3,
+ Arrays.asList(SupportedIlluminaFormat.values()),
+ Arrays.asList(SupportedIlluminaFormat.values()),
+ makeList("BaseCalls/L003/C1.1/s_3_2.bcl"),
+ ".bz2"
+ },
+ {
+ 4,
+ Arrays.asList(SupportedIlluminaFormat.values()),
+ Arrays.asList(SupportedIlluminaFormat.Pos, SupportedIlluminaFormat.Locs),
+ makeList("s_4_10_pos.txt", "L004/s_4_2.locs"),
+ null
+ }
};
}
- public static final void emptyRelativeFiles(final File baseFile, final List<String> relativeFilesToDelete) {
- for(final String relativeFile : relativeFilesToDelete) {
+ public static void emptyRelativeFiles(final File baseFile, final List<String> relativeFilesToDelete) {
+ for (final String relativeFile : relativeFilesToDelete) {
final File actualFile = new File(baseFile, relativeFile);
- if(!actualFile.exists()) {
+ if (!actualFile.exists()) {
throw new RuntimeException("Trying to empty a non-existent file" + actualFile.getAbsolutePath());
}
- if(actualFile.isDirectory()) {
- throw new RuntimeException("Trying to empty a directory(" + actualFile.getAbsolutePath() +")");
+ if (actualFile.isDirectory()) {
+ throw new RuntimeException("Trying to empty a directory(" + actualFile.getAbsolutePath() + ")");
} else {
- if(!actualFile.delete()) {
+ if (!actualFile.delete()) {
throw new RuntimeException("Couldn't remove previous file when emptying(" + actualFile.getAbsolutePath() + ")");
} else {
try {
- if(!actualFile.createNewFile()) {
+ if (!actualFile.createNewFile()) {
throw new RuntimeException("Couldn't create empty file: " + actualFile.getAbsolutePath() + ")");
}
- } catch(IOException ioe) {
+ } catch (final IOException ioe) {
throw new RuntimeException(ioe);
}
}
}
- if(!actualFile.exists()) {
+ if (!actualFile.exists()) {
throw new PicardException("File should exist: " + actualFile);
}
}
}
- public static final void deleteRelativeFiles(final File baseFile, final List<String> relativeFilesToDelete) {
- for(final String relativeFile : relativeFilesToDelete) {
+ public static void deleteRelativeFiles(final File baseFile, final List<String> relativeFilesToDelete) {
+ for (final String relativeFile : relativeFilesToDelete) {
final File actualFile = new File(baseFile, relativeFile);
- if(!actualFile.exists()) {
+ if (!actualFile.exists()) {
throw new RuntimeException("Trying to delete a non-existent file" + actualFile.getAbsolutePath());
}
- if(actualFile.isDirectory()) {
+ if (actualFile.isDirectory()) {
IoUtil.deleteDirectoryTree(actualFile);
} else {
- actualFile.delete();
+ IoUtil.deleteFiles(actualFile);
}
- if(actualFile.exists()) {
+ if (actualFile.exists()) {
throw new RuntimeException("File still exists after calling delete: " + actualFile);
}
}
@@ -376,23 +273,23 @@ public class IlluminaFileUtilTest {
deleteRelativeFiles(intensityDir, relativeFilesToDelete);
}
- @Test(dataProvider="missingTileFormats")
+ @Test(dataProvider = "missingTileFormats")
public void missingTileTest(final int lane,
final List<SupportedIlluminaFormat> formats,
final List<SupportedIlluminaFormat> formatsToGetTiles,
final List<String> relativeFilesToDelete,
final String compression) {
- for(final SupportedIlluminaFormat format : formats) {
- makeFiles(format, intensityDir, lane, DEFAULT_TILES, DEFAULT_CYCLES, DEFAULT_NUM_ENDS, compression);
+ for (final SupportedIlluminaFormat format : formats) {
+ makeFiles(format, intensityDir, lane, DEFAULT_TILES, DEFAULT_CYCLES, compression);
}
deleteRelativeFiles(relativeFilesToDelete);
PicardException pExc = null;
- try{
+ try {
final IlluminaFileUtil fUtil = new IlluminaFileUtil(new File(intensityDir, "BaseCalls"), lane);
fUtil.getActualTiles(formatsToGetTiles);
- } catch(final PicardException exception) {
+ } catch (final PicardException exception) {
pExc = exception;
}
@@ -400,15 +297,15 @@ public class IlluminaFileUtilTest {
Assert.assertTrue(pExc.getMessage().contains("Formats do not have the same number of tiles! "), "Wrong exception thrown for missing tile!");
}
- @DataProvider(name="perTileFileFormats")
+ @DataProvider(name = "perTileFileFormats")
public Object[][] perTileFileUtils() {
return new Object[][]{
- {SupportedIlluminaFormat.Locs, null, false, laneDir(DEFAULT_LANE)},
- {SupportedIlluminaFormat.Clocs, null, false, laneDir(DEFAULT_LANE)},
- {SupportedIlluminaFormat.Pos, ".gz", false, null},
- {SupportedIlluminaFormat.Pos, null, false, null},
- {SupportedIlluminaFormat.Filter, null, true, "BaseCalls/" + laneDir(DEFAULT_LANE)},
- {SupportedIlluminaFormat.Barcode, ".bz2", true, "BaseCalls"}
+ {SupportedIlluminaFormat.Locs, null, false, laneDir(DEFAULT_LANE)},
+ {SupportedIlluminaFormat.Clocs, null, false, laneDir(DEFAULT_LANE)},
+ {SupportedIlluminaFormat.Pos, ".gz", false, null},
+ {SupportedIlluminaFormat.Pos, null, false, null},
+ {SupportedIlluminaFormat.Filter, null, true, "BaseCalls/" + laneDir(DEFAULT_LANE)},
+ {SupportedIlluminaFormat.Barcode, ".bz2", true, "BaseCalls"}
};
}
@@ -416,14 +313,14 @@ public class IlluminaFileUtilTest {
return new File(parentDir, "s_" + lane + "_" + longTile(tile, longFormat) + extension + (compression != null ? compression : ""));
}
- public void testDefaultPerTileUtil(final IlluminaFileUtil.PerTileFileUtil ptfu, final String compression, final boolean longFormat, final File parentDir) {
+ public void testDefaultPerTileUtil(final PerTileFileUtil ptfu, final String compression, final boolean longFormat, final File parentDir) {
final IlluminaFileMap fm = ptfu.getFiles();
final IlluminaFileMap fmWTiles = ptfu.getFiles(DEFAULT_TILES);
Assert.assertEquals(fm.size(), DEFAULT_TILES.size());
- for(final Integer tile : DEFAULT_TILES) {
- final File tFile = fm.get(tile);
+ for (final Integer tile : DEFAULT_TILES) {
+ final File tFile = fm.get(tile);
final File tFile2 = fmWTiles.get(tile);
Assert.assertEquals(tFile.getAbsolutePath(), tFile2.getAbsolutePath());
Assert.assertEquals(tFile, makePerTileFile(parentDir, DEFAULT_LANE, tile, ptfu.extension, compression, longFormat));
@@ -433,10 +330,10 @@ public class IlluminaFileUtilTest {
final List<Integer> tiles = new ArrayList<Integer>(DEFAULT_TILE_TEST_SUBSET);
final IlluminaFileMap subsetMap = ptfu.getFiles(DEFAULT_TILE_TEST_SUBSET);
- for(final Integer tile : subsetMap.keySet()) {
+ for (final Integer tile : subsetMap.keySet()) {
tiles.remove(tile);
Assert.assertTrue(DEFAULT_TILE_TEST_SUBSET.contains(tile));
- final File tFile = subsetMap.get(tile);
+ final File tFile = subsetMap.get(tile);
Assert.assertEquals(tFile, makePerTileFile(parentDir, DEFAULT_LANE, tile, ptfu.extension, compression, longFormat));
Assert.assertTrue(tFile.exists());
Assert.assertTrue(tFile.length() > 0);
@@ -445,18 +342,18 @@ public class IlluminaFileUtilTest {
Assert.assertTrue(tiles.isEmpty());
}
- @Test(dataProvider="perTileFileFormats")
+ @Test(dataProvider = "perTileFileFormats")
public void perTileFileUtilsTest(final SupportedIlluminaFormat format, final String compression, final boolean longFormat, final String parentDir) {
- makeFiles(format, intensityDir, DEFAULT_LANE, DEFAULT_TILES, DEFAULT_CYCLES, DEFAULT_NUM_ENDS, compression);
+ makeFiles(format, intensityDir, DEFAULT_LANE, DEFAULT_TILES, DEFAULT_CYCLES, compression);
final IlluminaFileUtil fileUtil = new IlluminaFileUtil(basecallDir, DEFAULT_LANE);
- final IlluminaFileUtil.PerTileFileUtil ptfu = (IlluminaFileUtil.PerTileFileUtil)fileUtil.getUtil(format);
+ final PerTileFileUtil ptfu = (PerTileFileUtil) fileUtil.getUtil(format);
Assert.assertTrue(ptfu.filesAvailable());
testDefaultPerTileUtil(ptfu, compression, longFormat, (parentDir == null) ? intensityDir : new File(intensityDir, parentDir));
- final IlluminaFileUtil noFilesFu = new IlluminaFileUtil(basecallDir, DEFAULT_LANE+20);
- final IlluminaFileUtil.PerTileFileUtil noFilesPtfu = (IlluminaFileUtil.PerTileFileUtil)noFilesFu.getUtil(format);
+ final IlluminaFileUtil noFilesFu = new IlluminaFileUtil(basecallDir, DEFAULT_LANE + 20);
+ final PerTileFileUtil noFilesPtfu = (PerTileFileUtil) noFilesFu.getUtil(format);
Assert.assertFalse(noFilesPtfu.filesAvailable());
Assert.assertTrue(noFilesPtfu.getFiles().isEmpty());
Assert.assertTrue(noFilesPtfu.getFiles(DEFAULT_TILES).isEmpty());
@@ -466,35 +363,35 @@ public class IlluminaFileUtilTest {
return new File(parentDir, "C" + cycle + ".1/s_" + lane + "_" + tile + extension);
}
- public void testDefaultPerTilePerCycleUtil(final IlluminaFileUtil.PerTilePerCycleFileUtil pcfu, final File parentDir, final int [] cycles) {
- final CycleIlluminaFileMap cfm = pcfu.getFiles(cycles);
- final CycleIlluminaFileMap cfmWTiles = pcfu.getFiles(DEFAULT_TILES, cycles);
+ public void testDefaultPerTilePerCycleUtil(final PerTilePerCycleFileUtil pcfu, final File parentDir, final int[] cycles) {
+ final CycleIlluminaFileMap cfm = pcfu.getFiles(cycles);
+ final CycleIlluminaFileMap cfmWTiles = pcfu.getFiles(DEFAULT_TILES, cycles);
final CycleIlluminaFileMap cfmNoCycles;
- if(Arrays.equals(cycles, DEFAULT_CYCLES)) {
+ if (Arrays.equals(cycles, DEFAULT_CYCLES)) {
cfmNoCycles = pcfu.getFiles();
} else {
cfmNoCycles = null;
}
- Assert.assertEquals(cfm.size(), DEFAULT_TILES.size());
+ Assert.assertEquals(cfm.size(), cycles.length);
- for(final Integer tile : DEFAULT_TILES) {
- final CycleFilesIterator tFileIter = cfm.get(tile);
- final CycleFilesIterator tFileIter2 = cfmWTiles.get(tile);
- final CycleFilesIterator tFileIter3;
- if(cfmNoCycles != null) {
- tFileIter3 = cfmNoCycles.get(tile);
+ for (final int cycle : cycles) {
+ final IlluminaFileMap tFileIter = cfm.get(cycle);
+ final IlluminaFileMap tFileIter2 = cfmWTiles.get(cycle);
+ final IlluminaFileMap tFileIter3;
+ if (cfmNoCycles != null) {
+ tFileIter3 = cfmNoCycles.get(cycle);
} else {
tFileIter3 = null;
}
- for(final int cycle : cycles) {
- final File tcFile = tFileIter.next();
- final File tcFile2 = tFileIter2.next();
+ for (final Integer tile : DEFAULT_TILES) {
+ final File tcFile = tFileIter.get(tile);
+ final File tcFile2 = tFileIter2.get(tile);
Assert.assertEquals(tcFile.getAbsolutePath(), tcFile2.getAbsolutePath());
- if(tFileIter3 != null) {
- final File tfFile3 = tFileIter3.next();
+ if (tFileIter3 != null) {
+ final File tfFile3 = tFileIter3.get(tile);
Assert.assertEquals(tcFile.getAbsolutePath(), tfFile3.getAbsolutePath());
}
@@ -506,314 +403,213 @@ public class IlluminaFileUtilTest {
}
- public void testSubsetDefaultPerTilePerCycleUtil(final IlluminaFileUtil.PerTilePerCycleFileUtil pcfu, final File parentDir, int [] cycles) {
+ public void testSubsetDefaultPerTilePerCycleUtil(final PerTilePerCycleFileUtil pcfu, final File parentDir, final int[] cycles) {
final List<Integer> tiles = new ArrayList<Integer>(DEFAULT_TILE_TEST_SUBSET);
final CycleIlluminaFileMap subsetMap = pcfu.getFiles(DEFAULT_TILE_TEST_SUBSET, cycles);
final CycleIlluminaFileMap cfmNoCycles;
- if(Arrays.equals(cycles, DEFAULT_CYCLES)) {
+ if (Arrays.equals(cycles, DEFAULT_CYCLES)) {
cfmNoCycles = pcfu.getFiles(DEFAULT_TILE_TEST_SUBSET);
} else {
cfmNoCycles = null;
}
- for(final Integer tile : subsetMap.keySet()) {
- tiles.remove(tile);
- Assert.assertTrue(DEFAULT_TILE_TEST_SUBSET.contains(tile));
- final CycleFilesIterator tFileIter = subsetMap.get(tile);
- final CycleFilesIterator tFileIter2;
- if(cfmNoCycles != null) {
- tFileIter2 = cfmNoCycles.get(tile);
+ for (final int cycle : cycles) {
+ final IlluminaFileMap tFileIter = subsetMap.get(cycle);
+ final IlluminaFileMap tFileIter2;
+ if (cfmNoCycles != null) {
+ tFileIter2 = cfmNoCycles.get(cycle);
} else {
tFileIter2 = null;
}
- for(final int cycle : cycles) {
- final File tcFile = tFileIter.next();
- if(tFileIter2 != null) {
- Assert.assertEquals(tcFile, tFileIter2.next());
+ for (final Integer tile : subsetMap.get(cycle).keySet()) {
+ Assert.assertTrue(DEFAULT_TILE_TEST_SUBSET.contains(tile));
+ tiles.remove(tile);
+ final File tcFile = tFileIter.get(tile);
+ if (tFileIter2 != null) {
+ Assert.assertEquals(tcFile, tFileIter2.get(tile));
}
Assert.assertEquals(tcFile, makePerTilePerCycleFilePath(parentDir, DEFAULT_LANE, tile, cycle, pcfu.extension));
Assert.assertTrue(tcFile.exists());
Assert.assertTrue(tcFile.length() > 0);
}
-
- Assert.assertFalse(tFileIter.hasNext());
}
Assert.assertTrue(tiles.isEmpty());
}
- public static int [] cycleRange(final Range range) {
+ public static int[] cycleRange(final Range range) {
return cycleRange(range.start, range.end);
}
- public static int [] cycleRange(final int start, final int end) {
- final int [] cycles = new int[end - start + 1];
- for(int i = 0; i < cycles.length; i++) {
+ public static int[] cycleRange(final int start, final int end) {
+ final int[] cycles = new int[end - start + 1];
+ for (int i = 0; i < cycles.length; i++) {
cycles[i] = start + i;
}
return cycles;
}
- public static int [] cycleRange(final int end) {
+ public static int[] cycleRange(final int end) {
return cycleRange(1, end);
}
- @DataProvider(name="perTilePerCycleFileFormats")
+ @DataProvider(name = "perTilePerCycleFileFormats")
public Object[][] perTilePerCycleFileFormats() {
return new Object[][]{
- {SupportedIlluminaFormat.Bcl, "BaseCalls/" + laneDir(DEFAULT_LANE), DEFAULT_CYCLES, false, false },
- {SupportedIlluminaFormat.Bcl, "BaseCalls/" + laneDir(DEFAULT_LANE), cycleRange(4), true, true },
- {SupportedIlluminaFormat.Cif, laneDir(DEFAULT_LANE) , DEFAULT_CYCLES, false, false },
- {SupportedIlluminaFormat.Cif, laneDir(DEFAULT_LANE) , cycleRange(8,12), true, false },
- {SupportedIlluminaFormat.Cif, laneDir(DEFAULT_LANE) , cycleRange(8,12), false, false },
- {SupportedIlluminaFormat.Cnf, laneDir(DEFAULT_LANE) , DEFAULT_CYCLES, false, false },
- {SupportedIlluminaFormat.Cnf, laneDir(DEFAULT_LANE) , cycleRange(15,DEFAULT_LAST_CYCLE), false, false }
+ {SupportedIlluminaFormat.Bcl, "BaseCalls/" + laneDir(DEFAULT_LANE), DEFAULT_CYCLES, false, false},
+ {SupportedIlluminaFormat.Bcl, "BaseCalls/" + laneDir(DEFAULT_LANE), cycleRange(4), true, true},
};
}
- @Test(dataProvider="perTilePerCycleFileFormats")
- public void perTilePerCycleFileUtilsTest(final SupportedIlluminaFormat format, final String parentDir, final int [] cycles, boolean createEarlySkippedCycles, boolean createLateSkippedCycles) {
- if(createEarlySkippedCycles) {
- makeFiles(format, intensityDir, DEFAULT_LANE, DEFAULT_TILES, cycleRange(1, cycles[0]), DEFAULT_NUM_ENDS, null);
+ @Test(dataProvider = "perTilePerCycleFileFormats")
+ public void perTilePerCycleFileUtilsTest(final SupportedIlluminaFormat format, final String parentDir,
+ final int[] cycles, final boolean createEarlySkippedCycles,
+ final boolean createLateSkippedCycles) {
+ if (createEarlySkippedCycles) {
+ makeFiles(format, intensityDir, DEFAULT_LANE, DEFAULT_TILES, cycleRange(1, cycles[0]), null);
}
- makeFiles(format, intensityDir, DEFAULT_LANE, DEFAULT_TILES, cycles, DEFAULT_NUM_ENDS, null);
+ makeFiles(format, intensityDir, DEFAULT_LANE, DEFAULT_TILES, cycles, null);
- if(createLateSkippedCycles) {
- makeFiles(format, intensityDir, DEFAULT_LANE, DEFAULT_TILES, cycleRange(cycles[cycles.length-1] + 1, DEFAULT_LAST_CYCLE), DEFAULT_NUM_ENDS, null);
+ if (createLateSkippedCycles) {
+ makeFiles(format, intensityDir, DEFAULT_LANE, DEFAULT_TILES, cycleRange(cycles[cycles.length - 1] + 1, DEFAULT_LAST_CYCLE), null);
}
final IlluminaFileUtil fileUtil = new IlluminaFileUtil(basecallDir, DEFAULT_LANE);
- final IlluminaFileUtil.PerTilePerCycleFileUtil pcfu = (IlluminaFileUtil.PerTilePerCycleFileUtil)fileUtil.getUtil(format);
+ final PerTilePerCycleFileUtil pcfu = (PerTilePerCycleFileUtil) fileUtil.getUtil(format);
Assert.assertTrue(pcfu.filesAvailable());
testDefaultPerTilePerCycleUtil(pcfu, (parentDir == null) ? intensityDir : new File(intensityDir, parentDir), cycles);
testSubsetDefaultPerTilePerCycleUtil(pcfu, (parentDir == null) ? intensityDir : new File(intensityDir, parentDir), cycles);
- final IlluminaFileUtil noFilesFu = new IlluminaFileUtil(basecallDir, DEFAULT_LANE+20);
- final IlluminaFileUtil.PerTilePerCycleFileUtil noFilesPcfu = (IlluminaFileUtil.PerTilePerCycleFileUtil)noFilesFu.getUtil(format);
+ final IlluminaFileUtil noFilesFu = new IlluminaFileUtil(basecallDir, DEFAULT_LANE + 20);
+ final PerTilePerCycleFileUtil noFilesPcfu = (PerTilePerCycleFileUtil) noFilesFu.getUtil(format);
Assert.assertFalse(noFilesPcfu.filesAvailable());
Assert.assertTrue(noFilesPcfu.getFiles().isEmpty());
Assert.assertTrue(noFilesPcfu.getFiles(DEFAULT_TILES).isEmpty());
}
- @DataProvider(name="missingCycleDataRanges")
+ @DataProvider(name = "missingCycleDataRanges")
public Object[][] missingCycleDataRanges() {
- return new Object[][] {
- {makeList(new Range(10,15))},
- {makeList(new Range(9,12), new Range(14,15))}
+ return new Object[][]{
+ {makeList(new Range(10, 15))},
+ {makeList(new Range(9, 12), new Range(14, 15))}
};
}
- @Test(expectedExceptions = PicardException.class, dataProvider="missingCycleDataRanges")
+ @Test(expectedExceptions = PicardException.class, dataProvider = "missingCycleDataRanges")
public void perTilePerCycleFileUtilsMissingCycleTest(final List<Range> cycleRangesToMake) {
final SupportedIlluminaFormat format = SupportedIlluminaFormat.Bcl;
- final String parentDir = "BaseCalls/" + laneDir(DEFAULT_LANE);
- for(final Range range : cycleRangesToMake) {
- makeFiles(format, intensityDir, DEFAULT_LANE, DEFAULT_TILES, cycleRange(range), DEFAULT_NUM_ENDS, null);
+ for (final Range range : cycleRangesToMake) {
+ makeFiles(format, intensityDir, DEFAULT_LANE, DEFAULT_TILES, cycleRange(range), null);
}
final IlluminaFileUtil fileUtil = new IlluminaFileUtil(basecallDir, DEFAULT_LANE);
- final IlluminaFileUtil.PerTilePerCycleFileUtil pcfu = (IlluminaFileUtil.PerTilePerCycleFileUtil)fileUtil.getUtil(format);
+ final PerTilePerCycleFileUtil pcfu = (PerTilePerCycleFileUtil) fileUtil.getUtil(format);
Assert.assertTrue(pcfu.filesAvailable());
- int [] cycles = cycleRange(9,16);
- CycleIlluminaFileMap cfm = pcfu.getFiles(cycles);
+ final int[] cycles = cycleRange(9, 16);
+ final CycleIlluminaFileMap cfm = pcfu.getFiles(cycles);
cfm.assertValid(DEFAULT_TILES, cycles);
}
- @DataProvider(name="qseqTestData")
- public Object[][] qseqTestData() {
- return new Object[][]{
- //lane, compression
- {1, ".gz" },
- {8, ".bz2"},
- {10, null }
- };
- }
-
- @Test(dataProvider="qseqTestData")
- public void qseqFileUtilTest(final int lane, final String compression) {
- makeFiles(SupportedIlluminaFormat.Qseq, intensityDir, lane, DEFAULT_TILES, DEFAULT_CYCLES, DEFAULT_NUM_ENDS, compression);
- final IlluminaFileUtil fileUtil = new IlluminaFileUtil(basecallDir, lane);
- final IlluminaFileUtil.QSeqIlluminaFileUtil qseq = fileUtil.qseq();
-
- Assert.assertTrue(qseq.filesAvailable());
- Assert.assertEquals(qseq.numberOfEnds(), DEFAULT_NUM_ENDS);
- testQseqUtil(qseq, lane, compression);
-
- final IlluminaFileUtil noFilesFu = new IlluminaFileUtil(basecallDir, DEFAULT_LANE+20);
- Assert.assertFalse(noFilesFu.qseq().filesAvailable());
- Assert.assertEquals(qseq.numberOfEnds(), DEFAULT_NUM_ENDS);
- Assert.assertTrue(noFilesFu.qseq().getFiles().isEmpty());
- Assert.assertTrue(noFilesFu.qseq().getFiles(DEFAULT_TILES).isEmpty());
+ public static void makeFiles(final SupportedIlluminaFormat format, final File intensityDir, final int lane,
+ final List<Integer> tiles, final int[] cycles) {
+ makeFiles(format, intensityDir, lane, tiles, cycles, null);
}
- public void testQseqUtil(final IlluminaFileUtil.QSeqIlluminaFileUtil qseq, final int lane, final String compression) {
- final List<IlluminaFileMap> listOfFm = qseq.getFiles();
- final List<IlluminaFileMap> listOfFmWTiles = qseq.getFiles(DEFAULT_TILES);
-
- Assert.assertEquals(listOfFm.size(), DEFAULT_NUM_ENDS);
-
- for(int i = 0; i < DEFAULT_NUM_ENDS; i++) {
- final int currentEnd = i+1;
- final IlluminaFileMap fm = listOfFm.get(i);
- final IlluminaFileMap fmWTiles = listOfFmWTiles.get(i);
-
- for(final Integer tile : DEFAULT_TILES) {
- final File tFile = fm.get(tile);
- final File tFile2 = fmWTiles.get(tile);
- Assert.assertEquals(tFile.getAbsolutePath(), tFile2.getAbsolutePath());
- Assert.assertEquals(tFile, makeQSeqFilePath(basecallDir, lane, tile, currentEnd, compression));
- Assert.assertTrue(tFile.exists());
- Assert.assertTrue(tFile.length() > 0);
- }
- }
-
- final List<IlluminaFileMap> listOfsubsetMap = qseq.getFiles(DEFAULT_TILE_TEST_SUBSET);
-
- for(int i = 0; i < DEFAULT_NUM_ENDS; i++) {
- final int currentEnd = i+1;
- final IlluminaFileMap subsetMap = listOfsubsetMap.get(i);
-
- final List<Integer> tiles = new ArrayList<Integer>(DEFAULT_TILE_TEST_SUBSET);
-
- for(final Integer tile : subsetMap.keySet()) {
- tiles.remove(tile);
- final File tFile = subsetMap.get(tile);
- Assert.assertEquals(tFile, makeQSeqFilePath(basecallDir, lane, tile, currentEnd, compression));
- Assert.assertTrue(tFile.exists());
- Assert.assertTrue(tFile.length() > 0);
- }
- Assert.assertTrue(tiles.isEmpty());
- }
- }
-
- private static File makeQSeqFilePath(final File basecallDir, final int lane, final int tile, final int end, final String compression) {
- return new File(basecallDir, "s_" + lane +"_" + end + "_" + longTile(tile,true) + "_qseq.txt" + (compression != null ? compression : ""));
- }
-
- public static void makeFiles(final SupportedIlluminaFormat format, final File intensityDir, int lane, List<Integer> tiles, final int [] cycles, final int ends) {
- makeFiles(format, intensityDir, lane, tiles, cycles, ends, null);
- }
- public static void makeFiles(final SupportedIlluminaFormat format, final File intensityDir, int lane, List<Integer> tiles, final int [] cycles, final int ends, final String compression) {
+ public static void makeFiles(final SupportedIlluminaFormat format, final File intensityDir, final int lane,
+ final List<Integer> tiles, final int[] cycles, final String compression) {
String laneDir = String.valueOf(lane);
- while(laneDir.length() < 3) {
+ while (laneDir.length() < 3) {
laneDir = "0" + laneDir;
}
laneDir = "L" + laneDir;
- final File basecallDir = new File(intensityDir, "BaseCalls");
- final File basecallLaneDir = new File(basecallDir, laneDir);
+ final File basecallDir = new File(intensityDir, "BaseCalls");
+ final File basecallLaneDir = new File(basecallDir, laneDir);
final File intensityLaneDir = new File(intensityDir, laneDir);
- switch(format) {
+ switch (format) {
//per tile formats
case Barcode:
- makePerTileFiles(basecallDir, lane, tiles, maybeAddExt("_barcode.txt", compression), true);
+ makePerTileFiles(basecallDir, lane, tiles, maybeAddExt("_barcode.txt", compression), true);
break;
case Pos:
- makePerTileFiles(intensityDir, lane, tiles, maybeAddExt("_pos.txt", compression), false);
+ makePerTileFiles(intensityDir, lane, tiles, maybeAddExt("_pos.txt", compression), false);
break;
case Locs:
- makePerTileFiles(intensityLaneDir, lane, tiles, maybeAddExt(".locs", null), false);
+ makePerTileFiles(intensityLaneDir, lane, tiles, maybeAddExt(".locs", null), false);
break;
case Clocs:
- makePerTileFiles(intensityLaneDir, lane, tiles, maybeAddExt(".clocs", null), false);
+ makePerTileFiles(intensityLaneDir, lane, tiles, maybeAddExt(".clocs", null), false);
break;
case Filter:
- makePerTileFiles(basecallLaneDir, lane, tiles, maybeAddExt(".filter", null), true);
+ makePerTileFiles(basecallLaneDir, lane, tiles, maybeAddExt(".filter", null), true);
break;
//per tile per cycle formats
case Bcl:
- makePerTilePerCycleFiles(basecallLaneDir, lane, tiles, cycles, ".bcl");
- break;
-
- case Cif:
- makePerTilePerCycleFiles(intensityLaneDir, lane, tiles, cycles, ".cif");
- break;
-
- case Cnf:
- makePerTilePerCycleFiles(intensityLaneDir, lane, tiles, cycles, ".cnf");
- break;
-
- //Qseq is based on lane, tile, and end
- case Qseq:
- makeQSeqFiles(basecallDir, lane, tiles, ends, compression);
+ makePerTilePerCycleFiles(basecallLaneDir, lane, tiles, cycles, ".bcl");
break;
}
}
- private static void makeQSeqFiles(final File basecallDir, final int lane, final List<Integer> tiles, final int ends, final String compressionExt) {
- if(!basecallDir.exists()) {
- if(!basecallDir.mkdir()) {
- throw new RuntimeException("Couldn't create directory " + basecallDir.getAbsolutePath());
- }
- }
-
- for(final Integer tile : tiles) {
- for(int end = 1; end <= ends; end++) {
- writeNonEmptyFile(new File(basecallDir, "s_" + lane + "_" + end + "_" + longTile(tile, true) + maybeAddExt("_qseq.txt", compressionExt)));
- }
- }
- }
-
private static void makePerTileFiles(final File parentDir, final int lane, final List<Integer> tiles, final String ext, final boolean longName) {
- if(!parentDir.exists()) {
- if(!parentDir.mkdir()) {
+ if (!parentDir.exists()) {
+ if (!parentDir.mkdir()) {
throw new RuntimeException("Couldn't create directory " + parentDir.getAbsolutePath());
}
}
- for(final Integer tile : tiles) {
- writeNonEmptyFile(new File(parentDir, "s_" + lane + "_" + longTile(tile, longName) + ext));
+ for (final Integer tile : tiles) {
+ writeNonEmptyFile(new File(parentDir, "s_" + lane + "_" + longTile(tile, longName) + ext));
}
}
- private static void makePerTilePerCycleFiles(final File parentDir, final int lane, final List<Integer> tiles, final int [] cycles, final String ext) {
- if(!parentDir.exists()) {
- if(!parentDir.mkdir()) {
+ private static void makePerTilePerCycleFiles(final File parentDir, final int lane, final List<Integer> tiles, final int[] cycles, final String ext) {
+ if (!parentDir.exists()) {
+ if (!parentDir.mkdir()) {
throw new RuntimeException("Couldn't create directory " + parentDir.getAbsolutePath());
}
}
- for(final int cycle : cycles) {
+ for (final int cycle : cycles) {
final File cycleDir = new File(parentDir, "C" + cycle + ".1");
- if(!cycleDir.exists()) {
- if(!cycleDir.mkdir()) {
+ if (!cycleDir.exists()) {
+ if (!cycleDir.mkdir()) {
throw new RuntimeException("Couldn't create directory " + cycleDir.getAbsolutePath());
}
}
- for(final Integer tile : tiles) {
+ for (final Integer tile : tiles) {
writeNonEmptyFile(new File(cycleDir, "s_" + lane + "_" + tile + ext));
}
}
}
- private static List<String> makeCycleFileList(final File dir, final String ext, final int lane, final int [] cycles, final int ... tiles) {
+ private static List<String> makeCycleFileList(final File dir, final String ext, final int lane, final int[] cycles, final int... tiles) {
return makeCycleFileList(dir, ext, lane, cycles, false, tiles);
}
- private static List<String> makeCycleFileList(final File dir, final String ext, final int lane, final int [] cycles, final boolean longFmt, final int ... tiles) {
+ private static List<String> makeCycleFileList(final File dir, final String ext, final int lane, final int[] cycles, final boolean longFmt, final int... tiles) {
final List<String> files = new ArrayList<String>();
final File laneDir = new File(dir, laneDir(lane));
- for(final int cycle : cycles) {
+ for (final int cycle : cycles) {
final File cycleDir = new File(laneDir, "C" + cycle + ".1");
- for(final Integer tile : tiles) {
+ for (final Integer tile : tiles) {
files.add(cycleDir + "/s_" + lane + "_" + longTile(tile, longFmt) + ext);
}
}
@@ -823,27 +619,29 @@ public class IlluminaFileUtilTest {
private static void writeNonEmptyFile(final File file) {
try {
- final FileWriter fw = new FileWriter(file);
- fw.write("This is just so that the file doesn't appear to be of 0 length");
- fw.flush();
- fw.close();
- } catch (IOException e) {
+ final OutputStream outputStream = new DataOutputStream(new FileOutputStream(file));
+ final int expectedLength = 10;
+ outputStream.write(expectedLength);
+ // The negative beginning index is to accommodate the header. Fancy. Ever so fancy.
+ for (int i = -3; i < expectedLength; i++) outputStream.write(0x0);
+ outputStream.close();
+ } catch (final IOException e) {
throw new RuntimeException("Exception trying to create non-empty file!", e);
}
}
private static String laneDir(final int lane) {
String ldir = String.valueOf(lane);
- while(ldir.length() < 3) {
+ while (ldir.length() < 3) {
ldir = "0" + ldir;
}
return "L" + ldir;
}
private static String longTile(final int tile, final boolean makeLong) {
- if(makeLong) {
+ if (makeLong) {
String lt = String.valueOf(tile);
- while(lt.length() < 4) {
+ while (lt.length() < 4) {
lt = "0" + lt;
}
return lt;
@@ -851,9 +649,9 @@ public class IlluminaFileUtilTest {
return String.valueOf(tile);
}
}
-
+
private static String maybeAddExt(final String fileExt, final String compressionExt) {
- if(compressionExt != null) {
+ if (compressionExt != null) {
return fileExt + compressionExt;
} else {
return fileExt;
diff --git a/src/tests/java/net/sf/picard/illumina/parser/IlluminaIntensityParserTest.java b/src/tests/java/net/sf/picard/illumina/parser/IlluminaIntensityParserTest.java
deleted file mode 100644
index 3f4b3a5..0000000
--- a/src/tests/java/net/sf/picard/illumina/parser/IlluminaIntensityParserTest.java
+++ /dev/null
@@ -1,147 +0,0 @@
-package net.sf.picard.illumina.parser;
-
-import java.io.File;
-
-import org.testng.Assert;
-import org.testng.annotations.Test;
-
-public class IlluminaIntensityParserTest {
- private static final File TEST_DATA_DIR = new File("testdata/net/sf/picard/illumina/IlluminaTests/L001");
- private static final int LANE = 1;
- private static final int TILE_1_READS = 153010;
- private static final int TILE_2_READS = 149900;
- private static final int READS = TILE_1_READS + TILE_2_READS;
- private static final int [] CYCLES = new int[]{1,2,3,4};
- private static final int [] OUTPUT_LENGTHS = new int[]{4};
-
- private static CycleIlluminaFileMap makeFileMap(final String extension) {
- final CycleIlluminaFileMap fileMap = new CycleIlluminaFileMap();
- fileMap.put(1, new CycleFilesIterator(TEST_DATA_DIR, 1, 1, CYCLES, extension));
- fileMap.put(2, new CycleFilesIterator(TEST_DATA_DIR, 1, 2, CYCLES, extension));
- return fileMap;
- }
-
- private static CifParser makeCifParser(final String readStructure) {
- final OutputMapping outMap = new OutputMapping(new ReadStructure(readStructure));
- return new CifParser(TEST_DATA_DIR, LANE, makeFileMap(".cif"), outMap);
- }
-
- /**
- * Read noise files, configured as single-end, non-barcoded run with length=4.
- */
- @Test
- public void testSingleEnd() {
- final CifParser cifParser = makeCifParser("4T");
-
- int numReads;
- for (numReads = 0; cifParser.hasNext(); ++numReads) {
- final RawIntensityData rda = cifParser.next();
- for(final IntensityChannel iChan : IntensityChannel.values()) {
- Assert.assertEquals(rda.getRawIntensities()[0].getChannel(iChan).length, 4);
- }
- }
-
- Assert.assertEquals(numReads, READS);
- }
-
- /**
- * Read raw intensity files, configured as paired-end, barcoded run.
- */
- @Test
- public void testPairedEndWithBarcode() {
-
- final int [] outputLengths = new int[]{1, 2, 1};
- final CifParser cifParser = makeCifParser("1T2B1T");
-
- int numReads;
- for (numReads = 0; cifParser.hasNext(); ++numReads) {
- final RawIntensityData rda = cifParser.next();
- final FourChannelIntensityData [] fcids = rda.getRawIntensities();
- for(int i = 0; i <outputLengths.length; i++) {
- for(final IntensityChannel iChan : IntensityChannel.values()) {
- Assert.assertEquals(fcids[i].getChannel(iChan).length, outputLengths[i]);
- }
- }
- }
- Assert.assertEquals(numReads, READS);
- }
-
- @Test
- public void testSeekCnf() {
-
- final CycleIlluminaFileMap fileMap = makeFileMap(".cnf");
- final OutputMapping outMap = new OutputMapping(new ReadStructure("4T"));
- final CnfParser cnfParser = new CnfParser(TEST_DATA_DIR, LANE, fileMap, outMap);
- cnfParser.seekToTile(2);
- int numReads;
- int noiseIndex = 0;
- for (numReads = 0; cnfParser.hasNext(); ++numReads) {
- final FourChannelIntensityData [] fcids = cnfParser.next().getNoise();
-
- if(noiseIndex != noiseData.length && noiseData[noiseIndex].index == numReads) {
- final CnfTestReads testReads = noiseData[noiseIndex];
- //The cycles are arranged in channels but the comparisons below are done on a per cycle basis
- final FourChannelIntensityData fcid = fcids[0];
- final short [] a = fcid.getA();
- final short [] c = fcid.getC();
- final short [] g = fcid.getG();
- final short [] t = fcid.getT();
-
- for(int i = 0; i < a.length; i++) {
- Assert.assertEquals(a[i], testReads.acgtNoiseReads[i][0], "A values for read " + numReads + " on cycle " + (i+1) + " are not the same!");
- Assert.assertEquals(c[i], testReads.acgtNoiseReads[i][1], "C values for read " + numReads + " on cycle " + (i+1) + " are not the same!");
- Assert.assertEquals(g[i], testReads.acgtNoiseReads[i][2], "G values for read " + numReads + " on cycle " + (i+1) + " are not the same!");
- Assert.assertEquals(t[i], testReads.acgtNoiseReads[i][3], "T values for read " + numReads + " on cycle " + (i+1) + " are not the same!");
- }
- ++noiseIndex;
- }
- }
- Assert.assertEquals(numReads, TILE_2_READS);
- }
-
- private static class CnfTestReads {
- public CnfTestReads(final int index, final short [][] acgtNoiseReads) {
- this.index = index;
- this.acgtNoiseReads = acgtNoiseReads;
- }
- public int index;
- public short[][] acgtNoiseReads;
- }
-
- public static CnfTestReads [] noiseData = new CnfTestReads[]{
- new CnfTestReads(0, new short[][]{ new short[]{0, 9, 0, 0}, //cycle 1 (a,c,g,t)
- new short[]{0, 10, 0, 0},
- new short[]{0, 0, 0, 0},
- new short[]{0, 0, 0, 0}}),
-
- new CnfTestReads(19, new short[][]{ new short[]{0, 21, 0, 11},
- new short[]{0, 13, 0, 0},
- new short[]{0, 0, 0, 0},
- new short[]{0, 0, 0, 0}}),
-
- new CnfTestReads(39, new short[][]{ new short[]{10, 26, 0, 11},
- new short[]{0, 20, 0, 0},
- new short[]{0, 0, 0, 0},
- new short[]{0, 12, 0, 0}}),
-
- new CnfTestReads(74, new short[][]{ new short[]{9, 25, 0, 10},
- new short[]{0, 9, 0, 10},
- new short[]{0, 0, 0, 0},
- new short[]{0, 12, 0, 0}}),
-
- new CnfTestReads(90, new short[][]{ new short[]{8, 11, 0, 11},
- new short[]{0, 15, 0, 16},
- new short[]{0, 0, 0, 0},
- new short[]{0, 14, 0, 0}}),
-
- new CnfTestReads(98, new short[][]{ new short[]{6, 10, 0, 11},
- new short[]{0, 10, 0, 9},
- new short[]{0, 0, 0, 0},
- new short[]{0, 8, 0, 0}}),
-
- new CnfTestReads(99, new short[][]{ new short[]{9, 9, 0, 10},
- new short[]{10, 16, 0, 10},
- new short[]{0, 0, 0, 0},
- new short[]{0, 12, 0, 0}})
- };
-}
diff --git a/src/tests/java/net/sf/picard/illumina/parser/PerTilePerCycleParserTest.java b/src/tests/java/net/sf/picard/illumina/parser/PerTilePerCycleParserTest.java
index ab6bfcd..0348a2d 100644
--- a/src/tests/java/net/sf/picard/illumina/parser/PerTilePerCycleParserTest.java
+++ b/src/tests/java/net/sf/picard/illumina/parser/PerTilePerCycleParserTest.java
@@ -1,28 +1,32 @@
package net.sf.picard.illumina.parser;
-import static net.sf.samtools.util.CollectionUtil.makeList;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.NoSuchElementException;
+import java.util.Set;
+
+import static net.sf.samtools.util.CollectionUtil.makeList;
public class PerTilePerCycleParserTest {
public static final List<Integer> DEFAULT_TILES = makeList(1, 2, 3, 4);
- public static final int [] DEFAULT_OUTPUT_LENGTHS = new int[]{10,5,5};
- public static final int [] CYCLES = new int[]{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20};
+ public static final int[] DEFAULT_OUTPUT_LENGTHS = new int[]{10, 5, 5};
+ public static final int[] CYCLES = new int[]{1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20};
public static final int MAX_CYCLE = 20;
- public static final int NUM_CLUSTERS = 20;
public static final OutputMapping OUTPUT_MAPPING = new OutputMapping(new ReadStructure("20T"));
private class MockCycledIlluminaData implements IlluminaData {
- private List<String> values;
+ private final List<String> values;
+
public MockCycledIlluminaData() {
this.values = new ArrayList<String>();
}
- public void addValue(String value) {
+ public void addValue(final String value) {
values.add(value);
}
@@ -31,130 +35,95 @@ public class PerTilePerCycleParserTest {
}
}
- class MockPerTilePerCycleParser extends PerTilePerCycleParser<MockCycledIlluminaData> {
- private int [] expectedOutputLengths;
+ class MockPerTileCycleParser extends PerTileCycleParser<MockCycledIlluminaData> {
+ private final int[] expectedOutputLengths;
- public MockPerTilePerCycleParser(final File directory, final int lane, final CycleIlluminaFileMap tilesToCycleFiles, final OutputMapping outputMapping) {
+ public MockPerTileCycleParser(final File directory, final int lane, final CycleIlluminaFileMap tilesToCycleFiles, final OutputMapping outputMapping) {
super(directory, lane, tilesToCycleFiles, outputMapping);
expectedOutputLengths = outputMapping.getOutputReadLengths();
this.initialize();
}
@Override
- protected MockCycledIlluminaData makeData(final int[] outputLengths) {
- Assert.assertEquals(outputLengths, expectedOutputLengths);
- return new MockCycledIlluminaData();
-
- }
-
- @Override
- protected CycleFileParser<MockCycledIlluminaData> makeCycleFileParser(final File file, final int cycle, final int tileNumber) {
- return new CycleFileParser<MockCycledIlluminaData>() {
- int currentCluster = 0;
- final String filePrefix = str_del(file.getName(), cycle);
+ protected CycleFilesParser<MockCycledIlluminaData> makeCycleFileParser(final List<File> files) {
+ return new CycleFilesParser<MockCycledIlluminaData>() {
+ int currentCycle = 0;
@Override
public void close() {
+
}
@Override
- public void next(final MockCycledIlluminaData ild) {
- if(!hasNext()) {
+ public MockCycledIlluminaData next() {
+ final MockCycledIlluminaData ild = new MockCycledIlluminaData();
+ if (!hasNext()) {
throw new NoSuchElementException();
}
- ild.addValue(str_del(filePrefix, currentCluster++));
+ ild.addValue(str_del(files.get(currentCycle++)));
+ return ild;
}
@Override
public boolean hasNext() {
- return currentCluster < NUM_CLUSTERS;
+ return currentCycle < MAX_CYCLE;
}
};
}
- public Set<IlluminaDataType> supportedTypes() {
- return null;
- }
- }
-
- //Provides an iterator over files for one cycle for one multiple tiles
- class MontonicCycleFilesIterator extends CycleFilesIterator {
- private Iterator<String> iterator;
- private final List<String> fileNames;
-
- public MontonicCycleFilesIterator(final List<String> fileNames, int [] cycles) {
- super(null, 0, 0, cycles, null);
- this.iterator = fileNames.iterator();
- this.fileNames = fileNames;
- }
-
@Override
- public void reset() {
- this.iterator = fileNames.iterator();
- this.nextCycleIndex = 0;
+ public void initialize() {
+ seekToTile(currentTile);
}
- @Override
- public File next() {
- ++nextCycleIndex;
- return new File(iterator.next());
+ public Set<IlluminaDataType> supportedTypes() {
+ return null;
}
@Override
- public boolean hasNext() {
- return iterator.hasNext();
+ public void close() {
+ //no-op
}
}
- public List<String> getFileNames(final int tile, final int cluster, final int maxCycle) {
+ public List<String> getFileNames(final List<Integer> tiles) {
final List<String> fileNames = new ArrayList<String>();
- for(int i = 1; i <= maxCycle; i++) {
- fileNames.add(str_del(tile, i ,i, cluster));
- }
- return fileNames;
- }
-
- public List<String> getFileNames(final List<Integer> tiles, final int numClusters) {
- final List<String> fileNames = new ArrayList<String>();
- for(final Integer tile : tiles) {
- for(int i = 0; i < numClusters; i++) {
- fileNames.addAll(getFileNames(tile, i, MAX_CYCLE));
+ for (final Integer tile : tiles) {
+ for (int i = 1; i <= MAX_CYCLE; i++) {
+ fileNames.add(str_del(tile, i));
}
}
-
return fileNames;
}
- public List<CycleFilesIterator> getCycleFileIterators(final List<Integer> tiles, int [] cycles) {
- final List<CycleFilesIterator> iterators = new ArrayList<CycleFilesIterator>();
- for(final Integer tile : tiles) {
- final List<String> fileNames = new ArrayList<String>();
- for(int i = 0; i < cycles.length; i++) {
- fileNames.add(str_del(tile,cycles[i]));
+ public CycleIlluminaFileMap getIlluminaFileMaps(final List<Integer> tiles, final int[] cycles) {
+ final CycleIlluminaFileMap cycleFileMap = new CycleIlluminaFileMap();
+ for (final int cycle : cycles) {
+ final IlluminaFileMap fileMap = new IlluminaFileMap();
+ for (final Integer tile : tiles) {
+ fileMap.put(tile, new File(str_del(tile, cycle)));
}
-
- iterators.add(new MontonicCycleFilesIterator(fileNames, cycles));
+ cycleFileMap.put(cycle, fileMap);
}
-
- return iterators;
+ return cycleFileMap;
}
- public static String str_del(Object ... objs) {
- String out = objs[0].toString();
- for(int i = 1; i < objs.length; i++) {
- out += "_" + objs[i];
+ public static String str_del(final Object... objects) {
+ String out = objects[0].toString();
+ for (int i = 1; i < objects.length; i++) {
+ out += "_" + objects[i];
}
return out;
}
@Test
public void basicIterationTest() {
- final List<String> expectedValues = getFileNames(DEFAULT_TILES, NUM_CLUSTERS);
- final PerTilePerCycleParser<MockCycledIlluminaData> parser = makeParser();
+ final List<String> expectedValues = getFileNames(DEFAULT_TILES);
+ final PerTileCycleParser<MockCycledIlluminaData> parser = makeParser();
int index = 0;
- while(parser.hasNext()) {
+ while (parser.hasNext()) {
index = compareValues(parser.next().values, expectedValues, index);
}
@@ -163,7 +132,7 @@ public class PerTilePerCycleParserTest {
private int compareValues(final List<String> parserValues, final List<String> expectedValues, int index) {
- for(final String parserValue : parserValues) {
+ for (final String parserValue : parserValues) {
Assert.assertTrue(index < expectedValues.size());
Assert.assertEquals(parserValue, expectedValues.get(index), "With index " + index);
++index;
@@ -172,60 +141,52 @@ public class PerTilePerCycleParserTest {
return index;
}
- public PerTilePerCycleParser<MockCycledIlluminaData> makeParser() {
- CycleIlluminaFileMap fm = new CycleIlluminaFileMap();
- final List<CycleFilesIterator> iterators = getCycleFileIterators(DEFAULT_TILES, CYCLES);
- for(int i = 0; i < iterators.size(); i++) {
- fm.put(DEFAULT_TILES.get(i), iterators.get(i));
- }
-
- final PerTilePerCycleParser<MockCycledIlluminaData> parser = new MockPerTilePerCycleParser(new File("FakeFile"), 1, fm, OUTPUT_MAPPING);
- return parser;
+ public PerTileCycleParser<MockCycledIlluminaData> makeParser() {
+ final CycleIlluminaFileMap fileMap = getIlluminaFileMaps(DEFAULT_TILES, CYCLES);
+ return new MockPerTileCycleParser(new File("FakeFile"), 1, fileMap, OUTPUT_MAPPING);
}
- @DataProvider(name="seekingTests")
+ @DataProvider(name = "seekingTests")
public Object[][] seekingTests() {
- return new Object[][] {
- {1, 3, null, null},
- {22, 1, null, null},
- {38, 2, null, null},
- {75, 4, null, null},
- {1, 3, 70, 1},
- {1, 3, 45, 2},
- {12, 2, 59, 4},
- {45, 3, 70, 3},
- {14, 1, 5, 2}
+ return new Object[][]{
+ {1, 3, null, null},
+ {22, 1, null, null},
+ {38, 2, null, null},
+ {75, 4, null, null},
+ {1, 3, 70, 1},
+ {1, 3, 45, 2},
+ {12, 2, 59, 4},
+ {45, 3, 70, 3},
+ {14, 1, 5, 2}
};
}
@Test(dataProvider = "seekingTests")
- public void seekingIterationTest(Integer seekPos1, Integer newTile1, Integer seekPos2, Integer newTile2) {
- final List<String> expectedValues = getFileNames(DEFAULT_TILES, NUM_CLUSTERS);
- final PerTilePerCycleParser<MockCycledIlluminaData> parser = makeParser();
+ public void seekingIterationTest(final Integer seekPos1, final Integer newTile1, final Integer seekPos2, final Integer newTile2) {
+ final List<String> expectedValues = getFileNames(DEFAULT_TILES);
+ final PerTileCycleParser<MockCycledIlluminaData> parser = makeParser();
int index = 0;
- for(int i = 0; i <= seekPos1; i++) {
+ for (int i = 0; i <= seekPos1; i++) {
Assert.assertTrue(parser.hasNext());
index = compareValues(parser.next().values, expectedValues, index);
}
parser.seekToTile(newTile1);
- int startCluster = (newTile1-1) * NUM_CLUSTERS;
- index = startCluster * MAX_CYCLE;
- if(seekPos2 != null) {
- for(int i = startCluster; i <= seekPos2; i++) {
+ index = (newTile1 - 1) * MAX_CYCLE;
+ if (seekPos2 != null) {
+ for (int i = index; i <= seekPos2; i++) {
Assert.assertTrue(parser.hasNext());
index = compareValues(parser.next().values, expectedValues, index);
}
parser.seekToTile(newTile2);
- startCluster = (newTile2-1) * NUM_CLUSTERS;
- index = startCluster * MAX_CYCLE;
+ index = (newTile2 - 1) * MAX_CYCLE;
}
- for(int i = startCluster; i < NUM_CLUSTERS * DEFAULT_TILES.size(); i++) {
+ for (int i = index; i < MAX_CYCLE * DEFAULT_TILES.size(); i++) {
Assert.assertTrue(parser.hasNext());
index = compareValues(parser.next().values, expectedValues, index);
}
diff --git a/src/tests/java/net/sf/picard/illumina/parser/PosParserTest.java b/src/tests/java/net/sf/picard/illumina/parser/PosParserTest.java
index 9a28f92..005c478 100644
--- a/src/tests/java/net/sf/picard/illumina/parser/PosParserTest.java
+++ b/src/tests/java/net/sf/picard/illumina/parser/PosParserTest.java
@@ -157,6 +157,7 @@ public class PosParserTest {
}
Assert.assertFalse(parser.hasNext());
+ parser.close();
}
@DataProvider(name = "multiTileData")
@@ -195,5 +196,6 @@ public class PosParserTest {
}
Assert.assertFalse(parser.hasNext());
+ parser.close();
}
}
diff --git a/src/tests/java/net/sf/picard/illumina/parser/QSeqTdUtil.java b/src/tests/java/net/sf/picard/illumina/parser/QSeqTdUtil.java
deleted file mode 100644
index 9e4e365..0000000
--- a/src/tests/java/net/sf/picard/illumina/parser/QSeqTdUtil.java
+++ /dev/null
@@ -1,707 +0,0 @@
-package net.sf.picard.illumina.parser;
-
-import net.sf.picard.PicardException;
-
-import java.io.File;
-import java.util.*;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import static net.sf.picard.util.IlluminaUtilTest.iToB;
-
-public class QSeqTdUtil {
-
- private static Map<Integer, List<Integer>> laneToReadNos = new HashMap<Integer, List<Integer>>();
- private static Map<String, File> fnPrefixToQSeqFile = new HashMap<String, File>();
- private static Map<String, Integer> fnPrefixToNumReads = new HashMap<String, Integer>();
- private static Map<String, List<QseqReadData>> fnPrefixToQSeqReadData = new HashMap<String, List<QseqReadData>>();
-
-
- public static final String s_1_1 = "s_1_1";
- public static final String s_1_2 = "s_1_2";
- public static final String s_1_1_0001 = "s_1_1_0001";
- public static final String s_1_1_0002 = "s_1_1_0002";
- public static final String s_1_1_0003 = "s_1_1_0003";
- public static final String s_1_2_0001 = "s_1_2_0001";
- public static final String s_1_2_0002 = "s_1_2_0002";
- public static final String s_1_2_0003 = "s_1_2_0003";
-
- public static final String s_5_1 = "s_5_1";
- public static final String s_5_1_0001 = "s_5_1_0001";
-
- public static final String s_6_1 = "s_6_1";
- public static final String s_6_1_0001 = "s_6_1_0001";
- public static final String s_6_2_0001 = "s_6_2_0001";
- public static final String s_6_3_0001 = "s_6_3_0001";
-
- public static final String s_8_1_0001 = "s_8_1_0001";
- public static final String s_8_2_0001 = "s_8_2_0001";
-
- public static final byte A = (byte)65;
- public static final byte C = (byte)67;
- public static final byte G = (byte)71;
- public static final byte T = (byte)84;
- public static final byte P = (byte)46; //dot
- public static final String NO_TILE_PREFIX_STRING = "^s_(\\d)_(\\d)$";
- public static final Pattern NO_TILE_PREFIX_PATTERN = Pattern.compile(NO_TILE_PREFIX_STRING);
- public static final String PREFIX_PATTERN_STRING = "^s_(\\d)_(\\d)_(\\d{4})$";
- public static final Pattern PREFIX_PATTERN = Pattern.compile(PREFIX_PATTERN_STRING);
- private static final int LANE = 0;
- private static final int READ = 1;
- private static final int TILE = 2;
-
- public static final File PRIMARY_TESTDATA_DIR = new File("testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir");
-
- public static int getLaneFileSize(int lane) {
- switch(lane) {
- case 7:
- return 200;
- default:
- return 20;
- }
- }
-
- public static String makeFnPrefix(int lane, int end, int tile) {
- String prefix = "s_" + lane + "_" + end + "_";
- for(int i = 0; i < 4 - String.valueOf(tile).length(); i++) {
- prefix += "0";
- }
- prefix += tile;
- return prefix;
- }
-
- private static int[] varsFromPrefixAndRegex(final String prefix, final Pattern pattern, final String errMsg, int tokensExpected) {
- Matcher matcher = pattern.matcher(prefix);
- if(!matcher.find()) {
- throw new PicardException(errMsg);
- }
-
- int [] out = new int[tokensExpected];
- for(int i = 0; i < tokensExpected; i++) {
- out[i] = Integer.parseInt(matcher.group(i+1));
- }
- return out;
- }
-
- public static int[] varsFromNoTilePrefix(final String prefix) {
- return varsFromPrefixAndRegex(prefix, NO_TILE_PREFIX_PATTERN, "Couldn't find NO_TILE_PREFIX_PATTERN: " + NO_TILE_PREFIX_STRING + " in " + prefix, 2);
- }
-
- public static int[] varsFromPrefix(final String prefix) {
- return varsFromPrefixAndRegex(prefix, PREFIX_PATTERN, "Couldn't find PREFIX_PATTERN: " + PREFIX_PATTERN_STRING + " in " + prefix, 3);
- }
-
- public static void addPrefToFileMap(final String pref) {
- fnPrefixToQSeqFile.put(pref, new File(PRIMARY_TESTDATA_DIR, pref + "_qseq.txt"));
- }
-
- public static void addFileSize(final String pref, int numReads) {
- fnPrefixToNumReads.put(pref, numReads);
- }
-
- public static int getFileSize(final String pref) {
- return fnPrefixToNumReads.get(pref);
- }
-
- static {
- //lane 1
- laneToReadNos.put(1, Arrays.asList(0, 9, 19));
-
- String pref = makeFnPrefix(1,1,1);
- addPrefToFileMap(pref);
- addFileSize(pref, 20);
- fnPrefixToQSeqReadData.put(pref, Arrays.asList(
- makeQSeqReadData(new byte[][]{new byte[]{G, P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P, C, P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P, T,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P, T, P,P,P,P,P,P,P,P,P,P}},
- new int [][]{new int[] {28,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, 28,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, 27,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, 27,4,4,4,4,4,4,4,4,4,4}},
- false, 1793, 1420, 1, 1),
-
- makeQSeqReadData(new byte[][]{new byte[]{G, P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P, C, P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P, C,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P, C, P,P,P,P,P,P,P,P,P,P}},
- new int [][]{new int[] {25,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, 27,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, 8,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, 27,4,4,4,4,4,4,4,4,4,4}},
- false, 1793, 1718, 1, 1),
-
- makeQSeqReadData(new byte[][]{new byte[]{A, P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P, C, P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P, G,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P,P, G, P,P,P,P,P,P,P,P,P,P}},
- new int [][]{new int[] {7, 4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, 26,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, 16,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, 26,4,4,4,4,4,4,4,4,4,4}},
- false, 1793, 1011, 1, 1)
- ));
-
- pref = makeFnPrefix(1,1,2);
- addPrefToFileMap(pref);
- addFileSize(pref, 20);
- fnPrefixToQSeqReadData.put(pref, Arrays.asList(
- makeQSeqReadData(new byte[][]{new byte[]{G, P, T, C, C, P,P,P,P,P, P,P,A,P,T, C, C, C, C,G, T, G, G, A, T, G, A, A,A, A, T, G, C, T, G, T, A, C, A, T, G, T, T, C, T, T, G, T, T, G, A, T, A, A, C, A, A,T, G, G, G, C, A, A, G, G, T, C, T, A, G, G, A, C, A, G}},
- new int [][]{new int[] {15,4, 26,34,27,4,4,4,4,4, 4,4,8,4,24,34,34,31,7,29, 30,34,31,16,28,32,22,7,15,15, 28,33,34,32,33,24,21,32,29,27, 32,30,31,34,32,32,33,31,32,32, 20,29,22,32,33,16,6,21,29,22,29, 33,24,13,24,33,22,33,20,8, 22,26,20,33,27,29}},
- false, 1793, 1893, 1, 2),
-
- makeQSeqReadData(new byte[][]{new byte[]{C, P,G, A,G, P,P,P,P,P, P,P,T,P,G, G,G, T, A, G, G, A, A, A, C, A, C, A, G, C, C, T, T, G, C, T,C, C, A, C, A, G, C,G, C, A, C, T, G, T, C, A, G, C, A, A,G, A, C,G, C, T, C, C, T, T, T, C, T, T, C,G,G, A, G, A}},
- new int [][]{new int[] {30,4,24,7,24,4,4,4,4,4, 4,4,4,4,22,8,24,13,13,27, 25,25,29,18,29,16,26,22,22,27, 33,15,20,30,30,8,33,29,15,28, 16,17,7,17,32,21,28,19,25,19, 24,20,21,30,14,4,20,12,4,12, 26,16,26,21,20,19,17,26,14,12, 5,7,17,21,11,7}},
- false, 1793, 666, 1, 2),
-
- makeQSeqReadData(new byte[][]{new byte[]{C, P,T, C, C, P,P,P,P,P, P,P,T, P,T, A,T, T, T, A, C, T, A, T, T, T, T, C, T, G, A, T, T, T, T, T, A, A, A, A, T, G, A, C, A, G, T, G, G, C, A, A,T, T, A, C, C, A, T, T, T, A, T, A, C, T, G, T, G, T, T, A, T, T, T, G}},
- new int [][]{new int[] {30,4,23,34,30,4,4,4,4,4, 4,4,24,4,21,7,28,30,25,7, 28,31,33,32,32,31,31,33,31,32, 27,27,27,27,28,31,28,26,20,30, 31,24,10,30,32,31,25,30,24,31, 20,5,16,28,29,32,30,10,25,21, 21,21,23,28,32,24,30,22,30,24, 30,28,27,24,28,21}},
- false, 1794, 490, 1, 2)
- ));
-
- pref = makeFnPrefix(1,1,3);
- addPrefToFileMap(pref);
- addFileSize(pref, 20);
- fnPrefixToQSeqReadData.put(pref, Arrays.asList(
- makeQSeqReadData(new byte[][]{new byte[]{G, P,T, A,G, P,P,P,P,P, P,P,C,P,G, G, A, C,T, C, T, G, G, C, G, T, C,A, C, C, T, T,T, G, G,C, G, C, T, G, A,G, C,G, C, C, C, C, A,G, G, C, C, C, G,C, C, A, G, C, C, C, G, C, C,C, G, C, C, C, A, C,T,G, C, C}},
- new int [][]{new int[] {27,4,26,7,13,4,4,4,4,4, 4,4,7,4,13,21,13,7,26,33, 31,20,20,10,24,29,9,23,31,7, 29,9,31,26,7,13,26,31,22,20, 6,20,6,26,26,31,26,26,9,19, 27,20,27,17,9,31,26,14,29,27, 31,20,29,20,7,16,21,26,16,26, 22,8,6,11,13,13}},
- false, 1793, 1282, 1, 3),
-
- makeQSeqReadData(new byte[][]{new byte[]{G, P,G, G, G, P,P,P,P,P, P,P,T, P,C, C, A, T, T, G, G, T, T, T, C, T, G, A, A, A, G, T, A, T, T, C, A,C, A, T, C, A, T, T, T, G, G, G, A, T, A, C, C, A, G, A, T, A,G, C, T, C, A, A, T, A, C, T, C, T, C, T, G, A, G, T}},
- new int [][]{new int[] {23,4,29,33,27,4,4,4,4,4, 4,4,25,4,30,33,23,33,33,33, 33,30,33,33,34,32,34,30,31,21, 31,16,26,32,33,31,9,31,27,29, 33,24,29,30,31,31,33,30,24,27, 19,33,33,23,31,23,17,8,27,34, 31,34,32,25,30,23,33,31,34,31, 34,31,30,14,28,6}},
- false, 1793, 1709, 1, 3),
-
- makeQSeqReadData(new byte[][]{new byte[]{C, P,T, A, T, P,P,P,P,P, P,P,C, P,P,C, G, G, G, T, A, C, C, A, C, A, G, T, T, G, A, G, G, A, C, T, G, A, C, A, T, T, C, T, G, A, A, C, C, C, T, G, A, T, G, T, T, T, C, T, A, A, A, G, A, A, A, C, G, A, C, A, G, T, A, T}},
- new int [][]{new int[] {30,4,21,31,23,4,4,4,4,4, 4,4,30,4,4,30,31,30,31,21, 32,32,32,30,30,21,27,29,29,31, 21,14,22,30,32,30,30,21,29,27, 27,23,28,31,17,20,17,26,29,31, 23,19,27,24,29,20,23,31,30,22, 13,12,21,26,22,23,26,27,19,6, 24,12,27,25,21,23}},
- false, 1793, 456, 1, 3)
- ));
-
- pref = makeFnPrefix(1,2,1);
- addPrefToFileMap(pref);
- addFileSize(pref, 20);
- fnPrefixToQSeqReadData.put(pref, Arrays.asList(
- makeQSeqReadData(new byte[][]{new byte[]{C, P,P,P,A,P,P,P,P,P, P,P,P,P,P,P,P,P,P,P, P,A, P,P,P,P,P,P,P,P, P,P,P,P,P,P,P,P,P,P, P,P,P,C, P,P,P,P,P,P, P,P,P,P,P,P,P,P,P,P, P,P,P,P,P,T, P,P,P,P, P,P,P,P,P,P}},
- new int [][]{new int[] {30,4,4,4,9,4,4,4,4,4, 4,4,4,4,4,4,4,4,4,4, 4,11,4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4,4,4, 4,4,4,27,4,4,4,4,4,4, 4,4,4,4,4,4,4,4,4,4, 4,4,4,4,4,13,4,4,4,4, 4,4,4,4,4,4}},
- false, 1793, 1420, 1, 1),
-
- makeQSeqReadData(new byte[][]{new byte[]{A,P,P,P,A,P,P,P,P,P, P,P,P,P,P,P,P,P,P,P, P,A, P,P,P,P,P,P,P,P, P,P,P,P,P,P,P,P,P,P, P,P,P,A,P,P,P,P,P,P, P,P,P,P,P,P,P,P,P,P, P,P,P,P,P,G,P,P,P,P, P,P,P,P,P,P}},
- new int [][]{new int[] {7,4,4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4,4,4, 4,14,4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4,4,4, 4,4,4,6,4,4,4,4,4,4, 4,4,4,4,4,4,4,4,4,4, 4,4,4,4,4,7,4,4,4,4, 4,4,4,4,4,4}},
- false, 1793, 1718, 1, 1),
-
- makeQSeqReadData(new byte[][]{new byte[]{A, P,P,P,T,P,P,P,P,P, P,P,P,P,P,P,P,P,P,P, P,T,P,P,P,P,P,P,P,P, P,P,P,P,P,P,P,P,P,P, P,P,P,C, P,P,P,P,P,P, P,P,P,P,P,P,P,P,P,P, P,P,P,P,P,C,P,P,P,P, P,P,P,P,P,P}},
- new int [][]{new int[] {18,4,4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4,4,4, 4,7,4,4,4,4,4,4,4,4, 4,4,4,4,4,4,4,4,4,4, 4,4,4,30,4,4,4,4,4,4, 4,4,4,4,4,4,4,4,4,4, 4,4,4,4,4,9,4,4,4,4, 4,4,4,4,4,4}},
- false, 1793, 1011, 1, 1)
- ));
-
- pref = makeFnPrefix(1,2,2);
- addPrefToFileMap(pref);
- addFileSize(pref, 20);
- fnPrefixToQSeqReadData.put(pref, Arrays.asList(
- makeQSeqReadData(new byte[][]{new byte[]{G, G, G, C, A, G, G, G, G, G, C,T, T, T, T, T, C, T, C, A, C,T, C, T, C, T, C, T, C, A, T, A,T, C, T, T, C, T, A,G, G, G, T, A, A, C, T, A,C, A, T, G, A, A,C, A, C,A, C, G, C, T, T, C, T, C, T, C, C, C, C,T, T, C,C,G}},
- new int [][]{new int[] {32,33,33,33,19,28,33,33,33,25, 8,28,33,27,32,32,34,30,34,29, 8,30,34,31,34,30,34,33,33,18, 26,8,27,34,31,33,34,24,7,29, 30,32,18,31,12,31,28,8,31,21, 31,28,19,6,30,19,7,19,17,20, 34,24,28,33,27,34,31,34,33,31, 7,15,22,7,7,25}},
- false, 1793, 1893, 1, 2),
-
- makeQSeqReadData(new byte[][]{new byte[]{A, T, T, T, T, T, G, C, T, T, T, C, C, T, T, G, G, C, C, C, C, C, A, C, C, A, A, T, T, T, A, T, A, C, A, T, C, T, C, C, A, T, T, T, T, C, C, G, A,C, C, T, C, T, G, G,A, C, T, A, A, C, T, G, C,T,T, G, C, T, C, A, G, C, A,C}},
- new int [][]{new int[] {21,26,33,32,34,30,32,33,31,31, 29,31,23,26,31,29,31,33,33,33, 33,32,25,31,33,23,28,30,26,16, 29,21,31,32,32,27,33,19,32,33, 25,24,19,27,26,28,11,15,6,27, 31,27,32,23,22,8,22,33,28,22, 18,31,26,18,8,6,14,21,24,7, 27,11,21,22,6,4}},
- false, 1793, 1909, 1, 2),
-
- makeQSeqReadData(new byte[][]{new byte[]{A, T, A, A, A, C, T, T, G, A, A, A, A, T, A, A, T, T, T, T, C, T, A, T, G, A, T, A, C, A, G, C, T, T, T, C, A, G, G, T, A, G, A,A, A, A, A, T, G, A, A, T, T, T, T, C, G, T, C, G, T, G, T, T, T, A, A, C, A, A, T, G, T, T, G, T}},
- new int [][]{new int[] {32,33,33,34,33,34,32,32,34,31, 26,20,31,31,22,22,33,33,33,30, 34,34,33,33,33,30,31,33,34,33, 33,34,32,33,31,31,18,27,32,21, 29,29,8,24,24,30,15,27,33,31, 21,30,29,31,31,33,33,21,32,24, 29,33,20,32,27,31,21,27,4,10, 29,31,27,27,25,15}},
- false, 1794, 490, 1, 2)
- ));
-
- pref = makeFnPrefix(1,2,3);
- addPrefToFileMap(pref);
- addFileSize(pref, 20);
- fnPrefixToQSeqReadData.put(pref, Arrays.asList(
- makeQSeqReadData(new byte[][]{new byte[]{A,A,G, C, A, C, A, C,C, A, A, G, C, T, T, C, C, C, G, C, A, G, C, T, G, C,G, G,C, G, C, C, C, C, C, G,C, T, C, C, A,A,G,G, C, C, A,G, C,A, G, C, T, G, C, C, C, C, C, T, C, T, G, C, C, C,C, C, A,C, C, C, C, C, T, C}},
- new int [][]{new int[] {7,9,20,22,24,13,16,7,13,14, 14,29,33,31,12,16,22,10,28,13, 13,14,31,24,28,9,28,7,13,7, 13,26,27,13,16,6,29,26,27,25, 6,6,6,22,28,26,6,13,6,25, 28,28,25,20,20,16,24,18,23,9, 22,13,22,26,25,4,22,25,6,6, 26,31,26,21,15,24}},
- false, 1793, 1282, 1, 3),
-
- makeQSeqReadData(new byte[][]{new byte[]{A, G, C, C,A, C, T, G, T, C, C, C, G, T, G, T, A, T, A, A, C, T, T, G, G, C, A, T, T, A, G, A, G, C, A, C, C, A,G, G, T, C, T, G, T, T, G, G, A, T, G, G, T,G, G, T, G, G, C, A, G, G, C, C, C, A,A, T,T,A, A,T, T, T, T,T}},
- new int [][]{new int[] {11,30,31,8,22,31,33,31,21,33, 34,34,34,26,34,30,31,32,26,10, 31,32,26,33,33,33,28,26,33,32, 31,21,31,33,21,33,31,7,29,33, 23,34,32,32,21,27,33,30,21,24, 33,30,7,33,28,12,25,31,29,12, 22,31,23,20,25,4,13,8,8,18, 5,22,18,12,4,8}},
- false, 1793, 1709, 1, 3),
-
- makeQSeqReadData(new byte[][]{new byte[]{T, C, C, A, T, C, C, A, C, T, T, C, C, C, T, G, A, G, C, C, T, C, A, G, A, A, A, A, G, G, G, C, A, A, G, G, C, A, T, G, G, C, T, C, A, C, A, T, A, C, T, C, T, C, A,G, C, C, A, C, G, G, C, C, T,G,G, C, C,T, G, C, T, G, C, C}},
- new int [][]{new int[] {33,33,33,27,32,33,33,31,33,33, 33,33,33,33,28,31,31,32,33,33, 30,33,20,31,22,22,22,28,26,26, 32,33,32,24,32,26,33,30,28,29, 27,33,33,31,21,31,32,32,30,33, 29,33,24,29,9,29,32,32,24,32, 20,18,30,29,7,4,23,24,7,13, 24,29,26,27,25,7}},
- false, 1793, 456, 1, 3)
- ));
-
- laneToReadNos.put(5, Arrays.asList(0, 9, 19));
- pref = makeFnPrefix(5,1,1);
- addPrefToFileMap(pref);
- addFileSize(pref, 20);
- fnPrefixToQSeqReadData.put(pref, Arrays.asList(
- makeQSeqReadData(new byte[][]{new byte[]{G, A, C, T, T, T, G, G, G, A, A, G, G, G, T, C, A, T, T, A, C, T, G, C, C, C, T, T, G, T, A, G, A, A, A, G, A, A, C, A, C, C, T, C, A, T, G, T, T, C, C, T, T, A, T, C, G, A, G, A, G, C, G, G, C, C, G, C, T, G, C, T, G, A,T,C}},
- new int [][]{new int[] {23,27,32,34,34,34,34,31,34,33, 19,28,32,31,28,34,34,33,34,34, 33,23,18,32,34,34,33,32,32,33, 34,31,34,34,34,34,34,33,34,34, 34,33,33,34,34,30,30,30,28,33, 33,31,33,34,32,33,31,32,27,32, 22,33,19,20,27,30,19,23,20,24, 23,14,25,5,8,13}},
- true, 0, 357, 5, 1),
-
- makeQSeqReadData(new byte[][]{new byte[]{C, A, A, A, A, C,A, A, C, T, C, A, G, T, T, T, G, T, T, C, C, A, A, A, A, C, A, A, T, G, T, G, A, G, T, T, C, C, C, A, G, A, T, T, T, A, G, C, C, T, T, G, T, C, T, T, A, A, T, A, T, A, T, T, G, A, C, C, T, T, A, G, T, T, C, C}},
- new int [][]{new int[] {33,32,32,33,21,9,29,30,31,17, 31,33,33,33,33,34,22,28,34,32, 27,32,33,34,34,31,19,33,33,32, 33,34,29,34,33,34,34,31,25,32, 31,33,33,29,33,33,32,30,33,33, 34,34,24,23,33,28,32,33,33,33, 34,33,33,33,28,26,25,10,17,28, 22,25,30,19,14,10}},
- false, 0, 1484, 5, 1),
-
- makeQSeqReadData(new byte[][]{new byte[]{C, A, C, A, C, A, C, A, C, A, C, A, C, A, C, A, C, A, C, A, C, A, C, C, A, C, C, T, T, T, T, G, G, C, T, T, A, T, C, T, G, C, A, C, G, C, G, G, C, C, G, C, G, T, G, C, C, C,T, A, C, C, C, T, A, C, C, C, C, A, T,G, G,G, A, T}},
- new int [][]{new int[] {33,31,33,33,30,28,18,33,28,32, 33,33,24,33,31,33,33,31,33,33, 33,33,33,33,33,27,30,24,30,32, 32,22,27,32,31,32,33,30,33,33, 15,32,32,30,31,19,10,21,5,12, 20,22,13,11,22,20,16,6,15,11, 10,10,13,14,11,20,18,18,10,5, 5,16,6,11,20,18}},
- true, 0, 1250, 5, 1)
- ));
-
- laneToReadNos.put(6, Arrays.asList(0, 4, 9));
- pref = makeFnPrefix(6,1,1);
- addPrefToFileMap(pref);
- addFileSize(pref, 10);
- fnPrefixToQSeqReadData.put(pref, Arrays.asList(
- makeQSeqReadData(new byte[][]{new byte[]{T, A, G, A,G,A,T,G,G,C, P,C,T,P,P,P,P,P,P,P, P,P,T,P,P,P,P,P,P,C, P,P,P,P,P,P,P,P,G,P, P,P,T,C,C,A,G,A,C,C, G,C,C,C,A,T,T,C,T,C, T,G,C,C,T,G,C,C}},
- new int [][]{new int[] {30,32,30,2,2,2,2,2,2,2, 2,2,2,2,2,2,2,2,2,2, 2,2,2,2,2,2,2,2,2,2, 2,2,2,2,2,2,2,2,2,2, 2,2,2,2,2,2,2,2,2,2, 2,2,2,2,2,2,2,2,2,2, 2,2,2,2,2,2,2,2}},
- false, 4, 1969, 6, 1),
-
- makeQSeqReadData(new byte[][]{new byte[]{T, A, A, A, C, A,G,A,T,G, P,T,T,P,P,P,P,P,P,P, P,C,A,P,P,P,P,P,P,T, P,P,P,P,P,P,P,P,A,P, P,P,C,C,A,A,T,C,C,C, T,A,A,T,C,T,C,C,A,G, T,A,A,T,C,C,G,G}},
- new int [][]{new int[] {30,34,34,32,31,2,2,2,2,2, 2,2,2,2,2,2,2,2,2,2, 2,2,2,2,2,2,2,2,2,2, 2,2,2,2,2,2,2,2,2,2, 2,2,2,2,2,2,2,2,2,2, 2,2,2,2,2,2,2,2,2,2, 2,2,2,2,2,2,2,2}},
- false, 4, 1248, 6, 1),
-
- makeQSeqReadData(new byte[][]{new byte[]{C, A, A, C, T, C, T,T,G,T, P,G,T,P,P,P,P,P,P,P, P,G,T,P,P,P,P,P,P,A, P,P,P,P,P,P,P,P,G,P, P,P,A,A,T,A,T,A,T,T, C,T,G,A,A,A,C,T,C,A, G,C,A,A,T,G,T,T}},
- new int [][]{new int[] {33,33,33,34,33,33,2,2,2,2, 2,2,2,2,2,2,2,2,2,2, 2,2,2,2,2,2,2,2,2,2, 2,2,2,2,2,2,2,2,2,2, 2,2,2,2,2,2,2,2,2,2, 2,2,2,2,2,2,2,2,2,2, 2,2,2,2,2,2,2,2}},
- false, 4, 151, 6, 1)
- ));
-
- pref = makeFnPrefix(6,2,1);
- addPrefToFileMap(pref);
- addFileSize(pref, 10);
- fnPrefixToQSeqReadData.put(pref, Arrays.asList(
- makeQSeqReadData(new byte[][]{new byte[]{C, C, A,C, C, C, A,C}},
- new int [][]{new int[] {31,26,6,26,30,29,2,2}},
- false, 4, 1969, 6, 1),
-
- makeQSeqReadData(new byte[][]{new byte[]{G, C, A, C, C, C, G,A}},
- new int [][]{new int[] {20,31,24,31,10,31,2,2}},
- false, 4, 1248, 6, 1),
-
- makeQSeqReadData(new byte[][]{new byte[]{T, C, G, G, A, A, T, G}},
- new int [][]{new int[] {33,34,25,32,34,34,31,30}},
- false, 4, 151, 6, 1)
- ));
-
- pref = makeFnPrefix(6,3,1);
- addPrefToFileMap(pref);
- addFileSize(pref, 10);
- fnPrefixToQSeqReadData.put(pref, Arrays.asList(
- makeQSeqReadData(new byte[][]{new byte[]{C, C, T, C,T, A, A, T, C, C, C, A, G,C, A, C, T,A, T, C, C, G,A, G, A, C, C, A, A,A, T,C, A, G, G,C, A, A, A, T, C, A, C, T, T, G,A, A,G, T, C, A, G, G, A, G, T, T, C, G, A, G, A, C, C, A, G, C}},
- new int [][]{new int[] {29,29,22,9,19,17,11,31,13,28, 32,13,8,24,28,26,6,13,33,16, 23,8,24,25,21,33,29,26,8,10, 7,33,21,12,7,16,24,20,18,19, 28,23,27,32,26,8,31,7,13,21, 33,31,27,29,13,29,16,20,21,26, 24,29,22,33,26,33,21,28}},
- false, 4, 1969, 6, 1),
-
- makeQSeqReadData(new byte[][]{new byte[]{A,A, T, A, T, T, C, T, T, T, T, A, A, G, G, T, C, T, C, T, G, G, T, T, T, T,C, C, T, A, G, G, C, A, G, A, G, G, A, C, C, C, T, G, C, G, G, C, C, T, T, C, C, G, C, A, G, T, G, T, T, T, G, T, G, T, C, C}},
- new int [][]{new int[] {9,21,17,27,23,16,31,33,33,33, 29,23,34,34,27,33,34,32,34,21, 26,31,33,34,34,9,34,34,34,27, 34,27,31,28,31,33,34,34,33,33, 34,33,33,33,34,17,31,33,34,21, 14,31,34,34,34,32,34,32,34,30, 32,31,12,13,25,21,32,34}},
- false, 4, 1248, 6, 1),
-
- makeQSeqReadData(new byte[][]{new byte[]{T, A, A, C, T, T, T, C, A, G, A, G, G, C, C, C, T, T, C, A, G, G, A, G, G, C, C, C, T, G, G, C, C, T, G, T,C, A, A, G, T, A, C, C, T, T, T, A, C, A, G, T, G, A, T, G, G, G, T, A, T, A, G,A,C,T,T,T}},
- new int [][]{new int[] {33,34,34,34,33,34,34,33,31,34, 34,33,34,34,31,29,19,29,33,34, 31,33,34,31,31,30,33,34,19,15, 18,25,24,30,18,6,27,33,33,32, 31,33,31,27,24,22,33,32,27,23, 21,14,32,33,30,31,31,33,28,26, 12,28,2,2,2,2,2,2}},
- false, 4, 151, 6, 1)
- ));
-
- laneToReadNos.put(8, Arrays.asList(0, 9, 19));
- pref = makeFnPrefix(8,1,1);
- addPrefToFileMap(pref);
- addFileSize(pref, 20);
- fnPrefixToQSeqReadData.put(pref, Arrays.asList(
- makeQSeqReadData(new byte[][]{new byte[]{G, P,P,P}},
- new int [][]{new int[] {28,4,4,4}},
- false, 1793, 1420, 8, 1),
-
- makeQSeqReadData(new byte[][]{new byte[]{G, P,P,P}},
- new int [][]{new int[] {25,4,4,4}},
- false, 1793, 1718, 8, 1),
-
- makeQSeqReadData(new byte[][]{new byte[]{A, P,P,P}},
- new int [][]{new int[] {7,4,4,4}},
- false, 1793, 1011, 8, 1)
- ));
-
- pref = makeFnPrefix(8,2,1);
- addPrefToFileMap(pref);
- addFileSize(pref, 20);
- fnPrefixToQSeqReadData.put(pref, Arrays.asList(
- makeQSeqReadData(new byte[][]{new byte[]{C, P,P,P}},
- new int [][]{new int[] {30,4,4,4}},
- false, 1793, 1420, 8, 2),
-
- makeQSeqReadData(new byte[][]{new byte[]{A,P,P,P}},
- new int [][]{new int[] {7,4,4,4}},
- false, 1793, 1718, 8, 2),
-
- makeQSeqReadData(new byte[][]{new byte[]{A, P,P,P}},
- new int [][]{new int[] {18,4,4,4}},
- false, 1793, 1011, 8, 2)
- ));
- }
-
- private static QseqReadData makeQSeqReadData(final byte [][] bases, final int [][] qualities, final boolean pf,
- final int xCoord, final int yCoord, final int lane, final int tile) {
- final int [] outputLengths = new int[bases.length];
- for(int i = 0; i < outputLengths.length; i++) {
- outputLengths[i] = bases[i].length;
- }
- final QseqReadData qseqRd = new QseqReadData(outputLengths);
- for(int i = 0; i < bases.length; i++) {
- System.arraycopy(bases[i], 0, qseqRd.getBases()[i], 0, bases[i].length);
- System.arraycopy(iToB(qualities[i]), 0, qseqRd.getQualities()[i], 0, qualities[i].length);
- }
-
- qseqRd.setOrCheckPf(pf);
- qseqRd.setOrCheckXCoordinate(xCoord);
- qseqRd.setOrCheckYCoordinate(yCoord);
- qseqRd.setOrCheckLane(lane);
- qseqRd.setOrCheckTile(tile);
-
- return qseqRd;
- }
-
- private static void inMemorySplit(final byte[][] source, final byte[][] dest, final int dstOffset) {
- int srcIndex = 0;
- int dstIndex = 0;
- int srcPos = 0;
- int dstPos = dstOffset;
-
- while(dstPos > dest[dstIndex].length) {
- dstPos -= dest[dstIndex].length;
- ++dstIndex;
- }
-
- while(srcIndex < source.length) {
- if(dest[dstIndex].length > 0) {
- final int ln = Math.min(source[srcIndex].length - srcPos, dest[dstIndex].length - dstPos);
- System.arraycopy(source[srcIndex], srcPos, dest[dstIndex], dstPos, ln);
-
- srcPos += ln;
- dstPos += ln;
- }
-
- if(srcPos >= source[srcIndex].length) {
- srcPos = 0;
- ++srcIndex;
- }
-
- if(dstPos >= dest[dstIndex].length) {
- dstPos = 0;
- ++dstIndex;
- }
- }
- }
-
- private static void fillArrays(byte [][] array, byte value, int fillLength) {
- int arrIndex = 0;
- while(fillLength > 0) {
- final int filledThisRound = Math.min(array[arrIndex].length, fillLength);
- Arrays.fill(array[arrIndex], 0, filledThisRound, value);
- fillLength -= filledThisRound;
- ++arrIndex;
- }
- }
-
- private static void backFillArrays(byte [][] array, byte value, int fillLength) {
- int arrIndex = array.length - 1;
- while(fillLength > 0) {
- final int filledThisRound = Math.min(array[arrIndex].length, fillLength);
- Arrays.fill(array[arrIndex], array[arrIndex].length - filledThisRound, array[arrIndex].length-1, value);
- fillLength -= filledThisRound;
- --arrIndex;
- }
- }
-
- private static Map<Integer,QseqReadData> splitReadIntoLengths(final int thisReadLength, final int [] outputLengths, final Map<Integer, QseqReadData> templates, final int writeOffset) {
- int totalLength = 0;
- for(int i = 0; i < outputLengths.length; i++) {
- totalLength += outputLengths[i];
- }
-
- final Map<Integer,QseqReadData> outData = new HashMap<Integer, QseqReadData>();
- for(final Map.Entry<Integer, QseqReadData> readToTemplate : templates.entrySet()) {
- final QseqReadData template = readToTemplate.getValue();
- final QseqReadData qseqRd = new QseqReadData(outputLengths);
- fillArrays(qseqRd.getBases(), (byte)0, writeOffset);
- fillArrays(qseqRd.getQualities(), (byte)0, writeOffset);
- backFillArrays(qseqRd.getBases(), (byte)0, totalLength - thisReadLength - writeOffset);
- backFillArrays(qseqRd.getQualities(), (byte)0, totalLength - thisReadLength - writeOffset);
-
- inMemorySplit(template.getBases(), qseqRd.getBases(), writeOffset);
- inMemorySplit(template.getQualities(), qseqRd.getQualities(), writeOffset);
- qseqRd.setOrCheckPf(template.isPf());
- qseqRd.setOrCheckXCoordinate(template.getXCoordinate());
- qseqRd.setOrCheckYCoordinate(template.getYCoordinate());
- qseqRd.setOrCheckLane(template.getLane());
- qseqRd.setOrCheckTile(template.getTile());
- outData.put(readToTemplate.getKey(), qseqRd);
- }
-
- return outData;
- }
-
- private static int flatten(byte [][] bytes, byte [] out, int index) {
- int outIndex = index;
- for(int i = 0; i < bytes.length; i++) {
- for(int j = 0; j < bytes[i].length; j++) {
- out[outIndex++] = bytes[i][j];
- }
- }
- return outIndex;
- }
-
- private static QseqReadData combineReads(final QseqReadData qrd1, final QseqReadData qrd2) {
- int totalSize = 0;
- byte [][] bases1 = qrd1.getBases();
- byte [][] qualities1 = qrd1.getQualities();
-
- byte [][] bases2 = qrd2.getBases();
- byte [][] qualities2 = qrd2.getQualities();
-
- for(byte [] bases : bases1) {
- totalSize += bases.length;
- }
-
- for(byte [] bases : bases2) {
- totalSize += bases.length;
- }
-
- final QseqReadData outQrd = new QseqReadData(new int[]{totalSize});
- byte [] outBases = outQrd.getBases()[0];
- byte [] outQuals = outQrd.getQualities()[0];
- int bases2Start = flatten(bases1, outBases, 0);
- flatten(bases2, outBases, bases2Start);
- int quals2Start = flatten(qualities1, outQuals, 0); //should be the same as bases2Start
- flatten(qualities2, outQuals, quals2Start);
-
- outQrd.setOrCheckLane(qrd1.getLane());
- outQrd.setOrCheckTile(qrd1.getTile());
- outQrd.setOrCheckPf(qrd1.isPf());
- outQrd.setOrCheckXCoordinate(qrd1.getXCoordinate());
- outQrd.setOrCheckYCoordinate(qrd1.getYCoordinate());
- return outQrd;
- }
-
- private static Map<Integer, QseqReadData> combineAllReads(Map<Integer, QseqReadData> map1, Map<Integer, QseqReadData> map2) {
- final Map<Integer, QseqReadData> outMap = new HashMap<Integer, QseqReadData>();
- if(map1.size() != map2.size()) {
- throw new PicardException("Map1 and Map2 are not of the same size!");
- }
-
- for(Integer key : map1.keySet()) {
- final QseqReadData read1 = map1.get(key);
- final QseqReadData read2 = map2.get(key);
- if(read1 == null) {
- throw new PicardException("Null value in map 1 for key " + key);
- }
- if(read2 == null) {
- throw new PicardException("Null value in map 2 for key " + key);
- }
-
- outMap.put(key, combineReads(read1, read2));
- }
-
- return outMap;
- }
-
- private static <T,V> Map<T,V> toMap(List<T> keys, List<V> values) {
- if(keys.size() != values.size())
- throw new PicardException("Key list is not the same size as the value list!");
-
- Map<T, V> hmap = new HashMap<T, V>();
- for(int i = 0; i < keys.size(); i++) {
- hmap.put(keys.get(i), values.get(i));
- }
-
- return hmap;
- }
-
- public static Map<Integer, QseqReadData> addToKeys(Map<Integer, QseqReadData> map, int addend) {
- Map<Integer, QseqReadData> outMap = new HashMap<Integer, QseqReadData>();
- for(final Map.Entry<Integer, QseqReadData> entry : map.entrySet()) {
- outMap.put(entry.getKey() + addend, entry.getValue());
- }
- return outMap;
- }
-
- public static Map<Integer, QseqReadData> getReadData(int lane, int end, int tile) {
- return toMap(getReadNos(lane, 1), fnPrefixToQSeqReadData.get(makeFnPrefix(lane, end, tile)));
- }
-
- public static Map<Integer, QseqReadData> getReadData(final String fileNamePrefix) {
- int [] vars = varsFromPrefix(fileNamePrefix);
- return getReadData(vars[LANE], vars[READ], vars[TILE]);
- }
-
- public static Map<Integer, QseqReadData> getTiledReadData(final String fileNamePrefix_noTile, final List<Integer> tiles) {
- int [] vars = varsFromNoTilePrefix(fileNamePrefix_noTile);
- return getTiledReadData(vars[LANE], vars[READ], tiles);
- }
-
- public static Map<Integer, QseqReadData> getTiledReadData(int lane, int end, final List<Integer> tiles) {
- final Map<Integer, QseqReadData> outMap = new HashMap<Integer, QseqReadData>();
- int totalAddend = 0;
- for(final Integer tile : tiles) {
- outMap.putAll(addToKeys(getReadData(lane, end, tile), totalAddend));
- totalAddend += getLaneFileSize(lane);
- }
- return outMap;
- }
-
- //final int lane, final int [] writeLengths, final List<IlluminaFileMap> readNumberToTile, final Map<Integer, QseqReadData> testAgainst
- public static Map<Integer, QseqReadData> getTiledReadData(final List<String> fileNames) {
- final Map<Integer, QseqReadData> outMap = new HashMap<Integer, QseqReadData>();
- int totalAddend = 0;
- for(final String fn : fileNames) {
- int [] vars = varsFromPrefix(fn);
- outMap.putAll(addToKeys(getReadData(vars[LANE], vars[READ], vars[TILE]), totalAddend));
- totalAddend += getLaneFileSize(vars[LANE]);
- }
- return outMap;
- }
-
- public static Map<Integer, QseqReadData> getTiledReadData(final List<String> fileNames, int totalReadLength, int [] outputLengths, int offset) {
- return splitReadIntoLengths(totalReadLength, outputLengths, getTiledReadData(fileNames), offset);
- }
-
- //Note: we want to use this like getReadNos(1,1,1) if we had 3 tiles for lane 1
- public static List<Integer> getReadNos(int lane, int files) {
- final List<Integer> readNos = new ArrayList<Integer>();
- int addend = 0;
- int laneSize = getLaneFileSize(lane);
- final List<Integer> laneNos = laneToReadNos.get(lane);
- for(int i = 0; i < files; i++) {
- for(Integer rn : laneNos) {
- readNos.add(rn + addend);
- }
-
- addend += laneSize;
- }
-
- return readNos;
- }
-
- public static Map<Integer,QseqReadData> getSplitOffsetReadData(final String fileNamePrefix, int totalLength, int [] outputLengths, int offsets) {
- return splitReadIntoLengths(totalLength, outputLengths, getReadData(fileNamePrefix), offsets);
- }
-
- public static Map<Integer, QseqReadData> getSplitOffsetReadData(final String fileName_preTile, List<Integer> tiles, int totalLength, int [] outputLengths, int offset) {
- return splitReadIntoLengths(totalLength, outputLengths, getTiledReadData(fileName_preTile, tiles), offset);
- }
-
- public static Map<Integer, QseqReadData> combineReads(final Map<Integer, QseqReadData> ... ends) {
- Map<Integer, QseqReadData> outList = new HashMap<Integer, QseqReadData>();
- outList.putAll(ends[0]);
- for(int i = 1; i < ends.length; i++) {
- outList = combineAllReads(outList, ends[i]);
- }
-
- return outList;
- }
-
- public static Map<Integer, QseqReadData> combineReads(int totalLength, int [] outputLengths, int offsets, final Map<Integer, QseqReadData> ... ends) {
- return splitReadIntoLengths(totalLength, outputLengths, combineReads(ends), offsets);
- }
-
- public static List<File> getQseqs(final String ... prefixes) {
- final List<File> files = new ArrayList<File>();
- for(final String prefix : prefixes) {
- files.add(fnPrefixToQSeqFile.get(prefix));
- }
-
- return files;
- }
-
- public static Map<Integer, ClusterData> qseqDataToClusterMap(final List<Map<Integer, QseqReadData>> qseqDataPerRead, final OutputMapping om, final IlluminaDataType ... dataTypes) {
- //For each read data, combine the bases/quals in each read into 1 long read per readNo
- Map<Integer, QseqReadData> combinedRead = qseqDataPerRead.get(0);
- for(int i = 1; i < qseqDataPerRead.size(); i++) {
- combinedRead = combineAllReads(combinedRead, qseqDataPerRead.get(i));
- }
-
- final Map<Integer, ClusterData> clusterData = new HashMap<Integer, ClusterData>();
- for(final Map.Entry<Integer, QseqReadData> noToRead : combinedRead.entrySet()) {
- clusterData.put(noToRead.getKey(), flatQseqReadToClusterData(noToRead.getValue(), om, dataTypes));
- }
-
- return clusterData;
- }
-
- //QSeqRead should have ONLY 1 base and quality array in it's bases/qualities field
- private static ClusterData flatQseqReadToClusterData(QseqReadData value, OutputMapping om, IlluminaDataType[] dataTypes) {
- if(value.getBases().length != 1 || value.getQualities().length != 1) {
- throw new RuntimeException("QseqReadData must be flat! number of bases arrays(" + value.getBases().length + ") number of qual arrays(" + value.getQualities().length + ")");
- }
-
- final Range [] ranges = om.getCycleIndexRanges();
- final ReadData [] reads = new ReadData[ranges.length];
-
- int index = 0;
- for(final ReadDescriptor rd : om.getOutputDescriptors()) {
- reads[index] = new ReadData(rd.type);
- final Range cycleIndexRange = ranges[index];
-
- final byte [] bases = new byte[cycleIndexRange.length];
- final byte [] quals = new byte[cycleIndexRange.length];
-
- System.arraycopy(value.getBases()[0], cycleIndexRange.start, bases, 0, bases.length);
- System.arraycopy(value.getQualities()[0], cycleIndexRange.start, quals, 0, quals.length);
-
- reads[index].setBases(bases);
- reads[index].setQualities(quals);
- ++index;
- }
-
- final ClusterData cd = new ClusterData(reads);
- for(IlluminaDataType idt : dataTypes) {
- switch(idt) {
- case Position:
- cd.setTile(value.getTile());
- cd.setLane(value.getLane());
- cd.setX(value.getXCoordinate());
- cd.setY(value.getYCoordinate());
- break;
-
- case PF:
- cd.setPf(value.isPf());
- break;
- }
- }
-
- return cd;
- }
-
- public static final QseqReadData filterSkips(final OutputMapping om, final QseqReadData read) {
- final QseqReadData outRead = new QseqReadData(om.getOutputReadLengths());
- final Range [] ranges = om.getCycleIndexRanges(); //cycle ranges are indexes into the outputCycles array
- //and therefore start at 0
- final byte [][] bases = read.getBases();
- final byte [][] quals = read.getQualities();
-
- //there should be a one to relationship between ranges and output reads
- final byte [][] outBases = outRead.getBases();
- final byte [][] outQuals = outRead.getQualities();
-
- int arrayIndex = 0;
- int elementIndex = 0;
- int inputCycle = 0;
-
- for(int i = 0; i < ranges.length; i++) {
- final Range range = ranges[i];
- while(range.start > inputCycle + bases[arrayIndex].length) {
- inputCycle += bases[arrayIndex].length;
- ++arrayIndex;
- }
-
- int rangeCovered = 0;
- while(rangeCovered < range.length) {
- final int length = Math.min(range.length - rangeCovered, bases[arrayIndex].length - elementIndex);
- System.arraycopy(bases[arrayIndex], elementIndex, outBases[i], rangeCovered, length);
- System.arraycopy(quals[arrayIndex], elementIndex, outQuals[i], rangeCovered, length);
-
- rangeCovered += length;
-
- if(elementIndex + length == bases[arrayIndex].length) {
- elementIndex = 0;
- ++arrayIndex;
- } else {
- elementIndex += length;
- }
- }
- inputCycle += rangeCovered;
- }
-
- outRead.setOrCheckLane(read.getLane());
- outRead.setOrCheckPf(read.isPf());
- outRead.setOrCheckTile(read.getTile());
- outRead.setOrCheckXCoordinate(read.getXCoordinate());
- outRead.setOrCheckYCoordinate(read.getYCoordinate());
-
- return outRead;
- }
-
- public static final Map<Integer, QseqReadData> filterAllSkips(final Map<Integer, QseqReadData> testData, final OutputMapping om) {
- final Map<Integer, QseqReadData> filteredMap = new HashMap<Integer, QseqReadData>();
- for( final Map.Entry<Integer, QseqReadData> qrd : testData.entrySet() ) {
- filteredMap.put(qrd.getKey(), filterSkips(om, qrd.getValue()));
- }
-
- return filteredMap;
- }
-}
diff --git a/src/tests/java/net/sf/picard/illumina/parser/QseqParserTest.java b/src/tests/java/net/sf/picard/illumina/parser/QseqParserTest.java
deleted file mode 100644
index c31a3b2..0000000
--- a/src/tests/java/net/sf/picard/illumina/parser/QseqParserTest.java
+++ /dev/null
@@ -1,356 +0,0 @@
-package net.sf.picard.illumina.parser;
-
-import org.testng.Assert;
-import org.testng.annotations.Test;
-import org.testng.annotations.DataProvider;
-
-import java.util.*;
-
-import static net.sf.samtools.util.CollectionUtil.makeList;
-import static net.sf.picard.illumina.parser.QSeqTdUtil.*;
-import static net.sf.picard.illumina.parser.OutputMapping.TwoDIndex;
-
-public class QseqParserTest {
-
- //The actual testdata copied into source is in QseqTdUtil which provides test data (Td) for this an other tests
-
- @DataProvider(name = "qSeqSingleTile")
- public Object [][] qSeqOneEnds() {
- return new Object[][] {
- //using file s_1_1_0001.txt
- new Object[]{1, new IlluminaFileMap(makeList(1), getQseqs(s_1_1_0001)),
- new Range[]{new Range(0,75)},
- new TwoDIndex[]{new TwoDIndex(0,0)},
- new OutputMapping(new ReadStructure("76T")),
- getReadData(s_1_1_0001)},
-
- new Object[]{1, new IlluminaFileMap(makeList(1), getQseqs(s_1_1_0001)),
- new Range[]{new Range(0,37), new Range(38,75)},
- new TwoDIndex[]{new TwoDIndex(0,0), new TwoDIndex(1,0)},
- new OutputMapping(new ReadStructure("38T38T")),
- getSplitOffsetReadData(s_1_1_0001, 76, new int[]{38,38}, 0) //get read data for lane 1 end 1 tile 1, expect it to be 76 bases but split QseqReadData.getBases() into two arrays of size 38
- },
-
- new Object[]{1, new IlluminaFileMap(makeList(1), getQseqs(s_1_1_0001)),
- new Range[]{ new Range(0, 5), new Range(6, 43), new Range(44, 75)},
- new TwoDIndex[]{ new TwoDIndex(0, 26), new TwoDIndex(1, 0), new TwoDIndex(2, 0)},
- new OutputMapping(new ReadStructure("32T38B32T")),
- getSplitOffsetReadData(s_1_1_0001, 76, new int[]{32,38,32}, 26)
- },
-
-
- new Object[]{1, new IlluminaFileMap(makeList(1), getQseqs(s_1_1_0001)),
- new Range[]{ new Range(0, 31), new Range(32, 69), new Range(70, 75)},
- new TwoDIndex[]{ new TwoDIndex(0, 0), new TwoDIndex(1, 0), new TwoDIndex(2, 0)},
- new OutputMapping(new ReadStructure("32T38B32T")),
- getSplitOffsetReadData(s_1_1_0001, 76, new int[]{32,38,32}, 0)
- },
-
- new Object[]{1, new IlluminaFileMap(makeList(1), getQseqs(s_1_1_0001)),
- new Range[]{ new Range(0, 75)},
- new TwoDIndex[]{ new TwoDIndex(0, 0)},
- new OutputMapping(new ReadStructure("76B8T76B")),
- getSplitOffsetReadData(s_1_1_0001, 76, new int[]{76,8,76}, 0)
- },
-
- //using file s_1_1_0002_qseq.txt
- new Object[]{1, new IlluminaFileMap(makeList(1), getQseqs(s_1_1_0002)),
- new Range[]{ new Range(0, 75)},
- new TwoDIndex[]{ new TwoDIndex(2, 0)},
- new OutputMapping(new ReadStructure("76B8T76B")),
- getSplitOffsetReadData(s_1_1_0002, 76, new int[]{76,8,76}, 84)
- },
-
- new Object[]{1, new IlluminaFileMap(makeList(1), getQseqs(s_1_1_0002)),
- new Range[]{ new Range(0, 4), new Range(5, 36), new Range(37, 75)},
- new TwoDIndex[]{ new TwoDIndex(0, 0), new TwoDIndex(1, 0), new TwoDIndex(2, 0)},
- new OutputMapping(new ReadStructure("5T32B39T")),
- getSplitOffsetReadData(s_1_1_0002, 76, new int[]{5,32,39}, 0)
- }
- };
- }
-
- @DataProvider(name = "qSeqMultiTile")
- public Object [][] qSeqMultiTile() {
- return new Object[][] {
- new Object[]{1, new IlluminaFileMap(makeList(1,2), getQseqs(s_1_1_0001, s_1_1_0002)),
- new Range[]{ new Range(0,75)},
- new TwoDIndex[]{ new TwoDIndex(0,0)},
- new OutputMapping(new ReadStructure("76T")),
- getTiledReadData(s_1_1, makeList(1,2))
- },
- //using file s_1_1_0001.txt
- new Object[]{1, new IlluminaFileMap(makeList(1,2), getQseqs(s_1_1_0001, s_1_1_0002)),
- new Range[]{ new Range(0,37), new Range(38,75)},
- new TwoDIndex[]{ new TwoDIndex(0,0), new TwoDIndex(1, 0)},
- new OutputMapping(new ReadStructure("38T38T")),
- getSplitOffsetReadData(s_1_1, makeList(1,2), 76, new int[]{38,38}, 0)
- },
-
- //Using s_1_2_0001_qseq.txt as if it were s_1_1_0003_qseq.txt so we don't have to define more test data as static constants
- new Object[]{1, new IlluminaFileMap(makeList(1,2,3), getQseqs(s_1_1_0001, s_1_1_0002, s_1_2_0003)),
- new Range[]{ new Range(0,37), new Range(38,75)},
- new TwoDIndex[]{ new TwoDIndex(0,0), new TwoDIndex(1, 0)},
- new OutputMapping(new ReadStructure("38T38T")),
- getTiledReadData(makeList(s_1_1_0001, s_1_1_0002, s_1_2_0003), 76, new int[]{38,38}, 0)
- },
-
- new Object[]{1, new IlluminaFileMap(Arrays.asList(1,2,3), getQseqs(s_1_1_0001, s_1_1_0002, s_1_2_0003)),
- new Range[]{ new Range(0,20), new Range(21,59), new Range(60, 75)},
- new TwoDIndex[]{ new TwoDIndex(0,0), new TwoDIndex(1,0), new TwoDIndex(2,0)},
- new OutputMapping(new ReadStructure("21B39T16T")),
- getTiledReadData(makeList(s_1_1_0001, s_1_1_0002, s_1_2_0003), 76, new int[]{21,39, 16}, 0)
- }
- };
- }
-
- //SIMULATE THE FOLLOWING
- //read 1st end, middle end, last end, total
- //1-4 Output arrays, different positions
- @Test(dataProvider="qSeqSingleTile")
- public void qSeqReadParserTest(final int lane, final IlluminaFileMap tilesToReadFiles, final Range [] srcRanges, final TwoDIndex[] dstRanges, final OutputMapping om, final Map<Integer, QseqReadData> testAgainst) {
- final QseqReadParser filesParser = new QseqReadParser(lane, tilesToReadFiles, srcRanges, dstRanges, om);
- final Map<Integer, QseqReadData> filteredTestAgainst = filterAllSkips(testAgainst, om);
-
- final int [] outputLengths = om.getOutputReadLengths();
- int currentRead = 0;
- while(filesParser.hasNext()) {
- final QseqReadData qseqRead = new QseqReadData(outputLengths);
- filesParser.next(qseqRead);
- final QseqReadData testRead = filteredTestAgainst.get(currentRead);
- if(testRead != null) {
- testQSeqs(qseqRead, testRead);
- }
- currentRead++;
- }
- }
-
- @Test(dataProvider="qSeqMultiTile")
- public void qSeqReadParserTest_multiTile(final int lane, final IlluminaFileMap tilesToReadFiles, final Range [] srcRanges, final TwoDIndex[] dstRanges, final OutputMapping om, final Map<Integer, QseqReadData> testAgainst) {
- qSeqReadParserTest(lane, tilesToReadFiles, srcRanges, dstRanges, om, testAgainst);
- }
-
- @DataProvider(name="qSeqIntegrations")
- public Object[][] qSeqIntegrations() {
- return new Object[][] {
- //1 end 1 tile
- new Object[] {1, "76T", makeList(new IlluminaFileMap(makeList(1), getQseqs(s_1_1_0001))), getReadData(s_1_1_0001)},
-
- //1 end 2 tiles
- new Object[] {1, "38B38B", makeList(new IlluminaFileMap(makeList(1,2), getQseqs(s_1_1_0001, s_1_1_0002))),
- getSplitOffsetReadData(s_1_1, makeList(1,2), 76, new int[]{38,38}, 0)},
-
- //2 ends 1 tile
- new Object[] {1, "152T", makeList(new IlluminaFileMap(makeList(1), getQseqs(s_1_1_0001)), new IlluminaFileMap(makeList(1), getQseqs(s_1_2_0001))),
- combineReads(getReadData(s_1_1_0001), getReadData(s_1_2_0001))},
-
- //In this example tile 3 is tile 1 reused and therefore the resultant QSeqReadData will not read tile 3 but tile 1
- //2 ends 3 tiles
- new Object[] {1, "76T76T",
- makeList(new IlluminaFileMap(makeList(1,2,3), getQseqs(s_1_1_0001,s_1_1_0002, s_1_1_0003)), new IlluminaFileMap(makeList(1,2,3), getQseqs(s_1_2_0001, s_1_2_0002, s_1_2_0003))),
- combineReads(152, new int[]{76,76}, 0, getTiledReadData(makeList(s_1_1_0001, s_1_1_0002, s_1_1_0003)), getTiledReadData(makeList(s_1_2_0001, s_1_2_0002, s_1_2_0003)))},
-
- //3 ends 2 tiles 3rd end is the same as the first
- new Object[] {1, "38T38B76T76B",
- makeList(new IlluminaFileMap(makeList(1,2), getQseqs(s_1_1_0001,s_1_1_0002)), new IlluminaFileMap(makeList(1,2), getQseqs(s_1_2_0001, s_1_2_0002)), new IlluminaFileMap(makeList(1,2), getQseqs(s_1_1_0001,s_1_1_0002))),
- combineReads(228, new int[]{38, 38, 76, 76}, 0, getTiledReadData(makeList(s_1_1_0001, s_1_1_0002)), getTiledReadData(makeList(s_1_2_0001, s_1_2_0002)), getTiledReadData(makeList(s_1_1_0001, s_1_1_0002)))},
-
- //4 ends 3 tiles
- new Object[] {1, "38T38T76B76B76B",
- makeList(new IlluminaFileMap(makeList(1,2,3), getQseqs(s_1_1_0001,s_1_1_0002, s_1_1_0003)), new IlluminaFileMap(makeList(1,2,3), getQseqs(s_1_2_0001, s_1_2_0002, s_1_2_0003)), new IlluminaFileMap(makeList(1,2,3), getQseqs(s_1_1_0001,s_1_1_0002, s_1_1_0003)), new IlluminaFileMap(makeList(1,2,3), getQseqs(s_1_2_0001, s_1_2_0002, s_1_2_0003))),
- combineReads(304, new int[]{38, 38, 76, 76, 76}, 0, getTiledReadData(makeList(s_1_1_0001, s_1_1_0002, s_1_1_0003)), getTiledReadData(makeList(s_1_2_0001, s_1_2_0002, s_1_2_0003)), getTiledReadData(makeList(s_1_1_0001, s_1_1_0002, s_1_1_0003)), getTiledReadData(makeList(s_1_2_0001, s_1_2_0002, s_1_2_0003)))},
- };
- }
-
- @Test(dataProvider="qSeqIntegrations")
- public void qSeqParserTest(final int lane, final String readStructure, final List<IlluminaFileMap> readNumberToTile, final Map<Integer, QseqReadData> testAgainst) {
- final OutputMapping om = new OutputMapping(new ReadStructure(readStructure));
- final QseqParser qseqParser = new QseqParser(lane, readNumberToTile, new OutputMapping(new ReadStructure(readStructure)));
- final Map<Integer, QseqReadData> filteredTestAgainst = filterAllSkips(testAgainst, om);
-
- int currentRead = 0;
- while(qseqParser.hasNext()) {
- final QseqReadData qseqRead = qseqParser.next();
- final QseqReadData testRead = filteredTestAgainst.get(currentRead);
- if(testRead != null) {
- testQSeqs(qseqRead, testRead);
- }
- currentRead++;
- }
- }
-
- public void testQSeqs(final QseqReadData actual, final QseqReadData expected){
- if(actual == expected) return;
- final byte [][] actualBases = actual.getBases();
- final byte [][] expectedBases = expected.getBases();
- final byte [][] actualQualities = actual.getQualities();
- final byte [][] expectedQualities = expected.getQualities();
-
- Assert.assertEquals(actualBases.length, expectedBases.length);
- Assert.assertEquals(actualQualities.length, expectedQualities.length);
-
- for(int i = 0; i < actualBases.length; i++) {
- for(int j = 0; j < actualBases[i].length; j++) {
- Assert.assertEquals(actualBases[i][j], expectedBases[i][j]);
- Assert.assertEquals(actualQualities[i][j], expectedQualities[i][j]);
- }
- }
-
- Assert.assertEquals(actual.isPf(), expected.isPf());
- Assert.assertEquals(actual.getXCoordinate(), expected.getXCoordinate());
- Assert.assertEquals(actual.getYCoordinate(), expected.getYCoordinate());
- Assert.assertEquals(actual.getLane(), expected.getLane());
- Assert.assertEquals(actual.getTile(), expected.getTile());
- }
-
- @DataProvider(name = "validSplitRangeData")
- public static Object [][] validSplitRangeData() {
- return new Object [][] {
- //how output should be structure, lengths of qseqs, output ranges as a result
- {"76T", new int[]{76}, makeList(new Range(0, 75))},
- {"76T", new int[]{38, 38}, makeList(new Range(0, 37), new Range(38, 75))},
- {"76T76S", new int[]{76,76}, makeList(new Range(0, 75))},
- {"76T76S", new int[]{8, 30, 38, 38, 38}, makeList(new Range(0, 7), new Range(8, 37), new Range(38, 75))},
- {"8S76T8S", new int[]{8,76,8}, makeList(new Range(8,83))},
- {"8S76T8S", new int[]{76,8,8}, makeList(new Range(8,75), new Range(76, 83))},
- {"8S76T8S", new int[]{30, 8, 8, 30, 16}, makeList(new Range(8,29), new Range(30,37), new Range(38, 45), new Range(46, 75), new Range(76, 83))},
-
- {"101T101T", new int[]{11, 90, 101}, makeList(new Range(0,10), new Range(11, 100), new Range(101, 201))},
- {"101T16S101T", new int[]{218}, makeList(new Range(0,100), new Range(117, 217))},
- {"101T16S101S", new int[]{51, 25, 25, 117}, makeList(new Range(0,50), new Range(51, 75), new Range(76, 100))},
- {"101T16S101T", new int[]{51, 25, 25, 117}, makeList(new Range(0,50), new Range(51, 75), new Range(76, 100), new Range(117, 217))},
- {"101S16T", new int[]{50, 51, 16}, makeList(new Range(101, 116))},
-
- {"25T25T25T", new int[]{60, 15}, makeList(new Range(0,24), new Range(25,49), new Range(50, 59), new Range(60, 74))},
- {"25T30S25T25T", new int[]{30,75}, makeList(new Range(0,24), new Range(55,79), new Range(80, 104))},
- {"25T30S25T10S25T", new int[]{125}, makeList(new Range(0,24), new Range(55,79), new Range(90, 114))}
- };
- }
-
- @Test(dataProvider = "validSplitRangeData")
- public void testSplitOutputRangesOnQseqBoundaries(final String readStructure, final int [] readLengths, final List<Range> expectedRanges) {
- final List<Range> outputRanges = QseqParser.splitOutputRangesOnQseqBoundaries(readLengths, new OutputMapping(new ReadStructure(readStructure)));
- Assert.assertEquals(outputRanges, expectedRanges);
- }
-
- //TODO: NEED TO DO SOME INVALID ONES
-
- @DataProvider(name = "outputRangesToInputRangesData")
- public static Object [][] outputRangesToInputRangesData() {
- return new Object [][] {
- //QSeqRead Lengths, OutputRanges
- // InputRanges per Read
- {
- new int[]{75, 8, 75}, makeList(new Range(0, 74), new Range(75, 82), new Range(83, 157)),
- makeList(
- makeList(new Range(0, 74)),
- makeList(new Range(0, 7)),
- makeList(new Range(0, 74))
- )
- },
- {
- new int[]{75, 8, 75}, makeList(new Range(0, 74), new Range(75, 82), new Range(91, 157)),
- makeList(
- makeList(new Range(0, 74)),
- makeList(new Range(0, 7)),
- makeList(new Range(8, 74))
- )
- },
-
- {
- new int[]{101, 8, 8, 101}, makeList(new Range(15, 20), new Range(90, 100), new Range(109,113), new Range(117, 130), new Range(150, 180)),
- makeList(
- makeList(new Range(15, 20), new Range(90, 100)),
- new ArrayList<Range>(),
- makeList(new Range(0, 4)),
- makeList(new Range(0, 13), new Range(33,63))
- )
- },
- {
- new int[]{250, 250}, makeList(new Range(25, 249), new Range(250, 276), new Range(480, 499)),
- makeList(
- makeList(new Range(25, 249)),
- makeList(new Range(0, 26), new Range(230, 249))
- )
- },
- {
- new int[]{310}, makeList(new Range(0, 99), new Range(300, 309)),
- makeList(
- makeList(new Range(0,99), new Range(300,309))
- )
- }
- };
- }
-
- @Test(dataProvider = "outputRangesToInputRangesData")
- public void testOutputRangesToInputRanges(final int [] readLengths, final List<Range> outputRanges, final List<List<Range>> expectedResults) {
- final List<List<Range>> actualResults = QseqParser.outputRangesToInputRanges(readLengths, outputRanges);
- Assert.assertEquals(actualResults, expectedResults);
- }
-
- @DataProvider(name = "outputRangesTo2DTargetsPerReadData")
- public static Object [][] outputRangesTo2DTargetsPerReadData() {
- return new Object [][] {
- //QSeqRead Lengths, OutputRanges
- // InputRanges per Read
- {
- "76T8B76T",
- makeList(1,1,1),
- makeList(new Range(0, 75), new Range(76, 83), new Range(84, 157)),
- makeList(
- makeList(new TwoDIndex(0, 0)),
- makeList(new TwoDIndex(1, 0)),
- makeList(new TwoDIndex(2, 0))
- )
- },
- {
- "76T8B8S68T",
- makeList(1,1,1),
- makeList(new Range(0, 75), new Range(76, 83), new Range(92, 158)),
- makeList(
- makeList(new TwoDIndex(0, 0)),
- makeList(new TwoDIndex(1, 0)),
- makeList(new TwoDIndex(2, 0))
- )
- },
-
- { //less realistic scenario, but useful for testing
- "101T8B8B101T",
- makeList(2,0,1, 2),
- makeList(new Range(15, 20), new Range(90, 100), new Range(109,113), new Range(117, 130), new Range(150, 180)),
- makeList(
- makeList(new TwoDIndex(0, 15), new TwoDIndex(0, 90)),
- new ArrayList<TwoDIndex>(),
- makeList(new TwoDIndex(2, 0)),
- makeList(new TwoDIndex(3, 0), new TwoDIndex(3,33))
- )
- },
- { //Another less realistic scenario
- "250T27T190S43T",
- makeList(1,1,1),
- makeList(new Range(25, 249), new Range(250, 276), new Range(480, 499)),
- makeList(
- makeList(new TwoDIndex(0, 25)),
- makeList(new TwoDIndex(1, 0)),
- makeList(new TwoDIndex(2, 13))
- )
- },
- {
- "100T200S10T8S",
- makeList(1,1),
- makeList(new Range(0, 99), new Range(300, 309)),
- makeList(
- makeList(new TwoDIndex(0,0)),
- makeList(new TwoDIndex(1,0))
- )
- }
- };
- }
-
- @Test(dataProvider = "outputRangesTo2DTargetsPerReadData")
- public void testOutputRangesTo2DTargetsPerRead(String readStructure, final List<Integer> rangesPerRead, final List<Range> splitOutputRanges, final List<List<TwoDIndex>> expectedResults) {
- final List<List<TwoDIndex>> actualResults = QseqParser.outputRangesTo2DTargetsPerRead(rangesPerRead, splitOutputRanges, new OutputMapping(new ReadStructure(readStructure)));
- Assert.assertEquals(actualResults, expectedResults);
- }
-}
-
diff --git a/src/tests/java/net/sf/picard/illumina/parser/fakers/BclFileFakerTest.java b/src/tests/java/net/sf/picard/illumina/parser/fakers/BclFileFakerTest.java
new file mode 100644
index 0000000..445da40
--- /dev/null
+++ b/src/tests/java/net/sf/picard/illumina/parser/fakers/BclFileFakerTest.java
@@ -0,0 +1,59 @@
+package net.sf.picard.illumina.parser.fakers;
+
+import net.sf.picard.illumina.parser.readers.BclQualityEvaluationStrategy;
+import net.sf.picard.illumina.parser.readers.BclReader;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.io.File;
+
+/**
+ * The MIT License
+ * <p/>
+ * Copyright (c) 2014 The Broad Institute
+ * <p/>
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ * <p/>
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ * <p/>
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+public class BclFileFakerTest {
+
+ @Test
+ public void testFileLengthMatchesHeaderLength() throws Exception {
+ final File fakeFile = File.createTempFile("BclFileFakerTest", ".bcl");
+ fakeFile.deleteOnExit();
+
+ new BclFileFaker().fakeFile(fakeFile, 100000);
+ // .make() has a number of checks for the file
+ final BclReader bclReader = new BclReader(
+ fakeFile,
+ new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY), false);
+ Assert.assertEquals(100000, BclReader.getNumberOfClusters(fakeFile));
+ Assert.assertEquals(BclReader.getNumberOfClusters(fakeFile), fakeFile.length() - 4);
+ }
+
+ @Test
+ public void testGZFileIsActuallyGZipped() throws Exception {
+ final File fakeFile = File.createTempFile("BclFileFakerTest", ".bcl.gz");
+ fakeFile.deleteOnExit();
+
+ new BclFileFaker().fakeFile(fakeFile, 100000);
+ new BclReader(
+ fakeFile,
+ new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY), false);
+ }
+}
diff --git a/src/tests/java/net/sf/picard/illumina/parser/readers/BclReaderTest.java b/src/tests/java/net/sf/picard/illumina/parser/readers/BclReaderTest.java
index 865e3ae..1d4bb99 100644
--- a/src/tests/java/net/sf/picard/illumina/parser/readers/BclReaderTest.java
+++ b/src/tests/java/net/sf/picard/illumina/parser/readers/BclReaderTest.java
@@ -1,6 +1,7 @@
package net.sf.picard.illumina.parser.readers;
import net.sf.picard.PicardException;
+import net.sf.picard.illumina.parser.BclData;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
@@ -8,15 +9,19 @@ import org.testng.annotations.Test;
import java.io.File;
import java.util.Collection;
import java.util.LinkedList;
-import java.util.concurrent.*;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
public class BclReaderTest {
- public static File TestDataDir = new File("testdata/net/sf/picard/illumina/readerTests");
+ public static final File TestDataDir = new File("testdata/net/sf/picard/illumina/readerTests");
public static final File PASSING_BCL_FILE = new File(TestDataDir, "bcl_passing.bcl");
public static final File QUAL_0FAILING_BCL_FILE = new File(TestDataDir, "bcl_failing.bcl");
public static final File QUAL_1FAILING_BCL_FILE = new File(TestDataDir, "bcl_failing2.bcl");
- public static final File FILE_TOO_LARGE = new File(TestDataDir, "bcl_tooLarge.bcl");
+ public static final File FILE_TOO_LONG = new File(TestDataDir, "bcl_tooLong.bcl");
public static final File FILE_TOO_SHORT = new File(TestDataDir, "bcl_tooShort.bcl");
public static final char[] expectedBases = new char[]{
@@ -52,19 +57,20 @@ public class BclReaderTest {
@Test
public void readValidFile() {
final BclQualityEvaluationStrategy bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY);
- final BclReader reader = BclReader.make(PASSING_BCL_FILE, bclQualityEvaluationStrategy);
+ final BclReader reader = new BclReader(PASSING_BCL_FILE, bclQualityEvaluationStrategy, false);
final byte[] quals = qualsAsBytes();
- Assert.assertEquals(reader.numClusters, expectedBases.length);
+ Assert.assertEquals(reader.numClustersPerCycle[0], expectedBases.length);
int readNum = 0;
- while (readNum < reader.numClusters) {
- final BclReader.BclValue bv = reader.next();
- Assert.assertEquals(bv.base, expectedBases[readNum], " On num cluster: " + readNum);
- Assert.assertEquals(bv.quality, quals[readNum], " On num cluster: " + readNum);
+ while (readNum < reader.numClustersPerCycle[0]) {
+ final BclData bv = reader.next();
+ Assert.assertEquals(bv.bases[0][0], expectedBases[readNum], " On num cluster: " + readNum);
+ Assert.assertEquals(bv.qualities[0][0], quals[readNum], " On num cluster: " + readNum);
++readNum;
}
bclQualityEvaluationStrategy.assertMinimumQualities();
+ reader.close();
}
@DataProvider(name = "failingFiles")
@@ -72,8 +78,8 @@ public class BclReaderTest {
return new Object[][]{
{QUAL_0FAILING_BCL_FILE},
{QUAL_1FAILING_BCL_FILE},
- {new File(TestDataDir, "SomeNoneExistantFile.bcl")},
- {FILE_TOO_LARGE},
+ {new File(TestDataDir, "SomeNoneExistentFile.bcl")},
+ {FILE_TOO_LONG},
{FILE_TOO_SHORT}
};
}
@@ -81,11 +87,12 @@ public class BclReaderTest {
@Test(expectedExceptions = PicardException.class, dataProvider = "failingFiles")
public void failingFileTest(final File failingFile) {
final BclQualityEvaluationStrategy bclQualityEvaluationStrategy = new BclQualityEvaluationStrategy(BclQualityEvaluationStrategy.ILLUMINA_ALLEGED_MINIMUM_QUALITY);
- final BclReader reader = BclReader.make(failingFile, bclQualityEvaluationStrategy);
- Assert.assertEquals(reader.numClusters, expectedBases.length);
+ final BclReader reader = new BclReader(failingFile, bclQualityEvaluationStrategy, false);
+ Assert.assertEquals(reader.numClustersPerCycle[0], expectedBases.length);
while (reader.hasNext()) {
reader.next();
}
+ reader.close();
bclQualityEvaluationStrategy.assertMinimumQualities();
}
@@ -104,11 +111,13 @@ public class BclReaderTest {
callables.add(new Callable<Void>() {
@Override
public Void call() throws Exception {
- final BclReader reader = BclReader.make(even_i ? QUAL_1FAILING_BCL_FILE : QUAL_0FAILING_BCL_FILE, bclQualityEvaluationStrategy);
- Assert.assertEquals(reader.numClusters, expectedBases.length);
+ final BclReader reader = new BclReader(even_i ? QUAL_1FAILING_BCL_FILE : QUAL_0FAILING_BCL_FILE,
+ bclQualityEvaluationStrategy, false);
+ Assert.assertEquals(reader.numClustersPerCycle[0], expectedBases.length);
while (reader.hasNext()) {
reader.next();
}
+ reader.close();
return null;
}
});
@@ -137,11 +146,13 @@ public class BclReaderTest {
callables.add(new Callable<Void>() {
@Override
public Void call() throws Exception {
- final BclReader reader = BclReader.make(even_i ? QUAL_1FAILING_BCL_FILE : QUAL_0FAILING_BCL_FILE, bclQualityEvaluationStrategy);
- Assert.assertEquals(reader.numClusters, expectedBases.length);
+ final BclReader reader = new BclReader(even_i ? QUAL_1FAILING_BCL_FILE : QUAL_0FAILING_BCL_FILE,
+ bclQualityEvaluationStrategy, false);
+ Assert.assertEquals(reader.numClustersPerCycle[0], expectedBases.length);
while (reader.hasNext()) {
reader.next();
}
+ reader.close();
return null;
}
});
diff --git a/src/tests/java/net/sf/picard/illumina/parser/readers/PosFileReaderTest.java b/src/tests/java/net/sf/picard/illumina/parser/readers/PosFileReaderTest.java
index 1cdf344..a427cef 100644
--- a/src/tests/java/net/sf/picard/illumina/parser/readers/PosFileReaderTest.java
+++ b/src/tests/java/net/sf/picard/illumina/parser/readers/PosFileReaderTest.java
@@ -15,23 +15,23 @@ public class PosFileReaderTest {
public static final File PassingPosFile = new File(TestDir, "s_2_1101_pos.txt");
public static final int PassingTile = 1101;
public static final int PassingLane = 2;
- public static final float [][] PassingPosFloatCoord = {
- {17.80f, 0.30f}, {23.70f, 1.70f}, {18.50f, 3.90f}, {22.80f, 4.00f}, {15.90f, 4.20f},
- {19.10f, 5.60f}, {23.90f, 6.70f}, {16.70f, 7.00f}, {21.50f, 7.10f}, {18.90f, 9.30f},
- {17.10f, 10.30f}, {19.90f, 10.80f}, {15.90f, 11.90f}, {21.60f, 12.00f}, {24.80f, 12.40f},
- {17.90f, 14.20f}, {22.00f, 14.50f}, {23.60f, 15.20f}, {20.00f, 15.50f}, {16.30f, 17.30f}
+ public static final float[][] PassingPosFloatCoord = {
+ {17.80f, 0.30f}, {23.70f, 1.70f}, {18.50f, 3.90f}, {22.80f, 4.00f}, {15.90f, 4.20f},
+ {19.10f, 5.60f}, {23.90f, 6.70f}, {16.70f, 7.00f}, {21.50f, 7.10f}, {18.90f, 9.30f},
+ {17.10f, 10.30f}, {19.90f, 10.80f}, {15.90f, 11.90f}, {21.60f, 12.00f}, {24.80f, 12.40f},
+ {17.90f, 14.20f}, {22.00f, 14.50f}, {23.60f, 15.20f}, {20.00f, 15.50f}, {16.30f, 17.30f}
};
- public static final int [][] PassingPosQSeqCoord = {
- {1178, 1003}, {1237, 1017}, {1185, 1039}, {1228, 1040}, {1159, 1042},
- {1191, 1056}, {1239, 1067}, {1167, 1070}, {1215, 1071}, {1189, 1093},
- {1171, 1103}, {1199, 1108}, {1159, 1119}, {1216, 1120}, {1248, 1124},
- {1179, 1142}, {1220, 1145}, {1236, 1152}, {1200, 1155}, {1163, 1173}
+ public static final int[][] PassingPosQSeqCoord = {
+ {1178, 1003}, {1237, 1017}, {1185, 1039}, {1228, 1040}, {1159, 1042},
+ {1191, 1056}, {1239, 1067}, {1167, 1070}, {1215, 1071}, {1189, 1093},
+ {1171, 1103}, {1199, 1108}, {1159, 1119}, {1216, 1120}, {1248, 1124},
+ {1179, 1142}, {1220, 1145}, {1236, 1152}, {1200, 1155}, {1163, 1173}
};
@Test
public void validPosFileTest() {
final PosFileReader pfr = new PosFileReader(PassingPosFile);
- for(int i = 0; i < PassingPosFloatCoord.length; i++) {
+ for (int i = 0; i < PassingPosFloatCoord.length; i++) {
Assert.assertTrue(pfr.hasNext());
final AbstractIlluminaPositionFileReader.PositionInfo pi = pfr.next();
comparePositionInfo(pi, i);
@@ -41,13 +41,13 @@ public class PosFileReaderTest {
}
public static void comparePositionInfo(final AbstractIlluminaPositionFileReader.PositionInfo pi, final int index) {
- comparePositionInfo(pi, PassingPosFloatCoord[index][0], PassingPosFloatCoord[index][1],
- PassingPosQSeqCoord[index][0], PassingPosQSeqCoord[index][1],
- PassingLane, PassingTile, index);
+ comparePositionInfo(pi, PassingPosFloatCoord[index][0], PassingPosFloatCoord[index][1],
+ PassingPosQSeqCoord[index][0], PassingPosQSeqCoord[index][1],
+ PassingLane, PassingTile, index);
}
public static void comparePositionInfo(final AbstractIlluminaPositionFileReader.PositionInfo pi, final float xPos, final float yPos,
- final int xQSeqCoord, final int yQSeqCoord, final int lane, final int tile, final int index) {
+ final int xQSeqCoord, final int yQSeqCoord, final int lane, final int tile, final int index) {
Assert.assertEquals(pi.xPos, xPos, "Differs at index: " + index);
Assert.assertEquals(pi.yPos, yPos, "Differs at index: " + index);
Assert.assertEquals(pi.xQseqCoord, xQSeqCoord, "Differs at index: " + index);
@@ -62,26 +62,30 @@ public class PosFileReaderTest {
}
@DataProvider(name = "invalidDataFiles")
- public Object [][] invalidDataFiles() {
+ public Object[][] invalidDataFiles() {
return new Object[][]{
- {new File(TestDir, "s_1_1101_pos.txt")},
- {new File(TestDir, "s_1_1102_pos.txt")},
- {new File(TestDir, "s_1_1103_pos.txt")}
+ {new File(TestDir, "s_1_1101_pos.txt")},
+ {new File(TestDir, "s_1_1102_pos.txt")},
+ {new File(TestDir, "s_1_1103_pos.txt")}
};
}
- @Test(dataProvider="invalidDataFiles", expectedExceptions = PicardException.class)
+ @Test(dataProvider = "invalidDataFiles", expectedExceptions = PicardException.class)
public void failingDataPosFileTest(final File file) {
final PosFileReader pfr = new PosFileReader(file);
- while(pfr.hasNext()) {
- pfr.next();
+ try {
+ while (pfr.hasNext()) {
+ pfr.next();
+ }
+ } finally {
+ pfr.close();
}
- pfr.close();
}
@Test
public void zeroLengthFileTest() {
final PosFileReader pfr = new PosFileReader(new File(TestDir, "s_1_1104_pos.txt"));
Assert.assertFalse(pfr.hasNext());
+ pfr.close();
}
}
diff --git a/src/tests/java/net/sf/picard/reference/FastaSequenceIndexTest.java b/src/tests/java/net/sf/picard/reference/FastaSequenceIndexTest.java
index 366270c..a72d955 100644
--- a/src/tests/java/net/sf/picard/reference/FastaSequenceIndexTest.java
+++ b/src/tests/java/net/sf/picard/reference/FastaSequenceIndexTest.java
@@ -61,6 +61,7 @@ public class FastaSequenceIndexTest {
Assert.assertEquals(entry.getSize(),16571L,"Contig chrM size is incorrect");
Assert.assertEquals(entry.getBasesPerLine(),50,"Contig chrM bases per line is incorrect");
Assert.assertEquals(entry.getBytesPerLine(),51,"Contig chrM bytes per line is incorrect");
+
}
@Test(dataProvider="homosapiens")
diff --git a/src/tests/java/net/sf/picard/reference/IndexedFastaSequenceFileTest.java b/src/tests/java/net/sf/picard/reference/IndexedFastaSequenceFileTest.java
index 38636ab..12198c9 100644
--- a/src/tests/java/net/sf/picard/reference/IndexedFastaSequenceFileTest.java
+++ b/src/tests/java/net/sf/picard/reference/IndexedFastaSequenceFileTest.java
@@ -26,6 +26,7 @@ package net.sf.picard.reference;
import net.sf.picard.PicardException;
import net.sf.samtools.SAMSequenceRecord;
+import net.sf.samtools.util.CloserUtil;
import net.sf.samtools.util.StringUtil;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
@@ -70,6 +71,7 @@ public class IndexedFastaSequenceFileTest{
long startTime = System.currentTimeMillis();
Assert.assertNotNull(sequenceFile);
long endTime = System.currentTimeMillis();
+ CloserUtil.close(sequenceFile);
System.err.printf("testOpenFile runtime: %dms%n", (endTime - startTime)) ;
}
@@ -84,6 +86,8 @@ public class IndexedFastaSequenceFileTest{
Assert.assertEquals(sequence.getContigIndex(),0,"Sequence contig index is not correct");
Assert.assertEquals(StringUtil.bytesToString(sequence.getBases()),firstBasesOfChrM,"First n bases of chrM are incorrect");
+ CloserUtil.close(sequenceFile);
+
System.err.printf("testFirstSequence runtime: %dms%n", (endTime - startTime)) ;
}
@@ -97,6 +101,8 @@ public class IndexedFastaSequenceFileTest{
Assert.assertEquals(sequence.getContigIndex(),0,"Sequence contig index is not correct");
Assert.assertEquals(StringUtil.bytesToString(sequence.getBases()),extendedBasesOfChrM,"First n bases of chrM are incorrect");
+ CloserUtil.close(sequenceFile);
+
System.err.printf("testFirstSequenceExtended runtime: %dms%n", (endTime - startTime)) ;
}
@@ -115,6 +121,8 @@ public class IndexedFastaSequenceFileTest{
Assert.assertEquals(sequence.getContigIndex(),0,"Sequence contig index is not correct");
Assert.assertEquals(StringUtil.bytesToString(sequence.getBases()),truncated,"First n bases of chrM are incorrect");
+ CloserUtil.close(sequenceFile);
+
System.err.printf("testReadStartingInCenterOfFirstLine runtime: %dms%n", (endTime - startTime)) ;
}
@@ -133,6 +141,8 @@ public class IndexedFastaSequenceFileTest{
Assert.assertEquals(sequence.getContigIndex(),0,"Sequence contig index is not correct");
Assert.assertEquals(StringUtil.bytesToString(sequence.getBases()),truncated,"First n bases of chrM are incorrect");
+ CloserUtil.close(sequenceFile);
+
System.err.printf("testReadStartingInCenterOfMiddleLine runtime: %dms%n", (endTime - startTime)) ;
}
@@ -148,6 +158,9 @@ public class IndexedFastaSequenceFileTest{
Assert.assertEquals(sequence.getContigIndex(),0,"Sequence contig index is not correct");
Assert.assertEquals(StringUtil.bytesToString(sequence.getBases()),StringUtil.bytesToString(expectedSequence.getBases()),"chrM is incorrect");
+ CloserUtil.close(originalSequenceFile);
+ CloserUtil.close(sequenceFile);
+
System.err.printf("testFirstCompleteContigRead runtime: %dms%n", (endTime - startTime)) ;
}
@@ -159,6 +172,9 @@ public class IndexedFastaSequenceFileTest{
}
finally {
long endTime = System.currentTimeMillis();
+
+ CloserUtil.close(sequenceFile);
+
System.err.printf("testReadThroughEndOfContig runtime: %dms%n", (endTime - startTime)) ;
}
}
@@ -171,6 +187,9 @@ public class IndexedFastaSequenceFileTest{
}
finally {
long endTime = System.currentTimeMillis();
+
+ CloserUtil.close(sequenceFile);
+
System.err.printf("testReadPastEndOfContig runtime: %dms%n", (endTime - startTime)) ;
}
}
@@ -189,6 +208,9 @@ public class IndexedFastaSequenceFileTest{
Assert.assertEquals(sequence.getContigIndex(),1,"Sequence contig index is not correct");
Assert.assertEquals(StringUtil.bytesToString(sequence.getBases()),StringUtil.bytesToString(expectedSequence.getBases()),"chrX_random is incorrect");
+ CloserUtil.close(originalSequenceFile);
+ CloserUtil.close(sequenceFile);
+
System.err.printf("testLastCompleteContigRead runtime: %dms%n", (endTime - startTime)) ;
}
@@ -205,6 +227,8 @@ public class IndexedFastaSequenceFileTest{
Assert.assertEquals(sequence.getContigIndex(),1,"Sequence contig index is not correct");
Assert.assertEquals(StringUtil.bytesToString(sequence.getBases()),lastBasesOfChr20,"First n bases of chr1 are incorrect");
+ CloserUtil.close(sequenceFile);
+
System.err.printf("testFirstOfChr1 runtime: %dms%n", (endTime - startTime)) ;
}
@@ -220,6 +244,9 @@ public class IndexedFastaSequenceFileTest{
Assert.assertEquals(sequence.getContigIndex(), 0,"Sequence contig index is not correct");
Assert.assertEquals(StringUtil.bytesToString(sequence.getBases()),StringUtil.bytesToString(expectedSequence.getBases()),"chrM is incorrect");
+ CloserUtil.close(originalSequenceFile);
+ CloserUtil.close(sequenceFile);
+
System.err.printf("testFirstElementOfIterator runtime: %dms%n", (endTime - startTime)) ;
}
@@ -239,6 +266,9 @@ public class IndexedFastaSequenceFileTest{
Assert.assertEquals(sequence.length(),expectedSequence.length(),"Sequence size is not correct");
Assert.assertEquals(StringUtil.bytesToString(sequence.getBases()),StringUtil.bytesToString(expectedSequence.getBases()),"chr1 is incorrect");
+ CloserUtil.close(originalSequenceFile);
+ CloserUtil.close(sequenceFile);
+
System.err.printf("testNextElementOfIterator runtime: %dms%n", (endTime - startTime)) ;
}
@@ -259,6 +289,9 @@ public class IndexedFastaSequenceFileTest{
Assert.assertEquals(sequence.length(),expectedSequence.length(), "Sequence size is not correct");
Assert.assertEquals(StringUtil.bytesToString(sequence.getBases()),StringUtil.bytesToString(expectedSequence.getBases()),"chrM is incorrect");
+ CloserUtil.close(originalSequenceFile);
+ CloserUtil.close(sequenceFile);
+
System.err.printf("testReset runtime: %dms%n", (endTime - startTime)) ;
}
diff --git a/src/tests/java/net/sf/picard/reference/ReferenceSequenceFileWalkerTest.java b/src/tests/java/net/sf/picard/reference/ReferenceSequenceFileWalkerTest.java
index 5149376..71c6df8 100644
--- a/src/tests/java/net/sf/picard/reference/ReferenceSequenceFileWalkerTest.java
+++ b/src/tests/java/net/sf/picard/reference/ReferenceSequenceFileWalkerTest.java
@@ -1,6 +1,7 @@
package net.sf.picard.reference;
import net.sf.picard.PicardException;
+import net.sf.samtools.util.CloserUtil;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
@@ -33,6 +34,7 @@ public class ReferenceSequenceFileWalkerTest {
sequence = refWalker.get(index2);
Assert.assertEquals(sequence.getContigIndex(), index2);
+ CloserUtil.close(refWalker);
}
@@ -51,9 +53,14 @@ public class ReferenceSequenceFileWalkerTest {
final File refFile = new File(fileName);
final ReferenceSequenceFileWalker refWalker = new ReferenceSequenceFileWalker(refFile);
- refWalker.get(index1);
+ try {
+ refWalker.get(index1);
- refWalker.get(index2);
+ refWalker.get(index2);
+ }
+ finally {
+ CloserUtil.close(refWalker);
+ }
}
diff --git a/src/tests/java/net/sf/picard/sam/AddCommentsToBamTest.java b/src/tests/java/net/sf/picard/sam/AddCommentsToBamTest.java
new file mode 100644
index 0000000..1823997
--- /dev/null
+++ b/src/tests/java/net/sf/picard/sam/AddCommentsToBamTest.java
@@ -0,0 +1,63 @@
+package net.sf.picard.sam;
+
+import net.sf.picard.PicardException;
+import net.sf.samtools.BamFileIoUtils;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMTextHeaderCodec;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.LinkedList;
+import java.util.List;
+
+public class AddCommentsToBamTest {
+ private static final File TEST_DATA_DIR = new File("testdata/net/sf/picard/sam");
+ private static final File INPUT_FILE = new File(TEST_DATA_DIR, "aligned_queryname_sorted.bam");
+ private static final File SAM_FILE = new File(TEST_DATA_DIR, "summary_alignment_stats_test2.sam");
+
+ private static final List<String> commentList = new ArrayList(Arrays.asList("test1", "test2", "test3"));
+
+ @Test
+ public void testAddCommentsToBam() throws Exception {
+ final AddCommentsToBam addCommentToBam = new AddCommentsToBam();
+ addCommentToBam.INPUT = INPUT_FILE;
+ addCommentToBam.OUTPUT = File.createTempFile("addCommentsToBamTest.", BamFileIoUtils.BAM_FILE_EXTENSION);
+ addCommentToBam.COMMENT = commentList;
+ addCommentToBam.doWork();
+ final SAMFileHeader newHeader = new SAMFileReader(addCommentToBam.OUTPUT).getFileHeader();
+
+ // The original comments are massaged when they're added to the header. Perform the same massaging here,
+ // and then compare the lists
+ final List<String> massagedComments = new LinkedList<String>();
+ for (final String comment : commentList) {
+ massagedComments.add(SAMTextHeaderCodec.COMMENT_PREFIX + comment);
+ }
+
+ Assert.assertEquals(newHeader.getComments(), massagedComments);
+ }
+
+ @Test(expectedExceptions = PicardException.class)
+ public void testUsingSam() throws Exception {
+ final AddCommentsToBam addCommentToBam = new AddCommentsToBam();
+ addCommentToBam.INPUT = SAM_FILE;
+ addCommentToBam.OUTPUT = File.createTempFile("addCommentsToBamTest.samFile.", BamFileIoUtils.BAM_FILE_EXTENSION);
+ addCommentToBam.COMMENT = commentList;
+ addCommentToBam.doWork();
+ throw new IllegalStateException("We shouldn't be here!");
+ }
+
+ @Test(expectedExceptions = PicardException.class)
+ public void testUsingNewlines() throws Exception {
+ final AddCommentsToBam addCommentToBam = new AddCommentsToBam();
+ addCommentToBam.INPUT = INPUT_FILE;
+ addCommentToBam.OUTPUT = File.createTempFile("addCommentsToBamTest.newLine.", BamFileIoUtils.BAM_FILE_EXTENSION);
+ addCommentToBam.COMMENT = new ArrayList(Arrays.asList("this is\n a crazy\n test"));
+ addCommentToBam.doWork();
+ throw new IllegalStateException("We shouldn't be here!");
+ }
+
+}
diff --git a/src/tests/java/net/sf/picard/sam/CleanSamTest.java b/src/tests/java/net/sf/picard/sam/CleanSamTest.java
index a7ef22f..71ead29 100644
--- a/src/tests/java/net/sf/picard/sam/CleanSamTest.java
+++ b/src/tests/java/net/sf/picard/sam/CleanSamTest.java
@@ -78,21 +78,22 @@ public class CleanSamTest {
//identical test case using the SamFileTester to generate that SAM file on the fly
@Test(dataProvider = "testCleanSamTesterDataProvider")
- public void testCleanSamTester(final String expectedCigar, final int length, final int alignStart) throws IOException {
- final CleanSamTester cleanSamTester = new CleanSamTester(expectedCigar, length);
- cleanSamTester.addMappedFragment(0, alignStart, false, expectedCigar, qualityScore, -1);
+ public void testCleanSamTester(final String originalCigar, final String expectedCigar, final int defaultChromosomeLength, final int alignStart) throws IOException {
+ final CleanSamTester cleanSamTester = new CleanSamTester(expectedCigar, 100, defaultChromosomeLength);
+ // NB: this will add in the mate cigar, when enabled in SamPairUtil, for additional validation
+ cleanSamTester.addMappedPair(0, alignStart, alignStart, false, false, originalCigar, originalCigar, false, 50);
cleanSamTester.runTest();
}
@DataProvider(name = "testCleanSamTesterDataProvider")
public Object[][] testCleanSamTesterDataProvider() {
return new Object[][]{
- {"100M", 101, 2},
- {"99M1S", 101, 3},
- {"91M2D9M", 102, 1},
- {"91M2D8M1S", 101, 1},
- {"99M1I", 101, 3},
- {"90M10I", 101, 3},
+ {"100M", "100M", 101, 2}, // simple_filts.sam
+ {"100M", "99M1S", 101, 3}, // simple_overhang.sam
+ {"91M2D9M", "91M2D9M", 102, 1}, // fits_with_deletion.sam
+ {"91M2D9M", "91M2D8M1S", 101, 1}, // overhang_with_deletion.sam
+ {"99M1I", "99M1I", 101, 3}, // trailing_insertion.sam
+ {"90M10I", "90M10I", 101, 3} // long_trailing_insertion.sam
};
}
}
diff --git a/src/tests/java/net/sf/picard/sam/MergeBamAlignmentTest.java b/src/tests/java/net/sf/picard/sam/MergeBamAlignmentTest.java
index f9022ca..2f827a8 100644
--- a/src/tests/java/net/sf/picard/sam/MergeBamAlignmentTest.java
+++ b/src/tests/java/net/sf/picard/sam/MergeBamAlignmentTest.java
@@ -24,6 +24,7 @@
package net.sf.picard.sam;
import net.sf.picard.PicardException;
+import net.sf.samtools.BamFileIoUtils;
import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
@@ -341,7 +342,7 @@ public class MergeBamAlignmentTest {
final SamAlignmentMerger merger = new SamAlignmentMerger(unmapped, target, fasta, null, true, false,
false, Arrays.asList(aligned), 1, null, null, null, null, null, null,
Arrays.asList(SamPairUtil.PairOrientation.FR), SAMFileHeader.SortOrder.coordinate,
- new BestMapqPrimaryAlignmentSelectionStrategy());
+ new BestMapqPrimaryAlignmentSelectionStrategy(), false);
merger.mergeAlignment();
Assert.assertEquals(sorted, !merger.getForceSort());
@@ -448,7 +449,7 @@ public class MergeBamAlignmentTest {
@Test(expectedExceptions = {IllegalStateException.class, PicardException.class})
public void testOldQuerynameSortFails() throws IOException {
- final File merged = File.createTempFile("merged", ".bam");
+ final File merged = File.createTempFile("merged", BamFileIoUtils.BAM_FILE_EXTENSION);
merged.deleteOnExit();
final MergeBamAlignment merger = new MergeBamAlignment();
diff --git a/src/tests/java/net/sf/picard/sam/MergeSamFilesTest.java b/src/tests/java/net/sf/picard/sam/MergeSamFilesTest.java
index 0fcaba3..debdb50 100644
--- a/src/tests/java/net/sf/picard/sam/MergeSamFilesTest.java
+++ b/src/tests/java/net/sf/picard/sam/MergeSamFilesTest.java
@@ -23,6 +23,7 @@
*/
package net.sf.picard.sam;
+import net.sf.samtools.BamFileIoUtils;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader;
import org.testng.Assert;
@@ -39,7 +40,7 @@ public class MergeSamFilesTest {
@Test
public void unsortedInputSortedOutputTest() throws Exception {
File unsortedInputTestDataDir = new File(TEST_DATA_DIR, "unsorted_input");
- File mergedOutput = File.createTempFile("unsortedInputSortedOutputTest.", ".bam");
+ File mergedOutput = File.createTempFile("unsortedInputSortedOutputTest.", BamFileIoUtils.BAM_FILE_EXTENSION);
mergedOutput.deleteOnExit();
String[] args = {
"I=" + new File(unsortedInputTestDataDir, "1.sam").getAbsolutePath(),
diff --git a/src/tests/java/net/sf/picard/sam/ValidateSamFileTest.java b/src/tests/java/net/sf/picard/sam/ValidateSamFileTest.java
index 70a7837..0b3fbd2 100644
--- a/src/tests/java/net/sf/picard/sam/ValidateSamFileTest.java
+++ b/src/tests/java/net/sf/picard/sam/ValidateSamFileTest.java
@@ -50,6 +50,19 @@ public class ValidateSamFileTest {
private static final File TEST_DATA_DIR = new File("testdata/net/sf/picard/sam/ValidateSamFileTest");
@Test
+ public void testValidSamFile() throws Exception {
+ final SAMFileReader.ValidationStringency saveStringency = SAMFileReader.getDefaultValidationStringency();
+ SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.SILENT);
+ try {
+ final SAMFileReader samReader = new SAMFileReader(new File(TEST_DATA_DIR, "valid.sam"));
+ final Histogram<String> results = executeValidation(samReader, null);
+ Assert.assertTrue(results.isEmpty());
+ } finally {
+ SAMFileReader.setDefaultValidationStringency(saveStringency);
+ }
+ }
+
+ @Test
public void testSortOrder() throws IOException {
Histogram<String> results = executeValidation(new SAMFileReader(new File(TEST_DATA_DIR, "invalid_coord_sort_order.sam")), null);
Assert.assertEquals(results.get(SAMValidationError.Type.RECORD_OUT_OF_ORDER.getHistogramString()).getValue(), 1.0);
@@ -230,6 +243,11 @@ public class ValidateSamFileTest {
public ReferenceSequence getSubsequenceAt(final String contig, final long start, final long stop) {
throw new UnsupportedOperationException();
}
+
+ @Override
+ public void close() throws IOException {
+ //no-op
+ }
});
Assert.assertEquals(results.get(SAMValidationError.Type.INVALID_TAG_NM.getHistogramString()).getValue(), 1.0);
@@ -351,6 +369,32 @@ public class ValidateSamFileTest {
}
@Test
+ public void testPlatformMissing() throws Exception {
+ final SAMFileReader.ValidationStringency saveStringency = SAMFileReader.getDefaultValidationStringency();
+ SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.SILENT);
+ try {
+ final SAMFileReader samReader = new SAMFileReader(new File(TEST_DATA_DIR, "missing_platform_unit.sam"));
+ final Histogram<String> results = executeValidation(samReader, null);
+ Assert.assertEquals(results.get(SAMValidationError.Type.MISSING_PLATFORM_VALUE.getHistogramString()).getValue(), 1.0);
+ } finally {
+ SAMFileReader.setDefaultValidationStringency(saveStringency);
+ }
+ }
+
+ @Test
+ public void testDuplicateRGIDs() throws Exception {
+ final SAMFileReader.ValidationStringency saveStringency = SAMFileReader.getDefaultValidationStringency();
+ SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.SILENT);
+ try {
+ final SAMFileReader samReader = new SAMFileReader(new File(TEST_DATA_DIR, "duplicate_rg.sam"));
+ final Histogram<String> results = executeValidation(samReader, null);
+ Assert.assertEquals(results.get(SAMValidationError.Type.DUPLICATE_READ_GROUP_ID.getHistogramString()).getValue(), 1.0);
+ } finally {
+ SAMFileReader.setDefaultValidationStringency(saveStringency);
+ }
+ }
+
+ @Test
public void testIndexFileValidation() throws Exception {
final SAMFileReader.ValidationStringency saveStringency = SAMFileReader.getDefaultValidationStringency();
SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.SILENT);
@@ -366,6 +410,7 @@ public class ValidateSamFileTest {
private Histogram<String> executeValidation(final SAMFileReader samReader, final ReferenceSequenceFile reference) throws IOException {
final File outFile = File.createTempFile("validation", ".txt");
+ outFile.deleteOnExit();
final PrintWriter out = new PrintWriter(outFile);
new SamFileValidator(out, 8000).setValidateIndex(true).validateSamFileSummary(samReader, reference);
final LineNumberReader reader = new LineNumberReader(new FileReader(outFile));
diff --git a/src/tests/java/net/sf/picard/sam/testers/CleanSamTester.java b/src/tests/java/net/sf/picard/sam/testers/CleanSamTester.java
index 41aca58..ee6997a 100644
--- a/src/tests/java/net/sf/picard/sam/testers/CleanSamTester.java
+++ b/src/tests/java/net/sf/picard/sam/testers/CleanSamTester.java
@@ -18,8 +18,8 @@ public class CleanSamTester extends SamFileTester {
private final String expectedCigar;
private final CleanSam program = new CleanSam();
- public CleanSamTester(final String expectedCigar, final int length) {
- super(length, true);
+ public CleanSamTester(final String expectedCigar, final int readLength, final int defaultChromosomeLength) {
+ super(readLength, true, defaultChromosomeLength);
this.expectedCigar = expectedCigar;
}
@@ -27,14 +27,24 @@ public class CleanSamTester extends SamFileTester {
protected void test() {
try {
final SamFileValidator validator = new SamFileValidator(new PrintWriter(System.out), 8000);
+
+ // Validate it has the expected cigar
validator.setIgnoreWarnings(true);
validator.setVerbose(true, 1000);
validator.setErrorsToIgnore(Arrays.asList(SAMValidationError.Type.MISSING_READ_GROUP));
SAMFileReader samReader = new SAMFileReader(getOutput());
samReader.setValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
- final SAMRecord rec = samReader.iterator().next();
+ final SAMRecordIterator iterator = samReader.iterator();
+ while (iterator.hasNext()) {
+ final SAMRecord rec = iterator.next();
+ Assert.assertEquals(rec.getCigarString(), expectedCigar);
+ if (SAMUtils.hasMateCigar(rec)) {
+ Assert.assertEquals(SAMUtils.getMateCigarString(rec), expectedCigar);
+ }
+ }
samReader.close();
- Assert.assertEquals(rec.getCigarString(), expectedCigar);
+
+ // Run validation on the output file
samReader = new SAMFileReader(getOutput());
final boolean validated = validator.validateSamFileVerbose(samReader, null);
samReader.close();
diff --git a/src/tests/java/net/sf/picard/sam/testers/SamFileTester.java b/src/tests/java/net/sf/picard/sam/testers/SamFileTester.java
index 422efe7..d92292c 100644
--- a/src/tests/java/net/sf/picard/sam/testers/SamFileTester.java
+++ b/src/tests/java/net/sf/picard/sam/testers/SamFileTester.java
@@ -18,7 +18,7 @@ import java.util.Map;
public abstract class SamFileTester {
public static final String TEST_DATA_BASE_DIR = "testdata/net/sf/picard/sam/";
- private final SAMRecordSetBuilder samRecordSetBuilder = new SAMRecordSetBuilder();
+ private final SAMRecordSetBuilder samRecordSetBuilder;
protected final Map<String, Boolean> duplicateFlags = new HashMap<String, Boolean>();
private File outputDir;
private File output;
@@ -27,11 +27,19 @@ public abstract class SamFileTester {
private boolean deleteOnExit = true;
private final ArrayList<String> args = new ArrayList<String>();
- public SamFileTester(final int length, final boolean deleteOnExit) {
+ public SamFileTester(final int readLength, final boolean deleteOnExit, final int defaultChromosomeLength) {
this.deleteOnExit = deleteOnExit;
- samRecordSetBuilder.setReadLength(length);
+ this.samRecordSetBuilder = new SAMRecordSetBuilder(true, SAMFileHeader.SortOrder.coordinate, true, defaultChromosomeLength);
+ samRecordSetBuilder.setReadLength(readLength);
+ setOutputDir();
}
+ public SamFileTester(final int readLength, final boolean deleteOnExit) {
+ this.deleteOnExit = deleteOnExit;
+ this.samRecordSetBuilder = new SAMRecordSetBuilder();
+ samRecordSetBuilder.setReadLength(readLength);
+ setOutputDir();
+ }
public File getOutput() {
return output;
@@ -45,6 +53,13 @@ public abstract class SamFileTester {
return outputDir;
}
+ private void setOutputDir() {
+ this.outputDir = IoUtil.createTempDir(this.getClass().getSimpleName() + ".", ".tmp");
+ if(deleteOnExit){
+ outputDir.deleteOnExit();
+ }
+ }
+
public void setNoMateCigars(final boolean value) {
this.noMateCigars = value;
}
@@ -182,10 +197,6 @@ public abstract class SamFileTester {
*/
public void runTest() {
if (getProgram() != null) {
- outputDir = IoUtil.createTempDir(this.getClass().getSimpleName() + ".", ".tmp");
- if(deleteOnExit){
- outputDir.deleteOnExit();
- }
final File input = createInputFile();
output = new File(outputDir, "output.sam");
diff --git a/src/tests/java/net/sf/picard/util/ClippingUtilityTest.java b/src/tests/java/net/sf/picard/util/ClippingUtilityTest.java
index bb4e1a1..2fe7ff9 100644
--- a/src/tests/java/net/sf/picard/util/ClippingUtilityTest.java
+++ b/src/tests/java/net/sf/picard/util/ClippingUtilityTest.java
@@ -23,86 +23,358 @@
*/
package net.sf.picard.util;
+import net.sf.picard.sam.ReservedTagConstants;
import net.sf.picard.util.IlluminaUtil.IlluminaAdapterPair;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMRecord;
-import org.testng.annotations.Test;
-import org.testng.annotations.DataProvider;
-import org.testng.Assert;
+import net.sf.samtools.util.SequenceUtil;
import net.sf.samtools.util.StringUtil;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.HashMap;
+import java.util.Map;
/**
*
*/
public class ClippingUtilityTest {
- @Test(dataProvider="clipTestData")
- public void testBasicClip(final String testName, final String read, final String clip, final int minMatch, final double errRate, final int expected) {
- final byte[] r = (read == null) ? null : StringUtil.stringToBytes(read);
- final byte[] c = (clip == null) ? null : StringUtil.stringToBytes(clip);
-
- final int result = ClippingUtility.findIndexOfClipSequence(r, c, minMatch, errRate);
- Assert.assertEquals(result, expected, testName);
- }
-
- @Test(dataProvider="clipPairedTestData")
- public void testPairedEndClip(final String testName, final String read1, final String read2, final AdapterPair expected) {
-
- final SAMRecord rec1 = new SAMRecord(new SAMFileHeader());
- rec1.setReadString(read1);
- rec1.setFirstOfPairFlag(true);
- final SAMRecord rec2 = new SAMRecord(new SAMFileHeader());
- rec2.setReadString(read2);
- rec2.setSecondOfPairFlag(true);
-
- final AdapterPair result = ClippingUtility.adapterTrimIlluminaPairedReads(rec1, rec2,
- new AdapterPair[] { IlluminaAdapterPair.INDEXED, IlluminaAdapterPair.PAIRED_END });
- if (result != null) {
- Assert.assertEquals(result.getName(), expected.getName(), testName);
- }
- else {
- Assert.assertEquals(result, expected, testName);
- }
- }
+ @Test(dataProvider="clipTestData")
+ public void testBasicClip(final String testName, final String read, final String clip, final int minMatch, final double errRate, final int expected) {
+ final byte[] r = (read == null) ? null : StringUtil.stringToBytes(read);
+ final byte[] c = (clip == null) ? null : StringUtil.stringToBytes(clip);
+
+ final int result = ClippingUtility.findIndexOfClipSequence(r, c, minMatch, errRate);
+ Assert.assertEquals(result, expected, testName);
+
+ }
+
+
+
+ @Test(dataProvider = "clipTestData")
+ public void testSingleEndSamRecordClip(final String testName, final String read, final String clip, final int minMatch,
+ final double errRate, final int expected) {
+ if (read == null) return; // Silly case
+
+ final SingleEndAdapter adapter = new SingleEndAdapter(testName, clip);
+
+ for (final boolean reverse : new boolean[]{false, true}) {
+ final SAMRecord rec = new SAMRecord(null);
+ if (reverse) {
+ rec.setReadString(SequenceUtil.reverseComplement(read));
+ rec.setReadNegativeStrandFlag(true);
+ } else {
+ rec.setReadString(read);
+ }
+
+ final AdapterPair matchedAdapter = ClippingUtility.adapterTrimIlluminaSingleRead(rec, minMatch, errRate, adapter);
+ if (expected == -1) {
+ Assert.assertNull(matchedAdapter, testName);
+ Assert.assertNull(rec.getAttribute(ReservedTagConstants.XT), testName);
+ } else {
+ Assert.assertEquals(matchedAdapter, adapter, testName);
+ Assert.assertEquals(rec.getAttribute(ReservedTagConstants.XT), expected + 1, testName);
+
+ // Test that if minMatch is decreased, it still matches
+ for (int i = 1; i < minMatch - 3; ++i) {
+ Assert.assertEquals(ClippingUtility.adapterTrimIlluminaSingleRead(rec, minMatch - i, errRate, adapter), adapter, testName);
+ }
+
+ // Skip this test for high error rates, because almost anything will match.
+ if (errRate < 0.5) {
+ // Test that if minMatch is increased, it now fails to match
+ Assert.assertNull(ClippingUtility.adapterTrimIlluminaSingleRead(rec, minMatch + 1, errRate, adapter), testName);
+
+ // Test that if errRate is increased, it still matches
+ Assert.assertNotNull(ClippingUtility.adapterTrimIlluminaSingleRead(rec, minMatch, errRate + 0.1, adapter), testName);
+ }
+
+ // Very low error threshold should cause match failure
+ Assert.assertNull(ClippingUtility.adapterTrimIlluminaSingleRead(rec, minMatch, 0.01, adapter), testName);
+ }
+ }
+
+ }
+
+ @Test(dataProvider="clipPairedTestData")
+ public void testPairedEndClip(final String testName, final String read1, final String read2, final AdapterPair expected) {
+
+ final SAMRecord rec1 = new SAMRecord(new SAMFileHeader());
+ rec1.setReadString(read1);
+ rec1.setFirstOfPairFlag(true);
+ final SAMRecord rec2 = new SAMRecord(new SAMFileHeader());
+ rec2.setReadString(read2);
+ rec2.setSecondOfPairFlag(true);
+
+ final AdapterPair result = ClippingUtility.adapterTrimIlluminaPairedReads(rec1, rec2,
+ IlluminaAdapterPair.INDEXED, IlluminaAdapterPair.PAIRED_END);
+ if (result != null) {
+ Assert.assertEquals(result.getName(), expected.getName(), testName);
+ }
+ else {
+ Assert.assertNull(expected, testName);
+ }
+ }
+
+ @Test
+ public void testOneSidedMatchSupersededByTwoSidedMatch() {
+ final int readLength = 36;
+ final int adapterLength = 30;
+ final String read1 = patchAdapterSubsequenceIntoRead(makeBogusReadString(readLength), IlluminaAdapterPair.SINGLE_END.get3PrimeAdapterInReadOrder(), adapterLength);
+ final String read2 = patchAdapterSubsequenceIntoRead(makeBogusReadString(readLength), IlluminaAdapterPair.SINGLE_END.get5PrimeAdapterInReadOrder(), adapterLength);
+ final SAMRecord rec1 = new SAMRecord(null); rec1.setReadString(read1);
+ final SAMRecord rec2 = new SAMRecord(null); rec2.setReadString(read2);
+ AdapterPair result = ClippingUtility.adapterTrimIlluminaPairedReads(rec1, rec2, adapterLength - 2, 0.1,
+ IlluminaAdapterPair.PAIRED_END, IlluminaAdapterPair.SINGLE_END);
+ Assert.assertEquals(result, IlluminaAdapterPair.SINGLE_END);
+
+ // Confirm that without SINGLE_END, PAIRED_END would one-sided match, if match length is short enough.
+ result = ClippingUtility.adapterTrimIlluminaPairedReads(rec1, rec2, adapterLength/2, 0.1, IlluminaAdapterPair.PAIRED_END);
+ Assert.assertEquals(result, IlluminaAdapterPair.PAIRED_END);
+
+ // However, without shorter match length, one-sided match will fail.
+ Assert.assertNull(ClippingUtility.adapterTrimIlluminaPairedReads(rec1, rec2, adapterLength - 2, 0.1, IlluminaAdapterPair.PAIRED_END));
+ }
+
+ @Test(dataProvider = "testAdapterInAllReadPositionsDataProvider")
+ public void testAdapterInAllReadPositions(final int readLength) {
+ final int minAdapterLength = 6;
+ for (final IlluminaAdapterPair adapterPair : IlluminaAdapterPair.values()) {
+ final AdapterMarker marker = new AdapterMarker(adapterPair);
+ for (int adapterPosition = 0; adapterPosition < readLength; ++adapterPosition) {
+ final SAMRecord rec = createSamRecordWithAdapterSequence(readLength, adapterPair, adapterPosition);
+ final AdapterPair matchedAdapter = ClippingUtility.adapterTrimIlluminaSingleRead(rec, minAdapterLength, 0.1, adapterPair);
+ final Object xt = rec.getAttribute(ReservedTagConstants.XT);
+
+ rec.setAttribute(ReservedTagConstants.XT, null);
+ final AdapterPair truncatedAdapter = marker.adapterTrimIlluminaSingleRead(rec, minAdapterLength, 0.1);
+ final Object xtFromMarker = rec.getAttribute(ReservedTagConstants.XT);
+
+ if (adapterPosition <= readLength - minAdapterLength) {
+ Assert.assertEquals(matchedAdapter, adapterPair, "Failed at position " + adapterPosition);
+ Assert.assertEquals((Integer)xt, Integer.valueOf(adapterPosition + 1));
+ Assert.assertNotNull(truncatedAdapter);
+ Assert.assertEquals((Integer)xtFromMarker, Integer.valueOf(adapterPosition + 1));
+ } else {
+ Assert.assertNull(matchedAdapter);
+ Assert.assertNull(xt);
+ Assert.assertNull(truncatedAdapter);
+ Assert.assertNull(xtFromMarker);
+ }
+ }
+ }
+ }
+
+ private SAMRecord createSamRecordWithAdapterSequence(final int readLength, final IlluminaAdapterPair adapterPair, final int adapterPosition) {
+ final String adapterString = adapterPair.get3PrimeAdapterInReadOrder();
+ final int replacementLength = Math.min(adapterString.length(), readLength - adapterPosition);
+ final String adapterSubstring = adapterString.substring(0, replacementLength);
+ final String readBases = replaceSubstring(makeBogusReadString(readLength), adapterSubstring, adapterPosition, adapterSubstring.length());
+ final SAMRecord rec = new SAMRecord(null);
+ rec.setReadString(readBases);
+ return rec;
+ }
+
+ @DataProvider(name="testAdapterInAllReadPositionsDataProvider")
+ public Object[][] testAdapterInAllReadPositionsDataProvider() {
+ return new Object[][]{{100}, {36}};
+ }
@DataProvider(name="clipTestData")
public Object[][] getClipTestData() {
final String FORWARD = IlluminaAdapterPair.PAIRED_END.get3PrimeAdapter();
final String SE_FORWARD = IlluminaAdapterPair.SINGLE_END.get3PrimeAdapter();
final String REVERSE = IlluminaAdapterPair.PAIRED_END.get5PrimeAdapterInReadOrder();
- return new Object[][] {
- new Object[] {"Simple test 1", "AAAAACCCCCAGATCGGAAGAGCG", "AGATCGGAAGAGCG", 6, 0.15, 10},
- new Object[] {"Simple test 2", "AAAAACCCCCGGGGGAGATCGGAAGAGCG", "AGATCGGAAGAGCG", 6, 0.15, 15},
- new Object[] {"No adapter", "AAAAACCCCCGGGGGTTTTT", "AGATCGGAAGAGCG", 6, 0.15, -1},
- new Object[] {"Partial adapter", "AAAAACCCCCAGATCGGAA", "AGATCGGAAGAGCG", 6, 0.15, 10},
+ return new Object[][] {
+ {"Simple test 1", "AAAAACCCCCAGATCGGAAGAGCA", "AGATCGGAAGAGCG", 14, 0.15, 10},
+ {"Simple test 2", "AAAAACCCCCGGGGGAGATCGGAAGAGCA", "AGATCGGAAGAGCG", 14, 0.15, 15},
+ {"No adapter", "AAAAACCCCCGGGGGTTTTT", "AGATCGGAAGAGCG", 6, 0.15, -1},
+ {"Partial adapter", "AAAAACCCCCTGATCGGAA", "AGATCGGAAGAGCG", 9, 0.15, 10},
// no longer support clips in middle of read
-// new Object[] {"Adapter+Primer", "AAAAACCCCCAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG", "AGATCGGAAGAGCG", 6, 0.15, 10},
- new Object[] {"No sequence", null, "AGATCGGAAGAGCG", 6, 0.15, -1},
- new Object[] {"Read too short", "AGATCGGAAG", "AGATCGGAAGAGCG", 11, 0.15, -1},
- new Object[] {"All No Calls", "AAACCCNNNNNNNNNNNNNNNNNNNN", "AGATCGGAAGAGCG", 6, 0.15, -1},
- new Object[] {"From Test Data1", "CGGCATTCCTGCTGAACCGAGATCGGAAGAGCGTCGTGTAGGGAAAGGGGGTGGATCTCGGTGGGCGGCGTGTTGT", REVERSE, 5, 0.15, 19},
- new Object[] {"From Test Data2a", "CGGAAGAGCGGTTCAGCAGGAATGCCGAGATCGGAA", REVERSE, 5, 0.14, 27}, // XT:i:28
- new Object[] {"From Test Data2b", "CGGAAGAGCGGTTCAGCAGGAATGCCGAGATCGGAA", REVERSE, 10, 0.14, -1}, // only matches 9
- new Object[] {"From PE Test Data1", "CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGGT", FORWARD, 5, 0.14, 19},
- new Object[] {"From PE Test Data2", "CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGGT", REVERSE, 5, 0.14, -1},
- new Object[] {"From Test 8-clipped", "TGGGGTGGTTATTGTTGATTTTTGTTTGTGTGTTAGGTTGTTTGTGTTAGTTTTTTATTTTATTTTCGAGATCGGA", FORWARD, 8, 0.14, 68},
- new Object[] {"50% can be bad", "AAAAACCCCCAGATCGGAAGAGCG", "AGATCGGAAGAGCG", 5, 0.5, 18}, // 18?
-
- new Object[] {"From 30E54AAXX.5.a", "ATATCTGAAGATCTCGTATGCCGTCTTCTGCTTG", "AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG", 10, 0.14, 0}, // 0!? From KT test case
- new Object[] {"From 30E54AAXX.5.b", "ATATCTGAAGATCTCGTATGCCGTCTTCTGCTTG", SE_FORWARD, 10, 0.14, 0}, // 1?? From KT test case
+// {"Adapter+Primer", "AAAAACCCCCAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG", "AGATCGGAAGAGCG", 6, 0.15, 10},
+ {"No sequence", null, "AGATCGGAAGAGCG", 6, 0.15, -1},
+ {"Read too short", "AGATCGGAAG", "AGATCGGAAGAGCG", 11, 0.15, -1},
+ {"All No Calls", "AAACCCNNNNNNNNNNNNNNNNNNNN", "AGATCGGAAGAGCG", 6, 0.15, -1},
+ {"From Test Data1", "CGGCATTCCTGCTGAACCGAGATCGGAAGAGCGTCGTGTAGGGAAAGGGGGTGGATCTCGGTGGGCGGCGTGTTGT", REVERSE, 57, 0.15, 19},
+ {"From Test Data2a", "CGGAAGAGCGGTTCAGCAGGAATGCCGAGATCCGAA", REVERSE, 9, 0.14, 27}, // XT:i:28
+ {"From Test Data2b", "CGGAAGAGCGGTTCAGCAGGAATGCCGAGATCGGAA", REVERSE, 10, 0.14, -1}, // only matches 9
+ {"From PE Test Data1", "CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGGT", FORWARD, 17, 0.14, 19},
+ {"From PE Test Data2", "CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGGT", REVERSE, 5, 0.14, -1},
+ new Object[] {"From Test 8-clipped", "TGGGGTGGTTATTGTTGATTTTTGTTTGTGTGTTAGGTTGTTTGTGTTAGTTTTTTATTTTATTTTCGAGATCGAA", FORWARD, 8, 0.14, 68},
+ {"50% can be bad", "AAAAACCCCCAGGTCGGAAGAGCG", "AGATCGGAAGAGCG", 5, 0.5, 18}, // 18?
+
+ {"From 30E54AAXX.5.a", "ATATCTGAAGATCTCGTATGCCGTCTTCTGCTTG", "AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG", 34, 0.14, 0}, // 0!? From KT test case
+ {"From 30E54AAXX.5.b", "ATATCTGAAGATCTCGTATGCCGTCTTCTGCTTG", SE_FORWARD, 34, 0.14, 0}, // 1?? From KT test case
};
}
@DataProvider(name="clipPairedTestData")
public Object[][] getClipPairedTestData() {
return new Object[][] {
- new Object[] {"Basic positive paired test matching", "CTACTGGCGCTGAAACTGAGCAGCCAAGCAGATCGG", "GCTTGGCTGCTCAGTTTCAGCGCCAGTAGAGATCGG", IlluminaAdapterPair.INDEXED},
- // Tbis matches on one side and matches at higher stringency on that one side
- new Object[] {"Basic positive one-sided test matching", "CTACTGGCGCTGAAAAGATCGGAAGAGCGGTTCAGC", "AAAAAATTTTTTCCCCCCGGGGGGAAAAAATTTTTT", IlluminaAdapterPair.PAIRED_END},
- // Tbis matches on one side and does not match at higher stringency on that one side
- new Object[] {"Basic negative one-sided test matching", "GGCGCTGAAACTACTGGCGCTGAAAAGATCGGAAGA", "AAAAAATTTTTTCCCCCCGGGGGGAAAAAATTTTTT", null},
- // These match but at different positions. No clip should be done.
- new Object[] {"Mis-match paired test matching", "CTACTGGCGCTGAAACTGAGCAGCCAAGCAGATCGG", "AGCTTGGCTGCTCAGTTTCAGCGCCAGTAGAGATCG", null},
+ {"Basic positive paired test matching", "CTACTGGCGCTGAAACTGAGCAGCCAAGCAGATCGG", "GCTTGGCTGCTCAGTTTCAGCGCCAGTAGAGATCGG", IlluminaAdapterPair.INDEXED},
+ // This matches on first end and matches at higher stringency on that one side
+ {"Basic positive first end one-sided test matching", "CTACTGGCGCTGAAAAGATCGGAAGAGCGGTTCAGC", "AAAAAATTTTTTCCCCCCGGGGGGAAAAAATTTTTT", IlluminaAdapterPair.PAIRED_END},
+ // This matches on second end and matches at higher stringency on that one side
+ {"Basic positive second end one-sided test matching", "AAAAAATTTTTTCCCCCCGGGGGGAAAAAATTTTTT", "AAAAAATTTTTTCCCAGATCGGAAGAGCGTCGTGTA", IlluminaAdapterPair.PAIRED_END},
+ // This matches on one side and does not match at higher stringency on that one side
+ {"Basic negative one-sided test matching", "GGCGCTGAAACTACTGGCGCTGAAAAGATCGGAAGA", "AAAAAATTTTTTCCCCCCGGGGGGAAAAAATTTTTT", null},
+ // These match but at different positions. No clip should be done.
+ {"Mis-match paired test matching", "CTACTGGCGCTGAAACTGAGCAGCCAAGCAGATCGG", "AGCTTGGCTGCTCAGTTTCAGCGCCAGTAGAGATCG", null},
};
}
+
+ private static class SingleEndAdapter implements AdapterPair {
+ private final String name;
+ private final String threePrimeAdapter;
+
+ private SingleEndAdapter(final String name, final String threePrimeAdapter) {
+ this.name = name;
+ this.threePrimeAdapter = threePrimeAdapter;
+ }
+
+ @Override
+ public String get3PrimeAdapter() {
+ return threePrimeAdapter;
+ }
+
+ @Override
+ public String get3PrimeAdapterInReadOrder() {
+ return threePrimeAdapter;
+ }
+
+ @Override
+ public byte[] get3PrimeAdapterBytes() {
+ return StringUtil.stringToBytes(threePrimeAdapter);
+ }
+
+ @Override
+ public byte[] get3PrimeAdapterBytesInReadOrder() {
+ return get3PrimeAdapterBytes();
+ }
+
+ @Override
+ public String get5PrimeAdapter() {
+ throw new UnsupportedOperationException();
+ }
+
+ @Override
+ public String get5PrimeAdapterInReadOrder() {
+ throw new UnsupportedOperationException();
+ }
+
+ @Override
+ public byte[] get5PrimeAdapterBytes() {
+ throw new UnsupportedOperationException();
+ }
+
+ @Override
+ public byte[] get5PrimeAdapterBytesInReadOrder() {
+ throw new UnsupportedOperationException();
+ }
+
+ @Override
+ public String getName() {
+ return name;
+ }
+
+ }
+
+ /**
+ * @return A String of given length with 6 As, 6 Cs, 6 Gs, etc. until length is reached.
+ */
+ private static String makeBogusReadString(final int len) {
+ final StringBuilder builder = new StringBuilder(len);
+ final Map<Character, Character> nextChar = new HashMap<Character, Character>();
+ nextChar.put('A', 'C');
+ nextChar.put('C', 'G');
+ nextChar.put('G', 'T');
+ nextChar.put('T', 'A');
+ for (char curChar = 'A'; true; curChar = nextChar.get(curChar)) {
+ for (int i = 0; i < 6; ++i) {
+ if (builder.length() == len) return builder.toString();
+ builder.append(curChar);
+ }
+ }
+ }
+
+ private static String patchAdapterSubsequenceIntoRead(final String read, final String adapter, final int length) {
+ return replaceSubstring(read, adapter.substring(0, length), read.length() - length, read.length());
+ }
+
+ private static String replaceSubstring(final String s, final String replacement, final int position, final int charsToReplace) {
+ final StringBuilder sb = new StringBuilder(s);
+ sb.replace(position, position + charsToReplace, replacement);
+ return sb.toString();
+ }
+
+
+ @Test
+ public void testAdapterTruncation() {
+ final AdapterMarker marker = new AdapterMarker(30,
+ IlluminaUtil.IlluminaAdapterPair.INDEXED,
+ IlluminaUtil.IlluminaAdapterPair.DUAL_INDEXED,
+ IlluminaUtil.IlluminaAdapterPair.NEXTERA_V2,
+ IlluminaUtil.IlluminaAdapterPair.FLUIDIGM);
+ // INDEXED and DUAL_INDEXED should collapse at length 30
+ Assert.assertTrue(marker.getAdapters().length < 4, "Did not collapse: " + marker.getAdapters().length);
+ }
+
+ /**
+ * Confirm that after the requisite number of sightings of adapter, the list is trimmed
+ */
+ @Test(dataProvider = "testAdapterListTruncationDataProvider")
+ public void testAdapterListTruncation(final IlluminaAdapterPair adapterPair) {
+ final int thresholdForTruncatingAdapterList = 20;
+ final int readLength = 100;
+
+ // Throw all the adapter pairs into the marker. There is some danger in doing this because
+ // IlluminaAdapterPair.ALTERNATIVE_SINGLE_END has 3' that is a substring of some of the others. In the enum it appears
+ // last so it is tested last.
+ final AdapterMarker marker =
+ new AdapterMarker(IlluminaUtil.IlluminaAdapterPair.values()).
+ setThresholdForSelectingAdaptersToKeep(thresholdForTruncatingAdapterList);
+ int adapterPosition = 1;
+
+ Assert.assertTrue(adapterPosition + thresholdForTruncatingAdapterList < readLength - ClippingUtility.MIN_MATCH_BASES,
+ "Test is configured improperly -- eventually will not be enough adapter bases in read.");
+
+ int originalNumberOfAdapters = marker.getAdapters().length;
+ for (int i = 0; i < thresholdForTruncatingAdapterList; ++i) {
+
+ // First, a read with no adapter in it.
+ SAMRecord rec = new SAMRecord(null);
+ rec.setReadString(makeBogusReadString(readLength));
+ AdapterPair matchedPair = marker.adapterTrimIlluminaSingleRead(rec);
+ Assert.assertNull(matchedPair);
+ Assert.assertNull(rec.getAttribute(ReservedTagConstants.XT));
+
+ // Adapter list should not be truncated yet
+ Assert.assertEquals(marker.getAdapters().length, originalNumberOfAdapters);
+
+ // Then, a record with some adapter sequence in it.
+ rec = createSamRecordWithAdapterSequence(readLength, adapterPair, adapterPosition);
+ matchedPair = marker.adapterTrimIlluminaSingleRead(rec);
+ Assert.assertNotNull(matchedPair);
+ Assert.assertEquals(rec.getIntegerAttribute(ReservedTagConstants.XT).intValue(), adapterPosition + 1,
+ rec.getReadString() + " matched " + matchedPair);
+
+ // Put adapter in different place next time.
+ adapterPosition++;
+ }
+
+ Assert.assertEquals(marker.getAdapters().length, 1, "Did not truncate adapter list to 1 element");
+ Assert.assertTrue(marker.getAdapters()[0].getName().contains(adapterPair.getName()),
+ String.format("Expected '%s' to contain '%s'", marker.getAdapters()[0].getName(), adapterPair.getName()));
+ }
+
+ @DataProvider(name="testAdapterListTruncationDataProvider")
+ public Object[][] testAdapterListTruncationDataProvider() {
+ Object[][] ret = new Object[IlluminaAdapterPair.values().length][];
+ for (int i = 0; i < ret.length; ++i) {
+ ret[i] = new Object[]{IlluminaAdapterPair.values()[i]};
+ }
+ return ret;
+ }
}
diff --git a/src/tests/java/net/sf/picard/util/IntervalListTest.java b/src/tests/java/net/sf/picard/util/IntervalListTest.java
new file mode 100644
index 0000000..39f2b39
--- /dev/null
+++ b/src/tests/java/net/sf/picard/util/IntervalListTest.java
@@ -0,0 +1,387 @@
+package net.sf.picard.util;
+
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMSequenceRecord;
+import net.sf.samtools.util.CollectionUtil;
+import org.testng.Assert;
+import org.testng.annotations.*;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.LinkedList;
+import java.util.List;
+
+/**
+ * Tests the IntervalList class
+ */
+public class IntervalListTest {
+
+
+ final SAMFileHeader fileHeader;
+
+ final IntervalList list1, list2, list3;
+
+ public IntervalListTest() {
+ fileHeader = IntervalList.fromFile(new File("testdata/net/sf/picard/intervallist/IntervalListchr123_empty.interval_list")).getHeader();
+ fileHeader.setSortOrder(SAMFileHeader.SortOrder.unsorted);
+
+ list1 = new IntervalList(fileHeader);
+ list2 = new IntervalList(fileHeader);
+ list3 = new IntervalList(fileHeader);
+
+
+ list1.add(new Interval("1", 1, 100)); //de-facto: 1:1-200 1:202-300 2:100-150 2:200-300
+ list1.add(new Interval("1", 101, 200));
+ list1.add(new Interval("1", 202, 300));
+ list1.add(new Interval("2", 200, 300));
+ list1.add(new Interval("2", 100, 150));
+
+ list2.add(new Interval("1", 50, 150)); //de-facto 1:50-150 1:301-500 2:1-150 2:250-270 2:290-400
+ list2.add(new Interval("1", 301, 500));
+ list2.add(new Interval("2", 1, 150));
+ list2.add(new Interval("2", 250, 270));
+ list2.add(new Interval("2", 290, 400));
+
+ list3.add(new Interval("1", 25, 400)); //de-facto 1:25-400 2:200-600 3:50-470
+ list3.add(new Interval("2", 200, 600));
+ list3.add(new Interval("3", 50, 470));
+ }
+
+
+ @DataProvider(name = "intersectData")
+ public Object[][] intersectData() {
+ final IntervalList intersect123 = new IntervalList(fileHeader);
+ final IntervalList intersect12 = new IntervalList(fileHeader);
+ final IntervalList intersect13 = new IntervalList(fileHeader);
+ final IntervalList intersect23 = new IntervalList(fileHeader);
+
+ intersect123.add(new Interval("1", 50, 150));
+ intersect123.add(new Interval("2", 250, 270));
+ intersect123.add(new Interval("2", 290, 300));
+
+ intersect12.add(new Interval("1", 50, 150));
+ intersect12.add(new Interval("2", 100, 150));
+ intersect12.add(new Interval("2", 250, 270));
+ intersect12.add(new Interval("2", 290, 300));
+
+ intersect13.add(new Interval("1", 25, 200));
+ intersect13.add(new Interval("1", 202, 300));
+ intersect13.add(new Interval("2", 200, 300));
+
+ intersect23.add(new Interval("1", 50, 150));
+ intersect23.add(new Interval("1", 301, 400));
+ intersect23.add(new Interval("2", 250, 270));
+ intersect23.add(new Interval("2", 290, 400));
+
+
+ return new Object[][]{
+ new Object[]{Arrays.asList(list1, list2, list3), intersect123},
+ new Object[]{Arrays.asList(list1, list2), intersect12},
+ new Object[]{Arrays.asList(list2, list1), intersect12},
+ new Object[]{Arrays.asList(list2, list3), intersect23},
+ new Object[]{Arrays.asList(list3, list2), intersect23},
+ new Object[]{Arrays.asList(list1, list3), intersect13},
+ new Object[]{Arrays.asList(list3, list1), intersect13}
+ };
+ }
+
+ @Test(dataProvider = "intersectData")
+ public void testIntersectIntervalLists(final List<IntervalList> lists, final IntervalList list) {
+ Assert.assertEquals(
+ CollectionUtil.makeCollection(IntervalList.intersection(lists).iterator()),
+ CollectionUtil.makeCollection(list.iterator()));
+ }
+
+ @DataProvider(name = "mergeData")
+ public Object[][] mergeData() {
+ final IntervalList merge123 = new IntervalList(fileHeader);
+ final IntervalList merge12 = new IntervalList(fileHeader);
+ final IntervalList merge23 = new IntervalList(fileHeader);
+ final IntervalList merge13 = new IntervalList(fileHeader);
+
+
+ merge123.add(new Interval("1", 1, 100)); //de-facto: 1:1-200 1:202-300 2:100-150 2:200-300
+ merge123.add(new Interval("1", 101, 200));
+ merge123.add(new Interval("1", 202, 300));
+ merge123.add(new Interval("2", 200, 300));
+ merge123.add(new Interval("2", 100, 150));
+
+ merge123.add(new Interval("1", 50, 150)); //de-facto 1:50-150 1:301-500 2:1-150 2:250-270 2:290-400
+ merge123.add(new Interval("1", 301, 500));
+ merge123.add(new Interval("2", 1, 150));
+ merge123.add(new Interval("2", 250, 270));
+ merge123.add(new Interval("2", 290, 400));
+
+ merge123.add(new Interval("1", 25, 400)); //de-facto 1:25-400 2:200-600 3:50-470
+ merge123.add(new Interval("2", 200, 600));
+ merge123.add(new Interval("3", 50, 470));
+
+
+ merge12.add(new Interval("1", 1, 100)); //de-facto: 1:1-200 1:202-300 2:100-150 2:200-300
+ merge12.add(new Interval("1", 101, 200));
+ merge12.add(new Interval("1", 202, 300));
+ merge12.add(new Interval("2", 200, 300));
+ merge12.add(new Interval("2", 100, 150));
+
+ merge12.add(new Interval("1", 50, 150)); //de-facto 1:50-150 1:301-500 2:1-150 2:250-270 2:290-400
+ merge12.add(new Interval("1", 301, 500));
+ merge12.add(new Interval("2", 1, 150));
+ merge12.add(new Interval("2", 250, 270));
+ merge12.add(new Interval("2", 290, 400));
+
+ merge23.add(new Interval("1", 50, 150)); //de-facto 1:50-150 1:301-500 2:1-150 2:250-270 2:290-400
+ merge23.add(new Interval("1", 301, 500));
+ merge23.add(new Interval("2", 1, 150));
+ merge23.add(new Interval("2", 250, 270));
+ merge23.add(new Interval("2", 290, 400));
+
+ merge23.add(new Interval("1", 25, 400)); //de-facto 1:25-400 2:200-600 3:50-470
+ merge23.add(new Interval("2", 200, 600));
+ merge23.add(new Interval("3", 50, 470));
+
+
+ merge13.add(new Interval("1", 1, 100)); //de-facto: 1:1-200 1:202-300 2:100-150 2:200-300
+ merge13.add(new Interval("1", 101, 200));
+ merge13.add(new Interval("1", 202, 300));
+ merge13.add(new Interval("2", 200, 300));
+ merge13.add(new Interval("2", 100, 150));
+
+ merge13.add(new Interval("1", 25, 400)); //de-facto 1:25-400 2:200-600 3:50-470
+ merge13.add(new Interval("2", 200, 600));
+ merge13.add(new Interval("3", 50, 470));
+
+
+ return new Object[][]{
+ new Object[]{Arrays.asList(list1, list2, list3), merge123},
+ new Object[]{Arrays.asList(list1, list2), merge12},
+ new Object[]{Arrays.asList(list2, list3), merge23},
+ new Object[]{Arrays.asList(list1, list3), merge13}
+
+ };
+ }
+
+
+ @Test(dataProvider = "mergeData")
+ public void testMergeIntervalLists(final List<IntervalList> lists, final IntervalList list) {
+ Assert.assertEquals(
+ CollectionUtil.makeCollection(IntervalList.concatenate(lists).iterator()),
+ CollectionUtil.makeCollection(list.iterator()));
+ }
+
+
+ @DataProvider(name = "unionData")
+ public Object[][] unionData() {
+ final IntervalList union123 = new IntervalList(fileHeader);
+ final IntervalList union12 = new IntervalList(fileHeader);
+ final IntervalList union13 = new IntervalList(fileHeader);
+ final IntervalList union23 = new IntervalList(fileHeader);
+
+ union123.add(new Interval("1", 1, 500));
+ union123.add(new Interval("2", 1, 150));
+ union123.add(new Interval("2", 200, 600));
+ union123.add(new Interval("3", 50, 470));
+
+ union12.add(new Interval("1", 1, 200));
+ union12.add(new Interval("1", 202, 500));
+ union12.add(new Interval("2", 1, 150));
+ union12.add(new Interval("2", 200, 400));
+
+
+ union23.add(new Interval("1", 25, 500));
+ union23.add(new Interval("2", 1, 150));
+ union23.add(new Interval("2", 200, 600));
+ union23.add(new Interval("3", 50, 470));
+
+ union13.add(new Interval("1", 1, 400));
+ union13.add(new Interval("2", 100, 150));
+ union13.add(new Interval("2", 200, 600));
+ union13.add(new Interval("3", 50, 470));
+
+
+ return new Object[][]{
+ new Object[]{Arrays.asList(list1, list2, list3), union123},
+ new Object[]{Arrays.asList(list1, list2), union12},
+ new Object[]{Arrays.asList(list1, list2), union12},
+ new Object[]{Arrays.asList(list2, list3), union23},
+ new Object[]{Arrays.asList(list2, list3), union23},
+ new Object[]{Arrays.asList(list1, list3), union13},
+ new Object[]{Arrays.asList(list1, list3), union13}
+ };
+ }
+
+ @Test(dataProvider = "unionData", enabled = true)
+ public void testUnionIntervalLists(final List<IntervalList> lists, final IntervalList list) {
+ Assert.assertEquals(
+ CollectionUtil.makeCollection(IntervalList.union(lists).iterator()),
+ CollectionUtil.makeCollection(list.iterator()));
+ }
+
+ @DataProvider(name = "invertData")
+ public Object[][] invertData() {
+ final IntervalList invert1 = new IntervalList(fileHeader);
+ final IntervalList invert2 = new IntervalList(fileHeader);
+ final IntervalList invert3 = new IntervalList(fileHeader);
+
+ final IntervalList full = new IntervalList(fileHeader);
+ final IntervalList fullChopped = new IntervalList(fileHeader);
+ final IntervalList empty = new IntervalList(fileHeader);
+
+
+ invert1.add(new Interval("1", 201, 201));
+ invert1.add(new Interval("1", 301, fileHeader.getSequence("1").getSequenceLength()));
+ invert1.add(new Interval("2", 1, 99));
+ invert1.add(new Interval("2", 151, 199));
+ invert1.add(new Interval("2", 301, fileHeader.getSequence("2").getSequenceLength()));
+ invert1.add(new Interval("3", 1, fileHeader.getSequence("3").getSequenceLength()));
+
+ invert2.add(new Interval("1", 1, 49));
+ invert2.add(new Interval("1", 151, 300));
+ invert2.add(new Interval("1", 501, fileHeader.getSequence("1").getSequenceLength()));
+ invert2.add(new Interval("2", 151, 249));
+ invert2.add(new Interval("2", 271, 289));
+ invert2.add(new Interval("2", 401, fileHeader.getSequence("2").getSequenceLength()));
+ invert2.add(new Interval("3", 1, fileHeader.getSequence("3").getSequenceLength()));
+
+ invert3.add(new Interval("1", 1, 24));
+ invert3.add(new Interval("1", 401, fileHeader.getSequence("1").getSequenceLength()));
+ invert3.add(new Interval("2", 1, 199));
+ invert3.add(new Interval("2", 601, fileHeader.getSequence("2").getSequenceLength()));
+ invert3.add(new Interval("3", 1, 49));
+ invert3.add(new Interval("3", 471, fileHeader.getSequence("3").getSequenceLength()));
+
+ for (final SAMSequenceRecord samSequenceRecord : fileHeader.getSequenceDictionary().getSequences()) {
+ full.add(new Interval(samSequenceRecord.getSequenceName(), 1, samSequenceRecord.getSequenceLength()));
+
+ fullChopped.add(new Interval(samSequenceRecord.getSequenceName(), 1, samSequenceRecord.getSequenceLength() / 2));
+ fullChopped.add(new Interval(samSequenceRecord.getSequenceName(), samSequenceRecord.getSequenceLength() / 2 + 1, samSequenceRecord.getSequenceLength()));
+ }
+
+
+ return new Object[][]{
+ new Object[]{list1, invert1},
+ new Object[]{list2, invert2},
+ new Object[]{list3, invert3},
+ new Object[]{full, empty},
+ new Object[]{empty, full},
+ new Object[]{fullChopped, empty}
+ };
+ }
+
+
+ @Test(dataProvider = "invertData")
+ public void testInvertSquared(final IntervalList list, @SuppressWarnings("UnusedParameters") final IntervalList ignored) throws Exception {
+ final IntervalList inverseSquared = IntervalList.invert(IntervalList.invert(list));
+ final IntervalList originalClone = new IntervalList(list.getHeader());
+
+ for (final Interval interval : list) {
+ originalClone.add(interval);
+ }
+
+ Assert.assertEquals(
+ CollectionUtil.makeCollection(inverseSquared.iterator()),
+ CollectionUtil.makeCollection(originalClone.uniqued().iterator()));
+ }
+
+ @Test(dataProvider = "invertData")
+ public void testInvert(final IntervalList list, final IntervalList inverse) throws Exception {
+ Assert.assertEquals(
+ CollectionUtil.makeCollection(IntervalList.invert(list).iterator()),
+ CollectionUtil.makeCollection(inverse.iterator()));
+ }
+
+
+ @DataProvider(name = "subtractData")
+ public Object[][] subtractData() {
+ final IntervalList subtract12_from_3 = new IntervalList(fileHeader);
+ final IntervalList subtract1_from_2 = new IntervalList(fileHeader);
+ final IntervalList subtract2_from_3 = new IntervalList(fileHeader);
+ final IntervalList subtract1_from_3 = new IntervalList(fileHeader);
+ final IntervalList subtract3_from_1 = new IntervalList(fileHeader);
+
+
+ subtract12_from_3.add(new Interval("1", 201, 201));
+ subtract12_from_3.add(new Interval("2", 401, 600));
+ subtract12_from_3.add(new Interval("3", 50, 470));
+
+ subtract1_from_2.add(new Interval("1", 301, 500));
+ subtract1_from_2.add(new Interval("2", 1, 99));
+ subtract1_from_2.add(new Interval("2", 301, 400));
+
+
+ subtract2_from_3.add(new Interval("1", 25, 49));
+ subtract2_from_3.add(new Interval("1", 151, 300));
+ subtract2_from_3.add(new Interval("2", 200, 249));
+ subtract2_from_3.add(new Interval("2", 271, 289));
+ subtract2_from_3.add(new Interval("2", 401, 600));
+ subtract2_from_3.add(new Interval("3", 50, 470));
+
+ subtract1_from_3.add(new Interval("1", 201, 201));
+ subtract1_from_3.add(new Interval("1", 301, 400));
+ subtract1_from_3.add(new Interval("2", 301, 600));
+ subtract1_from_3.add(new Interval("3", 50, 470));
+
+ subtract3_from_1.add(new Interval("1", 1, 49)); //de-facto 1:25-400 2:200-600 3:50-470
+ subtract3_from_1.add(new Interval("2", 100, 150));
+
+
+ return new Object[][]{
+ new Object[]{CollectionUtil.makeList(list3), CollectionUtil.makeList(list1, list2), subtract12_from_3},
+ new Object[]{CollectionUtil.makeList(list2), CollectionUtil.makeList(list1), subtract1_from_2},
+ new Object[]{CollectionUtil.makeList(list3), CollectionUtil.makeList(list2), subtract2_from_3},
+ new Object[]{CollectionUtil.makeList(list3), CollectionUtil.makeList(list1), subtract1_from_3},
+ };
+ }
+
+
+ @Test(dataProvider = "subtractData")
+ public void testSubtractIntervalLists(final List<IntervalList> fromLists, final List<IntervalList> whatLists, final IntervalList list) {
+ Assert.assertEquals(
+ CollectionUtil.makeCollection(IntervalList.subtract(fromLists, whatLists).iterator()),
+ CollectionUtil.makeCollection(list.iterator()));
+ }
+
+
+ @DataProvider(name = "VCFCompData")
+ public Object[][] VCFCompData() {
+ return new Object[][]{
+ new Object[]{"testdata/net/sf/picard/intervallist/IntervalListFromVCFTest.vcf", "testdata/net/sf/picard/intervallist/IntervalListFromVCFTestComp.interval_list", false},
+ new Object[]{"testdata/net/sf/picard/intervallist/IntervalListFromVCFTest.vcf", "testdata/net/sf/picard/intervallist/IntervalListFromVCFTestCompInverse.interval_list", true},
+ new Object[]{"testdata/net/sf/picard/intervallist/IntervalListFromVCFTestManual.vcf", "testdata/net/sf/picard/intervallist/IntervalListFromVCFTestManualComp.interval_list", false},
+ new Object[]{"testdata/net/sf/picard/intervallist/IntervalListFromVCFTestManual.vcf", "testdata/net/sf/picard/intervallist/IntervalListFromVCFTestCompInverseManual.interval_list", true}
+ };
+ }
+
+
+ @Test(dataProvider = "VCFCompData")
+ public void testFromVCF(final String vcf, final String compInterval, final boolean invertVCF) {
+
+ final File vcfFile = new File(vcf);
+ final File compIntervalFile = new File(compInterval);
+
+ final IntervalList compList = IntervalList.fromFile(compIntervalFile);
+ final IntervalList list = invertVCF ? IntervalList.invert(IntervalList.fromVcf(vcfFile)) : IntervalList.fromVcf(vcfFile);
+
+ compList.getHeader().getSequenceDictionary().assertSameDictionary(list.getHeader().getSequenceDictionary());
+
+ final Collection<Interval> intervals = CollectionUtil.makeCollection(list.iterator());
+ final Collection<Interval> compIntervals = CollectionUtil.makeCollection(compList.iterator());
+
+ //assert that the intervals correspond
+ Assert.assertEquals(intervals, compIntervals);
+
+ final List<String> intervalNames = new LinkedList<String>();
+ final List<String> compIntervalNames = new LinkedList<String>();
+
+ for (final Interval interval : intervals) {
+ intervalNames.add(interval.getName());
+ }
+ for (final Interval interval : compIntervals) {
+ compIntervalNames.add(interval.getName());
+ }
+ //assert that the names match
+ Assert.assertEquals(intervalNames, compIntervalNames);
+
+ }
+
+}
\ No newline at end of file
diff --git a/src/tests/java/net/sf/picard/util/IntervalListToolsTest.java b/src/tests/java/net/sf/picard/util/IntervalListToolsTest.java
index 1b7b367..7b66603 100644
--- a/src/tests/java/net/sf/picard/util/IntervalListToolsTest.java
+++ b/src/tests/java/net/sf/picard/util/IntervalListToolsTest.java
@@ -32,6 +32,9 @@ import java.io.File;
import java.io.FilenameFilter;
import java.io.IOException;
import java.text.DecimalFormat;
+import java.util.List;
+import java.util.SortedSet;
+import java.util.TreeSet;
/**
* Very basic test for scatter functionality in IntervalListTools
@@ -143,4 +146,22 @@ public class IntervalListToolsTest {
}
return result;
}
+
+ @Test
+ public void testMerges() {
+ SortedSet<Interval> intervals = new TreeSet<Interval>() {{
+ add(new Interval("1", 500, 600, false, "foo"));
+ add(new Interval("1", 550, 650, false, "bar"));
+ add(new Interval("1", 625, 699, false, "splat"));
+ }};
+
+ Interval out = IntervalList.merge(intervals, false);
+ Assert.assertEquals(out.getStart(), 500);
+ Assert.assertEquals(out.getEnd(), 699);
+
+ intervals.add(new Interval("1", 626, 629, false, "whee"));
+ out = IntervalList.merge(intervals, false);
+ Assert.assertEquals(out.getStart(), 500);
+ Assert.assertEquals(out.getEnd(), 699);
+ }
}
diff --git a/src/tests/java/net/sf/picard/vcf/SplitVcfsTest.java b/src/tests/java/net/sf/picard/vcf/SplitVcfsTest.java
index 18caa9c..c64c743 100644
--- a/src/tests/java/net/sf/picard/vcf/SplitVcfsTest.java
+++ b/src/tests/java/net/sf/picard/vcf/SplitVcfsTest.java
@@ -5,7 +5,7 @@ import net.sf.samtools.util.CloseableIterator;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext.Type;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterBuilder;
import org.broadinstitute.variant.vcf.VCFFileReader;
import org.testng.Assert;
import org.testng.annotations.AfterClass;
@@ -71,11 +71,10 @@ public class SplitVcfsTest {
final File INPUT = new File("/Volumes/Disko Segundo/splitvcfs/CEUTrio.HiSeq.WGS.b37.snps_and_indels.recalibrated.filtered.phased.CURRENT.vcf.gz");
final VCFFileReader reader = new VCFFileReader(INPUT);
- final VariantContextWriter OUTPUT =
- VariantContextWriterFactory.create(
- new File("/Volumes/shm/CEUTrio-REDUCED.vcf"),
- null,
- VariantContextWriterFactory.NO_OPTIONS);
+ final VariantContextWriter OUTPUT = new VariantContextWriterBuilder()
+ .setOutputFile("/Volumes/shm/CEUTrio-REDUCED.vcf")
+ .clearOptions()
+ .build();
OUTPUT.writeHeader(reader.getFileHeader());
final CloseableIterator<VariantContext> iterator = reader.iterator();
diff --git a/src/tests/java/net/sf/picard/vcf/VcfFormatConverterTest.java b/src/tests/java/net/sf/picard/vcf/VcfFormatConverterTest.java
index 2300488..dfa7124 100644
--- a/src/tests/java/net/sf/picard/vcf/VcfFormatConverterTest.java
+++ b/src/tests/java/net/sf/picard/vcf/VcfFormatConverterTest.java
@@ -26,6 +26,7 @@
package net.sf.picard.vcf;
import net.sf.picard.PicardException;
+import org.broad.tribble.Tribble;
import org.testng.Assert;
import org.testng.annotations.Test;
@@ -91,7 +92,7 @@ public class VcfFormatConverterTest {
}
outputFile.deleteOnExit();
- new File(outputFile.getAbsolutePath() + ".idx").deleteOnExit();
+ new File(outputFile.getAbsolutePath() + Tribble.STANDARD_INDEX_EXTENSION).deleteOnExit();
final VcfFormatConverter vcfFormatConverter = new VcfFormatConverter();
vcfFormatConverter.INPUT = input;
vcfFormatConverter.OUTPUT = outputFile;
diff --git a/src/tests/java/net/sf/samtools/BAMFileIndexTest.java b/src/tests/java/net/sf/samtools/BAMFileIndexTest.java
index e642a3a..02741e1 100755
--- a/src/tests/java/net/sf/samtools/BAMFileIndexTest.java
+++ b/src/tests/java/net/sf/samtools/BAMFileIndexTest.java
@@ -214,8 +214,8 @@ public class BAMFileIndexTest
Assert.assertNotNull(mate);
Assert.assertEquals(mate.getReadName(), rec.getReadName());
Assert.assertEquals(mate.getReferenceIndex(), rec.getMateReferenceIndex());
- if (rec.getMateCigarString() != null) {
- Assert.assertEquals(mate.getCigarString(), rec.getMateCigarString());
+ if (SAMUtils.getMateCigarString(rec) != null) {
+ Assert.assertEquals(mate.getCigarString(), SAMUtils.getMateCigarString(rec));
}
Assert.assertEquals(mate.getAlignmentStart(), rec.getMateAlignmentStart());
Assert.assertFalse(mate.getFirstOfPairFlag() == rec.getFirstOfPairFlag());
@@ -277,7 +277,7 @@ public class BAMFileIndexTest
"one_end_mapped\t73\tchr7\t100\t255\t101M\t*\t0\t0\tCAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN\t)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&\tRG:Z:0\n" +
"one_end_mapped\t133\tchr7\t100\t0\t*\t=\t100\t0\tNCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA\t&/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1\tRG:Z:0\n";
final ByteArrayInputStream bis = new ByteArrayInputStream(StringUtil.stringToBytes(samText));
- final File bamFile = File.createTempFile("BAMFileIndexTest.", ".bam");
+ final File bamFile = File.createTempFile("BAMFileIndexTest.", BamFileIoUtils.BAM_FILE_EXTENSION);
bamFile.deleteOnExit();
final SAMFileReader textReader = new SAMFileReader(bis);
SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory();
diff --git a/src/tests/java/net/sf/samtools/BAMFileWriterTest.java b/src/tests/java/net/sf/samtools/BAMFileWriterTest.java
index c74b48c..6458657 100644
--- a/src/tests/java/net/sf/samtools/BAMFileWriterTest.java
+++ b/src/tests/java/net/sf/samtools/BAMFileWriterTest.java
@@ -54,7 +54,7 @@ public class BAMFileWriterTest {
*/
private void testHelper(final SAMRecordSetBuilder samRecordSetBuilder, final SAMFileHeader.SortOrder sortOrder, final boolean presorted) throws Exception {
SAMFileReader samReader = samRecordSetBuilder.getSamReader();
- final File bamFile = File.createTempFile("test.", ".bam");
+ final File bamFile = File.createTempFile("test.", BamFileIoUtils.BAM_FILE_EXTENSION);
bamFile.deleteOnExit();
samReader.getFileHeader().setSortOrder(sortOrder);
final SAMFileWriter bamWriter = new SAMFileWriterFactory().makeSAMOrBAMWriter(samReader.getFileHeader(), presorted, bamFile);
diff --git a/src/tests/java/net/sf/samtools/BamFileIoUtilsTest.java b/src/tests/java/net/sf/samtools/BamFileIoUtilsTest.java
new file mode 100644
index 0000000..124155c
--- /dev/null
+++ b/src/tests/java/net/sf/samtools/BamFileIoUtilsTest.java
@@ -0,0 +1,83 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2014 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+package net.sf.samtools;
+
+import net.sf.picard.PicardException;
+import net.sf.picard.sam.CompareSAMs;
+import net.sf.samtools.BamFileIoUtils;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMFileReader;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+
+public class BamFileIoUtilsTest {
+ private static final File TEST_DATA_DIR = new File("testdata/net/sf/picard/sam");
+ private static final File HEADER_PROVIDER = new File(TEST_DATA_DIR, "samHeaderProvider.sam");
+ private static final File INPUT_FILE = new File(TEST_DATA_DIR, "aligned_queryname_sorted.bam");
+
+ @Test
+ public void testReheader() throws Exception {
+ final SAMFileHeader samFileHeader = new SAMFileReader(HEADER_PROVIDER).getFileHeader();
+ final File outputFile = createOutputFile();
+ BamFileIoUtils.reheaderBamFile(samFileHeader, INPUT_FILE, outputFile);
+ assertReheader(outputFile, HEADER_PROVIDER);
+ }
+
+ @Test
+ public void testReapplySameHeader() throws Exception {
+ final SAMFileHeader samFileHeader = new SAMFileReader(INPUT_FILE).getFileHeader();
+ final File outputFile = createOutputFile();
+ BamFileIoUtils.reheaderBamFile(samFileHeader, INPUT_FILE, outputFile);
+
+ assertReheader(outputFile, INPUT_FILE);
+ final CompareSAMs compareSAMs = new CompareSAMs();
+ compareSAMs.instanceMain(new String[]{INPUT_FILE.getAbsolutePath(), outputFile.getAbsolutePath()});
+ Assert.assertTrue(compareSAMs.areEqual());
+ }
+
+ @Test(expectedExceptions = SAMException.class)
+ public void mismatchSortOrderTest() throws Exception {
+ final SAMFileHeader samFileHeader = new SAMFileReader(HEADER_PROVIDER).getFileHeader();
+ samFileHeader.setSortOrder(SAMFileHeader.SortOrder.coordinate);
+ BamFileIoUtils.reheaderBamFile(samFileHeader, INPUT_FILE, createOutputFile());
+ throw new IllegalStateException("We shouldn't be here");
+ }
+
+ private void assertReheader(final File outputFile, final File headerProvider) {
+ final SAMFileHeader origHeader = new SAMFileReader(headerProvider).getFileHeader();
+ final SAMFileHeader newHeader = new SAMFileReader(outputFile).getFileHeader();
+ Assert.assertEquals(origHeader, newHeader);
+ }
+
+ private File createOutputFile() throws IOException {
+ return File.createTempFile("reheaderTest.", BamFileIoUtils.BAM_FILE_EXTENSION);
+ }
+
+}
diff --git a/src/tests/java/net/sf/samtools/SAMFileWriterFactoryTest.java b/src/tests/java/net/sf/samtools/SAMFileWriterFactoryTest.java
index 049add7..2ea1ffe 100644
--- a/src/tests/java/net/sf/samtools/SAMFileWriterFactoryTest.java
+++ b/src/tests/java/net/sf/samtools/SAMFileWriterFactoryTest.java
@@ -38,12 +38,12 @@ public class SAMFileWriterFactoryTest {
@Test
public void ordinaryFileWriterTest() throws Exception {
- final File outputFile = File.createTempFile("tmp.", ".bam");
+ final File outputFile = File.createTempFile("tmp.", BamFileIoUtils.BAM_FILE_EXTENSION);
outputFile.delete();
outputFile.deleteOnExit();
String basename = outputFile.getName();
basename = basename.substring(0, basename.lastIndexOf("."));
- final File indexFile = new File(outputFile.getParent(), basename + ".bai");
+ final File indexFile = new File(outputFile.getParent(), basename + BAMIndex.BAMIndexSuffix);
indexFile.deleteOnExit();
final File md5File = new File(outputFile.getParent(), outputFile.getName() + ".md5");
md5File.deleteOnExit();
@@ -53,7 +53,7 @@ public class SAMFileWriterFactoryTest {
Assert.assertTrue(md5File.length() > 0);
}
- private void createSmallBam(File outputFile) {
+ private void createSmallBam(final File outputFile) {
final SAMFileWriterFactory factory = new SAMFileWriterFactory();
factory.setCreateIndex(true);
factory.setCreateMd5File(true);
diff --git a/src/tests/java/net/sf/samtools/SamPairUtilTest.java b/src/tests/java/net/sf/samtools/SamPairUtilTest.java
index f7792e3..36b1530 100644
--- a/src/tests/java/net/sf/samtools/SamPairUtilTest.java
+++ b/src/tests/java/net/sf/samtools/SamPairUtilTest.java
@@ -21,33 +21,41 @@
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
-package net.sf.picard.sam;
+package net.sf.samtools;
-import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMSequenceRecord;
-import net.sf.samtools.SamPairUtil;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
public class SamPairUtilTest {
-
@Test(dataProvider = "testGetPairOrientation")
- public void testGetPairOrientation(final String testName,
- final int read1Start, final int read1Length, final boolean read1Reverse,
- final int read2Start, final int read2Length, final boolean read2Reverse,
- final SamPairUtil.PairOrientation expectedOrientation) {
+ public void testGetPairOrientation(final String testName,
+ final int read1Start, final int read1Length, final boolean read1Reverse,
+ final int read2Start, final int read2Length, final boolean read2Reverse,
+ final SamPairUtil.PairOrientation expectedOrientation) {
final SAMFileHeader header = new SAMFileHeader();
header.addSequence(new SAMSequenceRecord("chr1", 100000000));
final SAMRecord rec1 = makeSamRecord(header, read1Start, read1Length, read1Reverse, true);
final SAMRecord rec2 = makeSamRecord(header, read2Start, read2Length, read2Reverse, false);
- SamPairUtil.setMateInfo(rec1, rec2, header);
+ SamPairUtil.setMateInfo(rec1, rec2, header, true);
Assert.assertEquals(SamPairUtil.getPairOrientation(rec1), expectedOrientation, testName + " first end");
Assert.assertEquals(SamPairUtil.getPairOrientation(rec2), expectedOrientation, testName + " second end");
}
+ @Test(dataProvider = "testSetMateInfoMateCigar")
+ public void testSetMateInfoMateCigar(final String testName,
+ final int read1Start, final boolean read1Reverse, final String read1Cigar,
+ final int read2Start, final boolean read2Reverse, final String read2Cigar) {
+ final SAMFileHeader header = new SAMFileHeader();
+ header.addSequence(new SAMSequenceRecord("chr1", 100000000));
+ final SAMRecord rec1 = makeSamRecord2(header, read1Start, read1Reverse, read1Cigar, true);
+ final SAMRecord rec2 = makeSamRecord2(header, read2Start, read2Reverse, read2Cigar, false);
+ SamPairUtil.setMateInfo(rec1, rec2, header, true);
+ Assert.assertEquals(SAMUtils.getMateCigarString(rec1), rec2.getCigarString(), testName + " first end");
+ Assert.assertEquals(SAMUtils.getMateCigarString(rec2), rec1.getCigarString(), testName + " second end");
+ }
+
private SAMRecord makeSamRecord(final SAMFileHeader header, final int alignmentStart, final int readLength,
final boolean reverse, final boolean firstOfPair) {
final SAMRecord rec = new SAMRecord(header);
@@ -69,6 +77,29 @@ public class SamPairUtilTest {
return rec;
}
+ private SAMRecord makeSamRecord2(final SAMFileHeader header, final int alignmentStart, boolean reverse,
+ String cigarString, final boolean firstOfPair) {
+ final SAMRecord rec = new SAMRecord(header);
+ final StringBuilder sb = new StringBuilder();
+ final Cigar cigar = TextCigarCodec.getSingleton().decode(cigarString);
+ final int readLength = cigar.getReadLength();
+ rec.setReferenceIndex(0);
+ final byte[] quals = new byte[readLength];
+ for (int i = 0; i < readLength; ++i) {
+ sb.append("A");
+ quals[i] = 20;
+ }
+ rec.setReadString(sb.toString());
+ rec.setBaseQualities(quals);
+ rec.setAlignmentStart(alignmentStart);
+ rec.setCigar(cigar);
+ rec.setReadPairedFlag(true);
+ rec.setReadNegativeStrandFlag(reverse);
+ if (firstOfPair) rec.setFirstOfPairFlag(true);
+ else rec.setSecondOfPairFlag(true);
+ return rec;
+ }
+
@DataProvider(name = "testGetPairOrientation")
public Object[][] testGetPairOrientationDataProvider() {
/**
@@ -101,4 +132,24 @@ public class SamPairUtilTest {
{"first end enclosed reverse tandem", 1, 50, false, 1, 100, false, SamPairUtil.PairOrientation.TANDEM},
};
}
+
+ @DataProvider(name = "testSetMateInfoMateCigar")
+ public Object[][] testSetMateInfoMateCigarDataProvider() {
+ /**
+ * @param testName
+ * @param read1Start
+ * @param read1Reverse
+ * @param read1Cigar
+ * @param read2Start
+ * @param read2Reverse
+ * @param read2Cigar
+ */
+ return new Object[][] {
+ {"50M/50M", 1, false, "50M", 500, true, "50M"},
+ {"50M/25M5I20M", 1, false, "50M", 500, true, "25M5I20M"},
+ {"25M5I20M/50M", 1, false, "25M5I20M", 500, true, "50M"},
+ {"50M/25M5D20M", 1, false, "50M", 500, true, "25M5D20M"},
+ {"25M5D20M/50M", 1, false, "25M5D20M", 500, true, "50M"},
+ };
+ }
}
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AAGGATGT-AAGGATGT-AAGGATGT.sam b/src/tests/java/net/sf/samtools/apps/.gitignore
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AAGGATGT-AAGGATGT-AAGGATGT.sam
rename to src/tests/java/net/sf/samtools/apps/.gitignore
diff --git a/src/tests/java/net/sf/samtools/util/IupacTest.java b/src/tests/java/net/sf/samtools/util/IupacTest.java
index 42d7505..6f55560 100644
--- a/src/tests/java/net/sf/samtools/util/IupacTest.java
+++ b/src/tests/java/net/sf/samtools/util/IupacTest.java
@@ -63,7 +63,7 @@ public class IupacTest {
@DataProvider(name = "basidDataProvider")
public Object[][] basicDataProvider() {
return new Object[][] {
- {".bam"},
+ {BamFileIoUtils.BAM_FILE_EXTENSION},
{".sam"}
};
}
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AAGGATGT-AAGGATGT.sam b/src/tests/java/org/broad/tribble/source/.gitignore
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AAGGATGT-AAGGATGT.sam
rename to src/tests/java/org/broad/tribble/source/.gitignore
diff --git a/src/tests/java/org/broadinstitute/variant/variantcontext/writer/TabixOnTheFlyIndexCreationTest.java b/src/tests/java/org/broadinstitute/variant/variantcontext/writer/TabixOnTheFlyIndexCreationTest.java
index f86e4b7..d51e74f 100644
--- a/src/tests/java/org/broadinstitute/variant/variantcontext/writer/TabixOnTheFlyIndexCreationTest.java
+++ b/src/tests/java/org/broadinstitute/variant/variantcontext/writer/TabixOnTheFlyIndexCreationTest.java
@@ -34,7 +34,6 @@ import org.broadinstitute.variant.vcf.VCFHeader;
import org.testng.annotations.Test;
import java.io.File;
-import java.io.FileOutputStream;
import java.util.EnumSet;
public class TabixOnTheFlyIndexCreationTest {
@@ -48,10 +47,11 @@ public class TabixOnTheFlyIndexCreationTest {
final File tabix = new File(vcf.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION);
vcf.deleteOnExit();
tabix.deleteOnExit();
- final FileOutputStream os = new FileOutputStream(vcf);
- final VariantContextWriter vcfWriter =
- VariantContextWriterFactory.createBlockCompressedVcf(vcf, os, headerFromFile.getSequenceDictionary(),
- EnumSet.of(Options.INDEX_ON_THE_FLY, Options.ALLOW_MISSING_FIELDS_IN_HEADER));
+ final VariantContextWriter vcfWriter = new VariantContextWriterBuilder()
+ .setOutputFile(vcf)
+ .setReferenceDictionary(headerFromFile.getSequenceDictionary())
+ .setOptions(EnumSet.of(Options.INDEX_ON_THE_FLY, Options.ALLOW_MISSING_FIELDS_IN_HEADER))
+ .build();
vcfWriter.writeHeader(headerFromFile);
final CloseableTribbleIterator<VariantContext> it = reader.iterator();
while (it.hasNext()) {
diff --git a/src/tests/java/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java b/src/tests/java/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java
index beaa5a3..86bb738 100644
--- a/src/tests/java/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java
+++ b/src/tests/java/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java
@@ -43,7 +43,6 @@ import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.*;
-
/**
* @author aaron
* <p/>
@@ -65,8 +64,11 @@ public class VCFWriterUnitTest extends VariantBaseTest {
additionalColumns = new HashSet<String>();
final SAMSequenceDictionary sequenceDict = createArtificialSequenceDictionary();
final VCFHeader header = createFakeHeader(metaData, additionalColumns, sequenceDict);
- final EnumSet<Options> options = EnumSet.of(Options.ALLOW_MISSING_FIELDS_IN_HEADER, Options.INDEX_ON_THE_FLY);
- final VariantContextWriter writer = VariantContextWriterFactory.create(fakeVCFFile, sequenceDict, options);
+ final VariantContextWriter writer = new VariantContextWriterBuilder()
+ .setOutputFile(fakeVCFFile)
+ .setReferenceDictionary(sequenceDict)
+ .setOptions(EnumSet.of(Options.ALLOW_MISSING_FIELDS_IN_HEADER, Options.INDEX_ON_THE_FLY))
+ .build();
writer.writeHeader(header);
writer.add(createVC(header));
writer.add(createVC(header));
@@ -171,7 +173,6 @@ public class VCFWriterUnitTest extends VariantBaseTest {
final SAMSequenceDictionary dict = createArtificialSequenceDictionary();
final VCFHeader header = createFakeHeader(metaData,Columns, dict);
- final EnumSet<Options> options = EnumSet.of(Options.ALLOW_MISSING_FIELDS_IN_HEADER,Options.INDEX_ON_THE_FLY);
final File tempDir = TestUtil.getTempDirectory("VCFWriter", "StaleIndex");
@@ -182,12 +183,16 @@ public class VCFWriterUnitTest extends VariantBaseTest {
if (extension.equals(".vcf.gz")) {
indexExtension = TabixUtils.STANDARD_INDEX_EXTENSION;
} else {
- indexExtension = ".idx";
+ indexExtension = Tribble.STANDARD_INDEX_EXTENSION;
}
final File vcfIndex = new File(vcf.getAbsolutePath() + indexExtension);
for(int count=1;count<2; count++){
- final VariantContextWriter writer = VariantContextWriterFactory.create(vcf, dict, options);
+ final VariantContextWriter writer = new VariantContextWriterBuilder()
+ .setOutputFile(vcf)
+ .setReferenceDictionary(dict)
+ .setOptions(EnumSet.of(Options.ALLOW_MISSING_FIELDS_IN_HEADER, Options.INDEX_ON_THE_FLY))
+ .build();
writer.writeHeader(header);
for (int i = 1; i < 17 ; i++) { // write 17 chromosomes
diff --git a/src/tests/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterBuilderUnitTest.java b/src/tests/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterBuilderUnitTest.java
new file mode 100644
index 0000000..b5e7f1a
--- /dev/null
+++ b/src/tests/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterBuilderUnitTest.java
@@ -0,0 +1,343 @@
+/*
+* Copyright (c) 2014 The Broad Institute
+*
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+*
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+*
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.variant.variantcontext.writer;
+
+import java.io.*;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.broad.tribble.Tribble;
+import org.broad.tribble.index.tabix.TabixIndex;
+import org.broad.tribble.util.TabixUtils;
+import org.testng.Assert;
+import org.testng.annotations.BeforeSuite;
+import org.testng.annotations.Test;
+
+import net.sf.samtools.Defaults;
+import net.sf.samtools.SAMSequenceDictionary;
+import net.sf.samtools.util.BlockCompressedOutputStream;
+import org.broad.tribble.AbstractFeatureReader;
+import org.broadinstitute.variant.VariantBaseTest;
+
+public class VariantContextWriterBuilderUnitTest extends VariantBaseTest {
+ private SAMSequenceDictionary dictionary;
+
+ private final File vcf = new File("test.vcf");
+ private final File vcfIdx = new File("test.vcf" + Tribble.STANDARD_INDEX_EXTENSION);
+ private final File vcfMD5 = new File("test.vcf.md5");
+ private final File bcf = new File("test.bcf");
+ private final File bcfIdx = new File("test.bcf" + Tribble.STANDARD_INDEX_EXTENSION);
+ private final File unknown = new File("test.unknown");
+
+ private List<File> blockCompressedVCFs;
+ private List<File> blockCompressedIndices;
+
+ @BeforeSuite
+ public void before() throws IOException {
+ dictionary = createArtificialSequenceDictionary();
+ vcf.deleteOnExit();
+ vcfIdx.deleteOnExit();
+ vcfMD5.deleteOnExit();
+ bcf.deleteOnExit();
+ bcfIdx.deleteOnExit();
+ unknown.deleteOnExit();
+
+ blockCompressedVCFs = new ArrayList<File>();
+ blockCompressedIndices = new ArrayList<File>();
+ for (final String extension : AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS) {
+ final File blockCompressed = new File("test.vcf" + extension);
+ blockCompressed.deleteOnExit();
+ blockCompressedVCFs.add(blockCompressed);
+
+ final File index = new File("test.vcf" + extension + TabixUtils.STANDARD_INDEX_EXTENSION);
+ index.deleteOnExit();
+ blockCompressedIndices.add(index);
+ }
+ }
+
+ @Test
+ public void testSetOutputFile() {
+ final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
+ .setReferenceDictionary(dictionary);
+
+ VariantContextWriter writer = builder.setOutputFile(vcf.getAbsolutePath()).build();
+ Assert.assertTrue(writer instanceof VCFWriter, "testSetOutputFile VCF String");
+ Assert.assertFalse(((VCFWriter) writer).getOutputStream() instanceof BlockCompressedOutputStream, "testSetOutputFile VCF String was compressed");
+
+ writer = builder.setOutputFile(vcf).build();
+ Assert.assertTrue(writer instanceof VCFWriter, "testSetOutputFile VCF File");
+ Assert.assertFalse(((VCFWriter)writer).getOutputStream() instanceof BlockCompressedOutputStream, "testSetOutputFile VCF File was compressed");
+
+ for (final String extension : AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS) {
+ final String filename = "test.vcf" + extension;
+ final File file = new File(filename);
+ file.deleteOnExit();
+
+ writer = builder.setOutputFile(filename).build();
+ Assert.assertTrue(writer instanceof VCFWriter, "testSetOutputFile " + extension + " String");
+ Assert.assertTrue(((VCFWriter) writer).getOutputStream() instanceof BlockCompressedOutputStream, "testSetOutputFile " + extension + " String was not compressed");
+
+ writer = builder.setOutputFile(file).build();
+ Assert.assertTrue(writer instanceof VCFWriter, "testSetOutputFile " + extension + " File");
+ Assert.assertTrue(((VCFWriter) writer).getOutputStream() instanceof BlockCompressedOutputStream, "testSetOutputFile " + extension + " File was not compressed");
+ }
+
+ writer = builder.setOutputFile(bcf).build();
+ Assert.assertTrue(writer instanceof BCF2Writer, "testSetOutputFile BCF String");
+
+ writer = builder.setOutputFile(bcf.getAbsolutePath()).build();
+ Assert.assertTrue(writer instanceof BCF2Writer, "testSetOutputFile BCF File");
+ }
+
+ @Test
+ public void testSetOutputFileType() {
+ final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
+ .setReferenceDictionary(dictionary)
+ .setOutputFile(unknown);
+
+ VariantContextWriter writer = builder.setOutputFileType(VariantContextWriterBuilder.OutputType.VCF).build();
+ Assert.assertTrue(writer instanceof VCFWriter, "testSetOutputFileType VCF");
+ Assert.assertFalse(((VCFWriter) writer).getOutputStream() instanceof BlockCompressedOutputStream, "testSetOutputFileType VCF was compressed");
+
+ writer = builder.setOption(Options.FORCE_BCF).build();
+ Assert.assertTrue(writer instanceof BCF2Writer, "testSetOutputFileType FORCE_BCF set -> expected BCF, was VCF");
+
+ // test that FORCE_BCF remains in effect, overriding the explicit setting of VCF
+ writer = builder.setOutputFileType(VariantContextWriterBuilder.OutputType.VCF).build();
+ Assert.assertTrue(writer instanceof BCF2Writer, "testSetOutputFileType FORCE_BCF set 2 -> expected BCF, was VCF");
+
+ writer = builder.unsetOption(Options.FORCE_BCF).build();
+ Assert.assertTrue(writer instanceof VCFWriter, "testSetOutputFileType FORCE_BCF unset -> expected VCF, was BCF");
+ Assert.assertFalse(((VCFWriter) writer).getOutputStream() instanceof BlockCompressedOutputStream, "testSetOutputFileType FORCE_BCF unset was compressed");
+
+ writer = builder.setOutputFileType(VariantContextWriterBuilder.OutputType.BLOCK_COMPRESSED_VCF).build();
+ Assert.assertTrue(writer instanceof VCFWriter, "testSetOutputFile BLOCK_COMPRESSED_VCF");
+ Assert.assertTrue(((VCFWriter) writer).getOutputStream() instanceof BlockCompressedOutputStream, "testSetOutputFileType BLOCK_COMPRESSED_VCF was not compressed");
+
+ writer = builder.setOutputFileType(VariantContextWriterBuilder.OutputType.BCF).build();
+ Assert.assertTrue(writer instanceof BCF2Writer, "testSetOutputFileType BCF");
+ }
+
+ @Test
+ public void testSetOutputStream() {
+ final OutputStream stream = new ByteArrayOutputStream();
+
+ final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
+ .setReferenceDictionary(dictionary)
+ .unsetOption(Options.INDEX_ON_THE_FLY)
+ .setOutputStream(stream);
+
+ VariantContextWriter writer = builder.build();
+ Assert.assertTrue(writer instanceof VCFWriter, "testSetOutputStream default");
+
+ writer = builder.setOption(Options.FORCE_BCF).build();
+ Assert.assertTrue(writer instanceof BCF2Writer, "testSetOutputStream FORCE_BCF set -> expected BCF stream, was VCF stream");
+
+ // test that FORCE_BCF remains in effect, overriding the explicit setting of VCF
+ writer = builder.setOutputVCFStream(stream).build();
+ Assert.assertTrue(writer instanceof BCF2Writer, "testSetOutputStream FORCE_BCF set 2 -> expected BCF stream, was VCF stream");
+
+ writer = builder.unsetOption(Options.FORCE_BCF).build();
+ Assert.assertTrue(writer instanceof VCFWriter, "testSetOutputStream FORCE_BCF unset -> expected VCF stream, was BCF stream");
+
+ writer = builder.setOutputBCFStream(stream).build();
+ Assert.assertTrue(writer instanceof BCF2Writer, "testSetOutputStream BCF");
+
+ writer = builder.setOutputVCFStream(stream).build();
+ Assert.assertTrue(writer instanceof VCFWriter, "testSetOutputStream VCF");
+ }
+
+ @Test
+ public void testAsync() {
+ final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
+ .setReferenceDictionary(dictionary)
+ .setOutputFile(vcf);
+
+ VariantContextWriter writer = builder.build();
+ Assert.assertEquals(writer instanceof AsyncVariantContextWriter, Defaults.USE_ASYNC_IO, "testAsync default");
+
+ writer = builder.setOption(Options.USE_ASYNC_IO).build();
+ Assert.assertTrue(writer instanceof AsyncVariantContextWriter, "testAsync option=set");
+
+ writer = builder.unsetOption(Options.USE_ASYNC_IO).build();
+ Assert.assertFalse(writer instanceof AsyncVariantContextWriter, "testAsync option=unset");
+ }
+
+ @Test
+ public void testBuffering() {
+ final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
+ .setReferenceDictionary(dictionary)
+ .setOutputFile(vcf)
+ .unsetOption(Options.INDEX_ON_THE_FLY); // so the potential BufferedOutputStream is not wrapped in a PositionalOutputStream
+
+ VariantContextWriter writer = builder.build();
+ Assert.assertTrue(((VCFWriter) writer).getOutputStream() instanceof BufferedOutputStream, "testBuffering was not buffered by default");
+
+ writer = builder.unsetBuffering().build();
+ Assert.assertFalse(((VCFWriter) writer).getOutputStream() instanceof BufferedOutputStream, "testBuffering was buffered when unset");
+
+ writer = builder.setBuffer(8192).build();
+ Assert.assertTrue(((VCFWriter) writer).getOutputStream() instanceof BufferedOutputStream, "testBuffering was not buffered when set");
+ }
+
+ @Test
+ public void testMD5() {
+ final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
+ .setReferenceDictionary(dictionary)
+ .setOutputFile(vcf);
+
+ VariantContextWriter writer = builder.build();
+ writer.close();
+ Assert.assertEquals(vcfMD5.exists(), Defaults.CREATE_MD5, "MD5 default setting not respected");
+
+ if (vcfMD5.exists())
+ vcfMD5.delete();
+
+ writer = builder.setCreateMD5().build();
+ writer.close();
+ Assert.assertTrue(vcfMD5.exists(), "MD5 not created when requested");
+ vcfMD5.delete();
+
+ writer = builder.unsetCreateMD5().build();
+ writer.close();
+ Assert.assertFalse(vcfMD5.exists(), "MD5 created when not requested");
+
+ writer = builder.setCreateMD5(false).build();
+ writer.close();
+ Assert.assertFalse(vcfMD5.exists(), "MD5 created when not requested via boolean parameter");
+
+ writer = builder.setCreateMD5(true).build();
+ writer.close();
+ Assert.assertTrue(vcfMD5.exists(), "MD5 not created when requested via boolean parameter");
+ vcfMD5.delete();
+
+ for (final File blockCompressed : blockCompressedVCFs) {
+ final File md5 = new File(blockCompressed + ".md5");
+ if (md5.exists())
+ md5.delete();
+ md5.deleteOnExit();
+ writer = builder.setOutputFile(blockCompressed).build();
+ writer.close();
+ Assert.assertTrue(md5.exists(), "MD5 digest not created for " + blockCompressed);
+ }
+ }
+
+ @Test
+ public void testIndexingOnTheFly() {
+ final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
+ .setReferenceDictionary(dictionary)
+ .setOption(Options.INDEX_ON_THE_FLY);
+
+ if (vcfIdx.exists())
+ vcfIdx.delete();
+ VariantContextWriter writer = builder.setOutputFile(vcf).build();
+ writer.close();
+ Assert.assertTrue(vcfIdx.exists(), String.format("VCF index not created for %s / %s", vcf, vcfIdx));
+
+ if (bcfIdx.exists())
+ bcfIdx.delete();
+ writer = builder.setOutputFile(bcf).build();
+ writer.close();
+ Assert.assertTrue(bcfIdx.exists(), String.format("BCF index not created for %s / %s", bcf, bcfIdx));
+
+ for (int i = 0; i < blockCompressedVCFs.size(); i++) {
+ final File blockCompressed = blockCompressedVCFs.get(i);
+ final File index = blockCompressedIndices.get(i);
+ if (index.exists())
+ index.delete();
+ writer = builder.setOutputFile(blockCompressed).setReferenceDictionary(dictionary).build();
+ writer.close();
+ Assert.assertTrue(index.exists(), String.format("Block-compressed index not created for %s / %s", blockCompressed, index));
+
+ // Tabix does not require a reference dictionary.
+ // Tribble does: see tests testRefDictRequiredForVCFIndexOnTheFly / testRefDictRequiredForBCFIndexOnTheFly
+
+ index.delete();
+ writer = builder.setReferenceDictionary(null).build();
+ writer.close();
+ Assert.assertTrue(index.exists(), String.format("Block-compressed index not created for %s / %s", blockCompressed, index));
+ }
+ }
+
+ @Test(expectedExceptions = IllegalArgumentException.class)
+ public void testInvalidImplicitFileType() {
+ new VariantContextWriterBuilder()
+ .setReferenceDictionary(dictionary)
+ .setOutputFile("test.bam")
+ .build();
+ }
+
+ @Test(expectedExceptions = IllegalArgumentException.class)
+ public void testSetInvalidFileType() {
+ new VariantContextWriterBuilder()
+ .setReferenceDictionary(dictionary)
+ .setOutputFile("test.bam")
+ .setOutputFileType(VariantContextWriterBuilder.OutputType.VCF_STREAM)
+ .build();
+ }
+
+ @Test(expectedExceptions = IllegalArgumentException.class)
+ public void testInvalidSetFileTypeForStream() {
+ new VariantContextWriterBuilder()
+ .setReferenceDictionary(dictionary)
+ .setOutputStream(new ByteArrayOutputStream())
+ .setOutputFileType(VariantContextWriterBuilder.OutputType.VCF)
+ .build();
+ }
+
+ @Test(expectedExceptions = IllegalArgumentException.class)
+ public void testUnsupportedIndexOnTheFlyForStreaming() {
+ new VariantContextWriterBuilder()
+ .setReferenceDictionary(dictionary)
+ .setOutputStream(new ByteArrayOutputStream())
+ .setOption(Options.INDEX_ON_THE_FLY)
+ .build();
+ }
+
+ @Test(expectedExceptions = IllegalArgumentException.class)
+ public void testUnsupportedDefaultIndexOnTheFlyForStreaming() {
+ new VariantContextWriterBuilder()
+ .setReferenceDictionary(dictionary)
+ .setOutputStream(new ByteArrayOutputStream())
+ .build();
+ }
+
+ @Test(expectedExceptions = IllegalArgumentException.class)
+ public void testRefDictRequiredForVCFIndexOnTheFly() {
+ new VariantContextWriterBuilder()
+ .setOutputFile(vcf)
+ .setOption(Options.INDEX_ON_THE_FLY)
+ .build();
+ }
+
+ @Test(expectedExceptions = IllegalArgumentException.class)
+ public void testRefDictRequiredForBCFIndexOnTheFly() {
+ new VariantContextWriterBuilder()
+ .setOutputFile(bcf)
+ .setOption(Options.INDEX_ON_THE_FLY)
+ .build();
+ }
+}
\ No newline at end of file
diff --git a/src/tests/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWritersUnitTest.java b/src/tests/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWritersUnitTest.java
index af8ac99..7ee9f9b 100644
--- a/src/tests/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWritersUnitTest.java
+++ b/src/tests/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWritersUnitTest.java
@@ -94,7 +94,11 @@ public class VariantContextWritersUnitTest extends VariantBaseTest {
@Override
public VariantContextWriter makeWriter(final File file, final EnumSet<Options> baseOptions) {
- return VariantContextWriterFactory.create(file, dictionary, baseOptions);
+ return new VariantContextWriterBuilder()
+ .setOutputFile(file)
+ .setReferenceDictionary(dictionary)
+ .setOptions(baseOptions)
+ .build();
}
@Override
@@ -143,7 +147,11 @@ public class VariantContextWritersUnitTest extends VariantBaseTest {
@Override
public VariantContextWriter makeWriter(final File file, final EnumSet<Options> baseOptions) {
- return VariantContextWriterFactory.create(file, dictionary, baseOptions);
+ return new VariantContextWriterBuilder()
+ .setOutputFile(file)
+ .setReferenceDictionary(dictionary)
+ .setOptions(baseOptions)
+ .build();
}
@Override
diff --git a/src/tests/java/org/broadinstitute/variant/vcf/IndexFactoryUnitTest.java b/src/tests/java/org/broadinstitute/variant/vcf/IndexFactoryUnitTest.java
index 080153d..fcf8382 100644
--- a/src/tests/java/org/broadinstitute/variant/vcf/IndexFactoryUnitTest.java
+++ b/src/tests/java/org/broadinstitute/variant/vcf/IndexFactoryUnitTest.java
@@ -35,7 +35,7 @@ import org.broadinstitute.variant.VariantBaseTest;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.writer.Options;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterBuilder;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
@@ -75,8 +75,11 @@ public class IndexFactoryUnitTest extends VariantBaseTest {
final AbstractFeatureReader source = AbstractFeatureReader.getFeatureReader(inputFile.getAbsolutePath(), new VCFCodec(), indexFromInputFile);
int counter = 0;
- final EnumSet<Options> options = EnumSet.of(Options.ALLOW_MISSING_FIELDS_IN_HEADER);
- VariantContextWriter writer = VariantContextWriterFactory.create(outputFile, dict, options);
+ VariantContextWriter writer = new VariantContextWriterBuilder()
+ .setOutputFile(outputFile)
+ .setReferenceDictionary(dict)
+ .setOptions(EnumSet.of(Options.ALLOW_MISSING_FIELDS_IN_HEADER))
+ .build();
writer.writeHeader((VCFHeader)source.getHeader());
CloseableTribbleIterator<VariantContext> it = source.iterator();
while (it.hasNext() && (counter++ < maxRecords || maxRecords == -1) ) {
diff --git a/src/tests/java/org/broadinstitute/variant/vcf/VCFCompoundHeaderLineUnitTest.java b/src/tests/java/org/broadinstitute/variant/vcf/VCFCompoundHeaderLineUnitTest.java
new file mode 100644
index 0000000..ef8b960
--- /dev/null
+++ b/src/tests/java/org/broadinstitute/variant/vcf/VCFCompoundHeaderLineUnitTest.java
@@ -0,0 +1,46 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+*
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+*
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+*
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.variant.vcf;
+
+import org.broadinstitute.variant.VariantBaseTest;
+import org.testng.annotations.Test;
+import org.testng.Assert;
+
+
+/**
+ * User: ebanks
+ * Date: Apr 2, 2014
+ */
+public class VCFCompoundHeaderLineUnitTest extends VariantBaseTest {
+
+ @Test
+ public void supportsVersionFields() {
+ final String line = "<ID=FOO,Number=1,Type=Float,Description=\"foo\",Version=3>";
+ final VCFCompoundHeaderLine headerline = new VCFInfoHeaderLine(line, VCFHeaderVersion.VCF4_2);
+ // if we don't support version fields then we should fail before we ever get here
+ Assert.assertTrue(true);
+ }
+}
diff --git a/src/tests/java/org/broadinstitute/variant/vcf/VCFHeaderUnitTest.java b/src/tests/java/org/broadinstitute/variant/vcf/VCFHeaderUnitTest.java
index 1c90769..9417809 100644
--- a/src/tests/java/org/broadinstitute/variant/vcf/VCFHeaderUnitTest.java
+++ b/src/tests/java/org/broadinstitute/variant/vcf/VCFHeaderUnitTest.java
@@ -25,10 +25,14 @@
package org.broadinstitute.variant.vcf;
+import org.broad.tribble.TribbleException;
+import org.broad.tribble.readers.AsciiLineReader;
+import org.broad.tribble.readers.AsciiLineReaderIterator;
import org.broad.tribble.readers.LineIteratorImpl;
import org.broad.tribble.readers.LineReaderUtil;
import org.broad.tribble.readers.PositionalBufferedStream;
import org.broadinstitute.variant.VariantBaseTest;
+import org.broadinstitute.variant.variantcontext.VariantContext;
import org.testng.Assert;
import org.testng.annotations.Test;
@@ -65,6 +69,42 @@ public class VCFHeaderUnitTest extends VariantBaseTest {
checkMD5ofHeaderFile(header, "b1d71cc94261053131f8d239d65a8c9f");
}
+ @Test
+ public void testVCFHeaderSampleRenamingSingleSampleVCF() throws Exception {
+ final VCFCodec codec = new VCFCodec();
+ codec.setRemappedSampleName("FOOSAMPLE");
+ final AsciiLineReaderIterator vcfIterator = new AsciiLineReaderIterator(new AsciiLineReader(new FileInputStream(variantTestDataRoot + "HiSeq.10000.vcf")));
+ final VCFHeader header = (VCFHeader)codec.readHeader(vcfIterator).getHeaderValue();
+
+ Assert.assertEquals(header.getNGenotypeSamples(), 1, "Wrong number of samples in remapped header");
+ Assert.assertEquals(header.getGenotypeSamples().get(0), "FOOSAMPLE", "Sample name in remapped header has incorrect value");
+
+ int recordCount = 0;
+ while ( vcfIterator.hasNext() && recordCount < 10) {
+ recordCount++;
+ final VariantContext vcfRecord = codec.decode(vcfIterator.next());
+
+ Assert.assertEquals(vcfRecord.getSampleNames().size(), 1, "Wrong number of samples in vcf record after remapping");
+ Assert.assertEquals(vcfRecord.getSampleNames().iterator().next(), "FOOSAMPLE", "Wrong sample in vcf record after remapping");
+ }
+ }
+
+ @Test(expectedExceptions = TribbleException.class)
+ public void testVCFHeaderSampleRenamingMultiSampleVCF() throws Exception {
+ final VCFCodec codec = new VCFCodec();
+ codec.setRemappedSampleName("FOOSAMPLE");
+ final AsciiLineReaderIterator vcfIterator = new AsciiLineReaderIterator(new AsciiLineReader(new FileInputStream(variantTestDataRoot + "ex2.vcf")));
+ final VCFHeader header = (VCFHeader)codec.readHeader(vcfIterator).getHeaderValue();
+ }
+
+ @Test(expectedExceptions = TribbleException.class)
+ public void testVCFHeaderSampleRenamingSitesOnlyVCF() throws Exception {
+ final VCFCodec codec = new VCFCodec();
+ codec.setRemappedSampleName("FOOSAMPLE");
+ final AsciiLineReaderIterator vcfIterator = new AsciiLineReaderIterator(new AsciiLineReader(new FileInputStream(variantTestDataRoot + "dbsnp_135.b37.1000.vcf")));
+ final VCFHeader header = (VCFHeader)codec.readHeader(vcfIterator).getHeaderValue();
+ }
+
/**
* a little utility function for all tests to md5sum a file
* Shameless taken from:
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diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1201.bcl b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1201.bcl
new file mode 100755
index 0000000..d121463
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1201.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_2101.bcl b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_2101.bcl
new file mode 100755
index 0000000..14ae6d2
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_2101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl
new file mode 100755
index 0000000..f248e20
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1201.bcl b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1201.bcl
new file mode 100755
index 0000000..dce6d70
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1201.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_2101.bcl b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_2101.bcl
new file mode 100755
index 0000000..cfac6aa
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_2101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl
new file mode 100755
index 0000000..7e21656
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1201.bcl b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1201.bcl
new file mode 100755
index 0000000..1a9d422
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1201.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_2101.bcl b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_2101.bcl
new file mode 100755
index 0000000..c69924d
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_2101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl
new file mode 100755
index 0000000..359ff7d
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1201.bcl b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1201.bcl
new file mode 100755
index 0000000..90eba55
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1201.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_2101.bcl b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_2101.bcl
new file mode 100755
index 0000000..60c0339
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_2101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_1101.filter b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_1101.filter
new file mode 100755
index 0000000..0ad05bc
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_1101.filter differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_1201.filter b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_1201.filter
new file mode 100755
index 0000000..19b6b51
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_1201.filter differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_2101.filter b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_2101.filter
new file mode 100755
index 0000000..951a583
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_2101.filter differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/s_1_1101_barcode.txt.gz b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/s_1_1101_barcode.txt.gz
new file mode 100755
index 0000000..4d89d1e
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/s_1_1101_barcode.txt.gz differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/s_1_1201_barcode.txt.gz b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/s_1_1201_barcode.txt.gz
new file mode 100755
index 0000000..eb4f41a
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/s_1_1201_barcode.txt.gz differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/s_1_2101_barcode.txt.gz b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/s_1_2101_barcode.txt.gz
new file mode 100755
index 0000000..e039100
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/s_1_2101_barcode.txt.gz differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/L001/s_1_1101.clocs b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/L001/s_1_1101.clocs
new file mode 100755
index 0000000..4245d39
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/L001/s_1_1101.clocs differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/L001/s_1_1201.clocs b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/L001/s_1_1201.clocs
new file mode 100755
index 0000000..8759b3d
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/L001/s_1_1201.clocs differ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/L001/s_1_2101.clocs b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/L001/s_1_2101.clocs
new file mode 100755
index 0000000..c482d87
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/L001/s_1_2101.clocs differ
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ACCAACTG-ACCAACTG-ACCAACTG.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AAAAAAAA.1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ACCAACTG-ACCAACTG-ACCAACTG.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/AAAAAAAA.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ACCAACTG-ACCAACTG.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AAAAAAAA.2.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ACCAACTG-ACCAACTG.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/AAAAAAAA.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGCAATTC-AGCAATTC-AGCAATTC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AAAAAAAA.barcode_1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGCAATTC-AGCAATTC-AGCAATTC.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/AAAAAAAA.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGCAATTC-AGCAATTC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AAAAGAAG.1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGCAATTC-AGCAATTC.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/AAAAGAAG.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGTTGCTT-AGTTGCTT-AGTTGCTT.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AAAAGAAG.2.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGTTGCTT-AGTTGCTT-AGTTGCTT.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/AAAAGAAG.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGTTGCTT-AGTTGCTT.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AAAAGAAG.barcode_1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGTTGCTT-AGTTGCTT.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/AAAAGAAG.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACAATGG.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACAATGG.1.fastq
new file mode 100644
index 0000000..79606c3
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACAATGG.1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1138:2141 1:Y:0:AACAATGG
+NTTACCAAGGTTTTCTGTTTAGTGA
++
+#1=DDFFFHHFHHJJJIHJIJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1206:2126 1:Y:0:AACAATGG
+NATTCTGCCATATTGGTCCGACAGT
++
+#1=DDFFFHHHHHJJJJJJJJJIJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1077:2139 1:Y:0:AACAATGG
+CACAGGCTTCCACGGACTTAACGTC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1112:2245 1:Y:0:AACAATGG
+TGCCATCTGCTCTGGGAAGCACCAG
++
+1:=DDDDDFBC:DEFIFFFIEF at BE
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACAATGG.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACAATGG.2.fastq
new file mode 100644
index 0000000..db34739
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACAATGG.2.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1138:2141 2:Y:0:AACAATGG
+TCCGATCTGCTTCAGGTCGATCAGA
++
+CCCFFFFFHGHHHJJIGHIJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1206:2126 2:Y:0:AACAATGG
+ATCTGTCCAGTGGTGCACTGAATGT
++
+CCCFFFFFHHHHHHIIJJJJIJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1077:2139 2:Y:0:AACAATGG
+NATTAGTTGGCGGATGAAGCAGATA
++
+#4=DFFFFHHHHHJJJJJJJJJIJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1112:2245 2:Y:0:AACAATGG
+TCGTAGTGTTGTAATTTCGTCTTCT
++
+?8?DBDDDCCFCAACGGFFCBFFAE
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACAATGG.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACAATGG.barcode_1.fastq
new file mode 100644
index 0000000..fa6ebcd
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACAATGG.barcode_1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1138:2141 :Y:0:AACAATGG
+AACAATGG
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1101:1206:2126 :Y:0:AACAATGG
+AACAATGG
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1077:2139 :Y:0:AACAATGG
+AACAATGG
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1112:2245 :Y:0:AACAATGG
+AACAATGG
++
+@@?BBDDD
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACGCATT.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACGCATT.1.fastq
new file mode 100644
index 0000000..fb4eb91
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACGCATT.1.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1197:2200 1:Y:0:AACGCATT
+GGGCGCCCCGTGAGGACCCAGTCCT
++
+ at C@FFADDFFCFCEHIIJIJJIEFC
+ at machine1:HiMom:abcdeACXX:1:1101:1308:2153 1:N:0:AACGCATT
+TTTTGGAAGAGACCTCAATTACTGT
++
+???DDDDD?:22AE:A2<3,AF?3A
+ at machine1:HiMom:abcdeACXX:1:1101:1452:2132 1:Y:0:AACGCATT
+NCGTCCTGGAAAACGGGGCGCGGCT
++
+#1=BDBDDFHHHHF at FHDHIGIIII
+ at machine1:HiMom:abcdeACXX:1:1201:1150:2161 1:Y:0:AACGCATT
+AAGTCACCTAATATCTTTTTTTTTT
++
+@@<??;?D?CFD,A4CDDHFBIIID
+ at machine1:HiMom:abcdeACXX:1:2101:1240:2197 1:N:0:AACGCATT
+ATAAAACATAGCAATATTTTCCTAT
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1336:2109 1:Y:0:AACGCATT
+NACTATCAGGATCGTGGCTATTTTG
++
+#1BDDFFFHHHHHJIJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1427:2081 1:Y:0:AACGCATT
+NCGAGTGCCTAGTGGGCCACTTTTG
++
+#4=DDBDFHHHHFHIJJJJIJJJJI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACGCATT.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACGCATT.2.fastq
new file mode 100644
index 0000000..fccce0a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACGCATT.2.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1197:2200 2:Y:0:AACGCATT
+ATATTCCACTGGAACCACAGAACCC
++
+@@@FFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1308:2153 2:N:0:AACGCATT
+TCTGTAAGGTAATCCCCGCATGTGT
++
+1?1=4===AFFDFFGFDGFB at CFB:
+ at machine1:HiMom:abcdeACXX:1:1101:1452:2132 2:Y:0:AACGCATT
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CCCFFFFFHHHHHJJJJJJJIJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1150:2161 2:Y:0:AACGCATT
+TTCTCACTACTGTGATTGTGCCACT
++
+ at C@FFFFFGHHHHGIIIICEHCFGH
+ at machine1:HiMom:abcdeACXX:1:2101:1240:2197 2:N:0:AACGCATT
+ACTGGAGATCCTTGTTACATGCCCA
++
+??+++A:DD?:ADEE@::C4:C<E:
+ at machine1:HiMom:abcdeACXX:1:2101:1336:2109 2:Y:0:AACGCATT
+AGACCAGAACAGCTCCAGGTGCTCC
++
+CCCFFFFFHHHHHJJJJJJCGHIJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1427:2081 2:Y:0:AACGCATT
+CCGACTTCCATGGCCACCGTCCTGC
++
+CCCFFFFFHHHHHJJJIIGFIIJJI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACGCATT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACGCATT.barcode_1.fastq
new file mode 100644
index 0000000..ae7cce7
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AACGCATT.barcode_1.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1197:2200 :Y:0:AACGCATT
+AACGCATT
++
+ at CCFDFFF
+ at machine1:HiMom:abcdeACXX:1:1101:1308:2153 :N:0:AACGCATT
+AACGCATT
++
+:?@B?@DD
+ at machine1:HiMom:abcdeACXX:1:1101:1452:2132 :Y:0:AACGCATT
+AACGCATT
++
+ at CCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1150:2161 :Y:0:AACGCATT
+AACGCATT
++
+@@@FDDDD
+ at machine1:HiMom:abcdeACXX:1:2101:1240:2197 :N:0:AACGCATT
+AACGCATT
++
+88+AD@?8
+ at machine1:HiMom:abcdeACXX:1:2101:1336:2109 :Y:0:AACGCATT
+AACGCATT
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1427:2081 :Y:0:AACGCATT
+AACGCATT
++
+CCCFFFFF
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ATTATGTT-ATTATGTT-ATTATGTT.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAAAATT.1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ATTATGTT-ATTATGTT-ATTATGTT.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAAAATT.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ATTATGTT-ATTATGTT.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAAAATT.2.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ATTATGTT-ATTATGTT.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAAAATT.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CACATCCT-CACATCCT-CACATCCT.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAAAATT.barcode_1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CACATCCT-CACATCCT-CACATCCT.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAAAATT.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGGTAT.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGGTAT.1.fastq
new file mode 100644
index 0000000..6326fe4
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGGTAT.1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1236:2121 1:Y:0:ACAGGTAT
+NGGTGCTTCATATCCCTCTAGAGGA
++
+#1=BDDFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1341:2116 1:Y:0:ACAGGTAT
+NAGAAGCCCCAGGAGGAAGACAGTC
++
+#1=DDFFFHHHHHHHJIIJJJJJGI
+ at machine1:HiMom:abcdeACXX:1:2101:1063:2206 1:Y:0:ACAGGTAT
+TCCTATTCGCCTACACAATTCTCCG
++
+CCCFFFFFHHHHHJJJJJJJHJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1325:2083 1:Y:0:ACAGGTAT
+NCAGAAGAAAGGGCCTTGTCGGAGG
++
+#1=DDDDDHHFHDGI at EEHG:?FA8
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGGTAT.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGGTAT.2.fastq
new file mode 100644
index 0000000..e3fc8e5
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGGTAT.2.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1236:2121 2:Y:0:ACAGGTAT
+TTGCGCTTACTTTGTAGCCTTCATC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1341:2116 2:Y:0:ACAGGTAT
+ATAACAGCGAGACTGGCAACTTAAA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1063:2206 2:Y:0:ACAGGTAT
+NTGCTAGGATGAGGATGGATAGTAA
++
+#1=DDDFFHHHHHJHIIJHIIIHHJ
+ at machine1:HiMom:abcdeACXX:1:2101:1325:2083 2:Y:0:ACAGGTAT
+TGTGCTCTTCCGATCTGGAGAAAAA
++
+#########################
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGGTAT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGGTAT.barcode_1.fastq
new file mode 100644
index 0000000..e99ec81
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGGTAT.barcode_1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1236:2121 :Y:0:ACAGGTAT
+ACAGGTAT
++
+CCCFFDDF
+ at machine1:HiMom:abcdeACXX:1:1201:1341:2116 :Y:0:ACAGGTAT
+ACAGGTAT
++
+CCCFFBDD
+ at machine1:HiMom:abcdeACXX:1:2101:1063:2206 :Y:0:ACAGGTAT
+ACAGGTAT
++
+CCCFFDFF
+ at machine1:HiMom:abcdeACXX:1:2101:1325:2083 :Y:0:ACAGGTAT
+ACAGGTAT
++
+@@@BD=DD
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGTTGA.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGTTGA.1.fastq
new file mode 100644
index 0000000..0bf30ad
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGTTGA.1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:2101:1048:2238 1:Y:0:ACAGTTGA
+NCTGCCGTGTCCTGACTTCTGGAAT
++
+#1:B?ADDACF<DCG;EG<FHH at CE
+ at machine1:HiMom:abcdeACXX:1:2101:1216:2193 1:Y:0:ACAGTTGA
+TTTTCTTGGCCTCTGTTTTTTTTTT
++
+BCCFDFFFHHFFHJIGIJJJJJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGTTGA.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGTTGA.2.fastq
new file mode 100644
index 0000000..06756b0
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGTTGA.2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:2101:1048:2238 2:Y:0:ACAGTTGA
+NGTCACATCGTTGAAGCACTGGATC
++
+#11ADDDB<CFFHCHGDBHGIIIII
+ at machine1:HiMom:abcdeACXX:1:2101:1216:2193 2:Y:0:ACAGTTGA
+AGGCATGACACTGCATTTTAAATAC
++
+@@@DDDDDHFFHHGGDFHFHIIHGG
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGTTGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGTTGA.barcode_1.fastq
new file mode 100644
index 0000000..494500e
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGTTGA.barcode_1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:2101:1048:2238 :Y:0:ACAGTTGA
+ACAGTTGA
++
+?@7DDDDA
+ at machine1:HiMom:abcdeACXX:1:2101:1216:2193 :Y:0:ACAGTTGA
+ACAGTTGA
++
+CCCFFFFF
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CACATCCT-CACATCCT.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACCAGTTG.1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CACATCCT-CACATCCT.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/ACCAGTTG.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CAGGAGCC-CAGGAGCC-CAGGAGCC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACCAGTTG.2.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CAGGAGCC-CAGGAGCC-CAGGAGCC.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/ACCAGTTG.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CAGGAGCC-CAGGAGCC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACCAGTTG.barcode_1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CAGGAGCC-CAGGAGCC.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/ACCAGTTG.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATAGCGA-CATAGCGA-CATAGCGA.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACGAAATC.1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATAGCGA-CATAGCGA-CATAGCGA.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/ACGAAATC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATAGCGA-CATAGCGA.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACGAAATC.2.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATAGCGA-CATAGCGA.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/ACGAAATC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATGCTTA-CATGCTTA-CATGCTTA.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACGAAATC.barcode_1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATGCTTA-CATGCTTA-CATGCTTA.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/ACGAAATC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTAAGAC.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTAAGAC.1.fastq
new file mode 100644
index 0000000..b707973
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTAAGAC.1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1259:2152 1:Y:0:ACTAAGAC
+CACCTATAATCCCAGCTACTCCAGA
++
+CCCFFFFFHHHHHJJJJJJIJJJIJ
+ at machine1:HiMom:abcdeACXX:1:1101:1261:2127 1:N:0:ACTAAGAC
+NTGAAATCTGGATAGGCTGGAGTTA
++
+#0-@@@###################
+ at machine1:HiMom:abcdeACXX:1:2101:1021:2209 1:Y:0:ACTAAGAC
+NGGCCCCACCCTCCTCCAGCACGTC
++
+#1=DDFFFHHHHHJJJJJJHIIHFH
+ at machine1:HiMom:abcdeACXX:1:2101:1262:2128 1:N:0:ACTAAGAC
+AGCAGAAGGGCAAAAGCTGGCTTGA
++
+9;<@:@###################
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTAAGAC.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTAAGAC.2.fastq
new file mode 100644
index 0000000..c5caacf
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTAAGAC.2.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1259:2152 2:Y:0:ACTAAGAC
+ATTTTTATATTTTTTTAGACATAGG
++
+CCCFFFFFGHHHHJJJJIGIIJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1261:2127 2:N:0:ACTAAGAC
+TTTTTTTTTTTTTTTTTTTTTTTTT
++
+CCCFFFFFHGHHHJJIFDDDDDDDD
+ at machine1:HiMom:abcdeACXX:1:2101:1021:2209 2:Y:0:ACTAAGAC
+NNGGAAGGCTGCTAGCTGGCCAGAG
++
+##08@>??@@??@?????????>?@
+ at machine1:HiMom:abcdeACXX:1:2101:1262:2128 2:N:0:ACTAAGAC
+TCTTGTGGTAACTTTTCTGACACCT
++
+-(---9@;@?:8>?4:>?@######
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTAAGAC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTAAGAC.barcode_1.fastq
new file mode 100644
index 0000000..4e1fb6b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTAAGAC.barcode_1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1259:2152 :Y:0:ACTAAGAC
+ACTAAGAC
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1101:1261:2127 :N:0:ACTAAGAC
+ACTAAGAC
++
+>7+ at A7A7
+ at machine1:HiMom:abcdeACXX:1:2101:1021:2209 :Y:0:ACTAAGAC
+ACTAAGAC
++
+ at CCDFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1262:2128 :N:0:ACTAAGAC
+ACTAAGAC
++
+1+8?ADD8
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATGCTTA-CATGCTTA.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTGTACC.1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATGCTTA-CATGCTTA.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTGTACC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCAGTTAG-CCAGTTAG-CCAGTTAG.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTGTACC.2.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCAGTTAG-CCAGTTAG-CCAGTTAG.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTGTACC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCAGTTAG-CCAGTTAG.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTGTACC.barcode_1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCAGTTAG-CCAGTTAG.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTGTACC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTGTATC.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTGTATC.1.fastq
new file mode 100644
index 0000000..97623fe
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTGTATC.1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1458:2109 1:Y:0:ACTGTATC
+NGAGACCATAGAGCGGATGCTTTCA
++
+#1=DDDFFHHGHGIJJIGIIJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1105:2131 1:Y:0:ACTGTATC
+TTGGAACACAGCGGGAATCACAGCA
++
+CCCFFFFFHHHHHJIJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1349:2084 1:Y:0:ACTGTATC
+NCAAGTAGCAGTGTCACGCCTTAGC
++
+#1=DDBDDADFDDBEH at HC=CEGG@
+ at machine1:HiMom:abcdeACXX:1:2101:1365:2094 1:Y:0:ACTGTATC
+NAAGGTGAAGGCCGGCGCGCTCGCC
++
+#1=BDDDFFHHHHJGGGIGFIHIIJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTGTATC.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTGTATC.2.fastq
new file mode 100644
index 0000000..1605b41
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTGTATC.2.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1458:2109 2:Y:0:ACTGTATC
+GATACGAACACACAAGAACTTTTTT
++
+CCCFFFFFHHHHHJJJJJJJJJJJI
+ at machine1:HiMom:abcdeACXX:1:2101:1105:2131 2:Y:0:ACTGTATC
+CAGCAGCAGCAACAGCAGAAACATG
++
+CCCFFFFFHHHHHJJJJJIJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1349:2084 2:Y:0:ACTGTATC
+AGTCTGAATCATTGGTGTCTGAAGA
++
+<5;??=>=>>?##############
+ at machine1:HiMom:abcdeACXX:1:2101:1365:2094 2:Y:0:ACTGTATC
+GCTCTTCCGATCTTGTGCTCTTCCG
++
+CCCFFFFDHFHHGJJIIJIJJIHII
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTGTATC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTGTATC.barcode_1.fastq
new file mode 100644
index 0000000..a5cae5c
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTGTATC.barcode_1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1458:2109 :Y:0:ACTGTATC
+ACTGTATC
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1105:2131 :Y:0:ACTGTATC
+ACTGTATC
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1349:2084 :Y:0:ACTGTATC
+ACTGTATC
++
+=;7+22<A
+ at machine1:HiMom:abcdeACXX:1:2101:1365:2094 :Y:0:ACTGTATC
+ACTGTACC
++
+########
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCTACCAT-CCTACCAT-CCTACCAT.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGAAAAGA.1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCTACCAT-CCTACCAT-CCTACCAT.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/AGAAAAGA.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCTACCAT-CCTACCAT.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGAAAAGA.2.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCTACCAT-CCTACCAT.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/AGAAAAGA.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CTACCAGG-CTACCAGG-CTACCAGG.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGAAAAGA.barcode_1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CTACCAGG-CTACCAGG-CTACCAGG.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/AGAAAAGA.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGCATGGA.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGCATGGA.1.fastq
new file mode 100644
index 0000000..27ac39f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGCATGGA.1.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1406:2222 1:Y:0:AGCATGGA
+CTCCCCCCGGGCTGAACCAGGGTAC
++
+CCCFFDDDDHDFHIIIIIIIII9DG
+ at machine1:HiMom:abcdeACXX:1:1201:1291:2158 1:Y:0:AGCATGGA
+AGAAGGGGAAAGCCTTCATCTTGGC
++
+BCBFFFFFHHHHHJJJJJIIFIJIJ
+ at machine1:HiMom:abcdeACXX:1:2101:1370:2116 1:Y:0:AGCATGGA
+NTGGTGGTCCATAGAGATTTGAAAC
++
+#1:4BD7DACF?FCA:4+<ACHIIH
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGCATGGA.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGCATGGA.2.fastq
new file mode 100644
index 0000000..308b145
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGCATGGA.2.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1406:2222 2:Y:0:AGCATGGA
+GGCTGGACTCCCCTGGTTCTGGGCA
++
+;?@DDDBD?FHDFGIIIGIGHHIII
+ at machine1:HiMom:abcdeACXX:1:1201:1291:2158 2:Y:0:AGCATGGA
+CGTGTGCTCTTCCGATCTGATGGGC
++
+ at CCFFFDD?FHHFGEHHIIDHIIII
+ at machine1:HiMom:abcdeACXX:1:2101:1370:2116 2:Y:0:AGCATGGA
+CACCATCTGACATCATGTTTGAAAG
++
+@@@DFFFDFFHDHIGBHHII<HEDB
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGCATGGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGCATGGA.barcode_1.fastq
new file mode 100644
index 0000000..83c6cb0
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGCATGGA.barcode_1.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1406:2222 :Y:0:AGCATGGA
+AGCATGGA
++
+C@@DBFEF
+ at machine1:HiMom:abcdeACXX:1:1201:1291:2158 :Y:0:AGCATGGA
+AGCATGGA
++
+ at CCFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1370:2116 :Y:0:AGCATGGA
+AGCATGGA
++
+?:8A?3:B
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTAAGG.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTAAGG.1.fastq
new file mode 100644
index 0000000..0c29862
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTAAGG.1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1263:2236 1:N:0:AGGTAAGG
+CTTTGAAGACATTGTGAGATCTGTA
++
+<==A<42 at C+A4A?,2A@=4 at 7A??
+ at machine1:HiMom:abcdeACXX:1:2101:1054:2162 1:Y:0:AGGTAAGG
+NCCAGGTGTCTTCCCGGGCCCTGCC
++
+#1=DDFBDFHHHHJJJJJIJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1163:2203 1:Y:0:AGGTAAGG
+TCTCCATGTGAAACAAGCAAAAAGA
++
+CCCFFFFFHHHHGJJJIJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1249:2231 1:Y:0:AGGTAAGG
+GTTATTGATAGGATACTGTACAAAC
++
+ at BCFFFFDHHHHFIJJJJJJJJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTAAGG.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTAAGG.2.fastq
new file mode 100644
index 0000000..e6ec62a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTAAGG.2.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1263:2236 2:N:0:AGGTAAGG
+AGTTCTTCAGTAATTTTAGTACTGC
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1054:2162 2:Y:0:AGGTAAGG
+NGGACAGGGAAGGGAAGGAAGGGTG
++
+#4=DDFDFHHHHHJIJIIDHHGICG
+ at machine1:HiMom:abcdeACXX:1:2101:1163:2203 2:Y:0:AGGTAAGG
+TTGGTTCACTTATGTATTTATGAAT
++
+ at CCFDFFFHHHHHJHIIJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1249:2231 2:Y:0:AGGTAAGG
+TCTCTCGGCCTTCCACTCTAGCATA
++
+@@@FFFFFFHHGHIJJJGJIIJHIJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTAAGG.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTAAGG.barcode_1.fastq
new file mode 100644
index 0000000..a8d8a51
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTAAGG.barcode_1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1263:2236 :N:0:AGGTAAGG
+AGGTAAGG
++
+########
+ at machine1:HiMom:abcdeACXX:1:2101:1054:2162 :Y:0:AGGTAAGG
+AGGTAAGG
++
+B at BDDFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1163:2203 :Y:0:AGGTAAGG
+AGGTAAGG
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1249:2231 :Y:0:AGGTAAGG
+AGGTAAGG
++
+@@CBDFFF
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTCGCA.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTCGCA.1.fastq
new file mode 100644
index 0000000..b8fd6ca
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTCGCA.1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1150:2228 1:Y:0:AGGTCGCA
+GCTACTCAGTAGACAGTCCCACCCT
++
+@@CADDDDFCFHHIIIIGGIIGGGI
+ at machine1:HiMom:abcdeACXX:1:1101:1491:2120 1:Y:0:AGGTCGCA
+NGGCAGGTGCCCCCACTTGACTCTC
++
+#1?DFFFFGHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1190:2194 1:Y:0:AGGTCGCA
+AACCTGGCGCTAAACCATTCGTAGA
++
+CCCFFFFFHHHHHJJJJJJJJIJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1188:2195 1:Y:0:AGGTCGCA
+TTAGACCGTCGTGAGACAGGTTAGT
++
+ at CCFFFFFHHHHHJJJJJIIEHIJH
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTCGCA.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTCGCA.2.fastq
new file mode 100644
index 0000000..b8537f5
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTCGCA.2.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1150:2228 2:Y:0:AGGTCGCA
+ATGGGAGGCGATTCCTAGGGGGTTG
++
+8?=DD8;@BH6DHD<FGGGEIGHIG
+ at machine1:HiMom:abcdeACXX:1:1101:1491:2120 2:Y:0:AGGTCGCA
+GGCCAGGCTGAACTTCTGAGCTGCT
++
+CCCFFFFFHHHGHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1190:2194 2:Y:0:AGGTCGCA
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1188:2195 2:Y:0:AGGTCGCA
+GCACATACACCAAATGTCTGAACCT
++
+CCCFFFFFHHHHHJJJHIJJJJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTCGCA.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTCGCA.barcode_1.fastq
new file mode 100644
index 0000000..3c18d15
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTCGCA.barcode_1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1150:2228 :Y:0:AGGTCGCA
+AGGTCGCA
++
+@@@DDFFF
+ at machine1:HiMom:abcdeACXX:1:1101:1491:2120 :Y:0:AGGTCGCA
+AGGTCGCA
++
+BCCDFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1190:2194 :Y:0:AGGTCGCA
+AGGTCGCA
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1188:2195 :Y:0:AGGTCGCA
+AGGTCGCA
++
+BCCDFFFF
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTATCAA.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTATCAA.1.fastq
new file mode 100644
index 0000000..cccbe53
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTATCAA.1.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1100:2207 1:Y:0:ATTATCAA
+ACGACAGACGTTCTTTCTTTGCTGC
++
+CCCFFFFFHHFHHJIJJJJJHIJJH
+ at machine1:HiMom:abcdeACXX:1:1101:1157:2135 1:Y:0:ATTATCAA
+NGGACATTGTAATCATTTCTTACAA
++
+#1=DD?DDHHHHHGGHIIIIIIIII
+ at machine1:HiMom:abcdeACXX:1:1101:1269:2170 1:Y:0:ATTATCAA
+ACAGTGTGGGAGGCAGACGAAGAGA
++
+@@@DDDDDFA:C at EGA?FD<FFHII
+ at machine1:HiMom:abcdeACXX:1:1201:1018:2217 1:N:0:ATTATCAA
+NTTTCTCTGGGCGCAAAGATGTTCA
++
+#07;8=8<<99(:=@@/@7>>6=?>
+ at machine1:HiMom:abcdeACXX:1:1201:1118:2198 1:Y:0:ATTATCAA
+CAAGTGTACAGGATTAGACTGGGTT
++
+BCCFDEBDHHHHHIJJJGIIIJJGH
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTATCAA.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTATCAA.2.fastq
new file mode 100644
index 0000000..b725e93
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTATCAA.2.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1100:2207 2:Y:0:ATTATCAA
+AGGCTNNNNNNNNNNNNGNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1157:2135 2:Y:0:ATTATCAA
+TTTAAAGTCTTAATCAAAGATGATA
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1269:2170 2:Y:0:ATTATCAA
+TTCCAAGCCTGTGCTTTAAGGAAAA
++
+@@<ADBDBDF8DDCFH at GIE@@GGH
+ at machine1:HiMom:abcdeACXX:1:1201:1018:2217 2:N:0:ATTATCAA
+NNNNNNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1201:1118:2198 2:Y:0:ATTATCAA
+AATAAACTTTATTAAAGCAGTTAAA
++
+C at CFFFFFHDHHHGIIIJJJIJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTATCAA.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTATCAA.barcode_1.fastq
new file mode 100644
index 0000000..9d77783
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTATCAA.barcode_1.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1100:2207 :Y:0:ATTATCAA
+ATTATCAA
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1101:1157:2135 :Y:0:ATTATCAA
+ATTATCAA
++
+C at CFFFFF
+ at machine1:HiMom:abcdeACXX:1:1101:1269:2170 :Y:0:ATTATCAA
+ATTATCAA
++
+@@@DDDF?
+ at machine1:HiMom:abcdeACXX:1:1201:1018:2217 :N:0:ATTATCAA
+ATTATCAA
++
+;<;:BBDD
+ at machine1:HiMom:abcdeACXX:1:1201:1118:2198 :Y:0:ATTATCAA
+ATTATCAA
++
+@@@DDBDD
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTCCTCT.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTCCTCT.1.fastq
new file mode 100644
index 0000000..3ed772b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTCCTCT.1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1309:2210 1:Y:0:ATTCCTCT
+ACACCAACCACCCAACTATCTATAA
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1018:2133 1:Y:0:ATTCCTCT
+NAAAACTTGAGGATGCTATGCAAGC
++
+#1:B:ADDDDDDDEEAEBF9FFEBF
+ at machine1:HiMom:abcdeACXX:1:1201:1073:2225 1:Y:0:ATTCCTCT
+GGGGCTGAGACCTTTGCTGATGGTG
++
+@@@FFFFFHHHGHJJJJJIIIGICH
+ at machine1:HiMom:abcdeACXX:1:1201:1242:2207 1:Y:0:ATTCCTCT
+ATGGCAAAGTGGTGTCTGAGACCAA
++
+BCCFFFFFGHHHHHIIIJFHIJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTCCTCT.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTCCTCT.2.fastq
new file mode 100644
index 0000000..31f3e57
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTCCTCT.2.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1309:2210 2:Y:0:ATTCCTCT
+AGTGGGCTAGGGCATTTTTAATCTT
++
+@@?DFFDFHHHDFHJIJJIJGIIIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1018:2133 2:Y:0:ATTCCTCT
+NNNNNNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1201:1073:2225 2:Y:0:ATTCCTCT
+CGTGTGCTCTTCCGATCTGGAGGGT
++
+ at BBDFFFFHHHHHJJJJJJJJJJJ:
+ at machine1:HiMom:abcdeACXX:1:1201:1242:2207 2:Y:0:ATTCCTCT
+ATCTTTTATTGGCCTCCTGCTCCCC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTCCTCT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTCCTCT.barcode_1.fastq
new file mode 100644
index 0000000..bb2bfeb
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTCCTCT.barcode_1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1309:2210 :Y:0:ATTCCTCT
+ATTCCTCT
++
+?@@ADEEF
+ at machine1:HiMom:abcdeACXX:1:1201:1018:2133 :Y:0:ATTCCTCT
+ATTCCTCT
++
+8??=BBBA
+ at machine1:HiMom:abcdeACXX:1:1201:1073:2225 :Y:0:ATTCCTCT
+ATTCCTCT
++
+B@@BDEFF
+ at machine1:HiMom:abcdeACXX:1:1201:1242:2207 :Y:0:ATTCCTCT
+ATTCCTCT
++
+?BBDDDFF
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAACTCTC.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAACTCTC.1.fastq
new file mode 100644
index 0000000..3d04499
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAACTCTC.1.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1140:2120 1:Y:0:CAACTCTC
+NCCCCAACATTCTAATTATGCCTCA
++
+#1:BDFFDHFFDFIJJJIIJIIIII
+ at machine1:HiMom:abcdeACXX:1:1101:1328:2225 1:Y:0:CAACTCTC
+GAAATGCATCTGTCTTAGAAACTGG
++
+??@=BDDDFDD<<,<2:C<F:FFEA
+ at machine1:HiMom:abcdeACXX:1:1201:1127:2112 1:N:0:CAACTCTC
+NGTCAAGGATGTTCGTCGTGGCAAC
++
+#1=BDDDDDDDDDID<AE?@<CEEE
+ at machine1:HiMom:abcdeACXX:1:1201:1452:2143 1:Y:0:CAACTCTC
+TATCCCCTCTAAGACGGACCTGGGT
++
+CCCFFFFFHHHHHJJIIIJJJJJJG
+ at machine1:HiMom:abcdeACXX:1:1201:1486:2146 1:N:0:CAACTCTC
+GTTCTCTGTCCCCAGGTCCTGTCTC
++
+===A7<7222<<=C=?+<7>@?ACB
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAACTCTC.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAACTCTC.2.fastq
new file mode 100644
index 0000000..86e9f33
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAACTCTC.2.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1140:2120 2:Y:0:CAACTCTC
+TTTTTTTTTTTTTAACTTTGCAAAT
++
+@@@DDDDDHHHHFB at 9FHI@BFH@@
+ at machine1:HiMom:abcdeACXX:1:1101:1328:2225 2:Y:0:CAACTCTC
+AGGAAATTAGGACTTACCTGACATA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1201:1127:2112 2:N:0:CAACTCTC
+TAATCACCTGAGCAGTGAAGCCAGC
++
+@<@?BDDDHD?FDBHI?AHGGGDFH
+ at machine1:HiMom:abcdeACXX:1:1201:1452:2143 2:Y:0:CAACTCTC
+TTTTAGTCTTAGCATTTACTTTCCC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1486:2146 2:N:0:CAACTCTC
+TTTTTTTTTTTTTTTTTTTTTGGGC
++
+<<<@??@??@???????########
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAACTCTC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAACTCTC.barcode_1.fastq
new file mode 100644
index 0000000..e0a8164
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAACTCTC.barcode_1.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1140:2120 :Y:0:CAACTCTC
+CAACTCTC
++
+@@@DDFDF
+ at machine1:HiMom:abcdeACXX:1:1101:1328:2225 :Y:0:CAACTCTC
+CAACTCTC
++
+??;=A:B=
+ at machine1:HiMom:abcdeACXX:1:1201:1127:2112 :N:0:CAACTCTC
+CAACTCTC
++
+=??BA?BD
+ at machine1:HiMom:abcdeACXX:1:1201:1452:2143 :Y:0:CAACTCTC
+CAACTCTC
++
+BC at DDFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1486:2146 :N:0:CAACTCTC
+CAACTCTC
++
+?@@1:DBD
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CTACCAGG-CTACCAGG.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAATAGAC.1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CTACCAGG-CTACCAGG.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/CAATAGAC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACACGA-GCACACGA-GCACACGA.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAATAGAC.2.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACACGA-GCACACGA-GCACACGA.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/CAATAGAC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACACGA-GCACACGA.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAATAGAC.barcode_1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACACGA-GCACACGA.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/CAATAGAC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAATAGTC.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAATAGTC.1.fastq
new file mode 100644
index 0000000..bdf2139
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAATAGTC.1.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1316:2126 1:Y:0:CAATAGTC
+NAAAAAAAAAAAAAAAAAAAAAAAA
++
+#1BDFFFFHHHHHJJJJFDDDDDDD
+ at machine1:HiMom:abcdeACXX:1:1101:1399:2128 1:Y:0:CAATAGTC
+NTGCCCTTCGTCCTGGGAAACGGGG
++
+#1BDFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1054:2151 1:Y:0:CAATAGTC
+NTAGTGCTGGGCACTAAGTAATACC
++
+#4=DDDFFHHHHHJJJJJHIJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1345:2181 1:Y:0:CAATAGTC
+GGATAATCCTATTTATTACCTCAGA
++
+BBBDDFFFHHHHHJJJJJJJJJIJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1392:2184 1:Y:0:CAATAGTC
+TTTCAGATTGGTCATTGTTAGTGTA
++
+??@BDDDEHBHADHHIIEHDHFHFF
+ at machine1:HiMom:abcdeACXX:1:2101:1172:2152 1:N:0:CAATAGTC
+AACACGGACAAAGGAGTCTAACACG
++
+<<<??8@@#################
+ at machine1:HiMom:abcdeACXX:1:2101:1491:2093 1:Y:0:CAATAGTC
+NCTATGCCGATCGGGTGTCCGCACT
++
+#1=DDDDDHHFHHIIEHHHBGHGII
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAATAGTC.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAATAGTC.2.fastq
new file mode 100644
index 0000000..5029765
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAATAGTC.2.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1316:2126 2:Y:0:CAATAGTC
+TCTTTTTTTTTTTTTTTTTTTTTTT
++
+CCCFFFFFHHHHHJJJJHFDDDDDD
+ at machine1:HiMom:abcdeACXX:1:1101:1399:2128 2:Y:0:CAATAGTC
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CCCFFFFFHHHHHIJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1054:2151 2:Y:0:CAATAGTC
+GTCAGGCACTGAGAATATATGGGTG
++
+CBCFFFFFHHHHHJJJJJJJJJJEG
+ at machine1:HiMom:abcdeACXX:1:1201:1345:2181 2:Y:0:CAATAGTC
+ATACGGATGTGTTTAGGAGTGGGAC
++
+CCCFFFFFHHHHHIIJJHJFHIJIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1392:2184 2:Y:0:CAATAGTC
+ATCTTTATTCATTTGTATGATCTTA
++
+@@BFFFFFHFFHFHIHIIJIJJJJI
+ at machine1:HiMom:abcdeACXX:1:2101:1172:2152 2:N:0:CAATAGTC
+ATCGTTTCTGGGGACTAGTGAGGCG
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1491:2093 2:Y:0:CAATAGTC
+AGAGACGGGGTCTCGCTATGTTGCC
++
+BCCDFFFFHHHHHJIIJJJJIJIJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAATAGTC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAATAGTC.barcode_1.fastq
new file mode 100644
index 0000000..1d92fa2
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAATAGTC.barcode_1.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1316:2126 :Y:0:CAATAGTC
+CAATAGAC
++
+1>>7A###
+ at machine1:HiMom:abcdeACXX:1:1101:1399:2128 :Y:0:CAATAGTC
+CAATAGTC
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1054:2151 :Y:0:CAATAGTC
+CAATAGTC
++
+CCCFFFDF
+ at machine1:HiMom:abcdeACXX:1:1201:1345:2181 :Y:0:CAATAGTC
+CAATAGTC
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1392:2184 :Y:0:CAATAGTC
+CAATAGTC
++
+ at CCFFDDE
+ at machine1:HiMom:abcdeACXX:1:2101:1172:2152 :N:0:CAATAGTC
+CAATAGTC
++
+########
+ at machine1:HiMom:abcdeACXX:1:2101:1491:2093 :Y:0:CAATAGTC
+CAATAGTC
++
+@@@FDEBD
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACATCT-GCACATCT-GCACATCT.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGAT.1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACATCT-GCACATCT-GCACATCT.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGAT.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACATCT-GCACATCT.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGAT.2.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACATCT-GCACATCT.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGAT.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GGTCCAGA-GGTCCAGA-GGTCCAGA.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGAT.barcode_1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GGTCCAGA-GGTCCAGA-GGTCCAGA.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGAT.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGTA.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGTA.1.fastq
new file mode 100644
index 0000000..39cb19f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGTA.1.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1420:2213 1:Y:0:CAGCGGTA
+TACCTGGTTGATCCTGCCAGTAGCA
++
+@@CFFFFDDHHGHJGGHIJJIHGBH
+ at machine1:HiMom:abcdeACXX:1:1201:1364:2113 1:Y:0:CAGCGGTA
+NCACTCATTTTCTTATGTGGGATAT
++
+#1=DDFDFHHHHHIJJIFHIIHHHI
+ at machine1:HiMom:abcdeACXX:1:2101:1072:2170 1:Y:0:CAGCGGTA
+ATCACCGCACTCATTTCCCGCTTCC
++
+CCCFFFFFHHHACEEGHIIBHIIII
+ at machine1:HiMom:abcdeACXX:1:2101:1123:2095 1:Y:0:CAGCGGTA
+NTGGACAACATGTTCGAGAGCTACA
++
+#1=BBDDDFFFFDGFGIG?F;HHFI
+ at machine1:HiMom:abcdeACXX:1:2101:1151:2236 1:N:0:CAGCGGTA
+TTAAAGAGGTTCAGGGATGCAGAGT
++
+#########################
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGTA.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGTA.2.fastq
new file mode 100644
index 0000000..3f02733
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGTA.2.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1420:2213 2:Y:0:CAGCGGTA
+TTCACTGTACCGGCCGTGCGTACTT
++
+ at CCFFFFDHHHFGIJJJJJJGHIGG
+ at machine1:HiMom:abcdeACXX:1:1201:1364:2113 2:Y:0:CAGCGGTA
+TAAAGAGAGCCAGTGGAGTTACGAC
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1072:2170 2:Y:0:CAGCGGTA
+NGGGGAGACAGAGAGGATCAGAAGT
++
+#4=BDDFDHHDFHEGFEGGIJIIIG
+ at machine1:HiMom:abcdeACXX:1:2101:1123:2095 2:Y:0:CAGCGGTA
+TCCGCCTCCAGCTTCAGCTTCTCCT
++
+@@@FDDFFHHHHHJHGGJIJJJEHH
+ at machine1:HiMom:abcdeACXX:1:2101:1151:2236 2:N:0:CAGCGGTA
+TTTGAAGCCTCTTTATCCTTGGCAT
++
+#########################
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGTA.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGTA.barcode_1.fastq
new file mode 100644
index 0000000..7d6da72
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGTA.barcode_1.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1420:2213 :Y:0:CAGCGGTA
+CAGCGGTA
++
+ at C@FFFDF
+ at machine1:HiMom:abcdeACXX:1:1201:1364:2113 :Y:0:CAGCGGTA
+CAGCGGTA
++
+C at CFFF@D
+ at machine1:HiMom:abcdeACXX:1:2101:1072:2170 :Y:0:CAGCGGTA
+CAGCGGTA
++
+B@@DFDDF
+ at machine1:HiMom:abcdeACXX:1:2101:1123:2095 :Y:0:CAGCGGTA
+CAGCGGTA
++
+@?@DDF@@
+ at machine1:HiMom:abcdeACXX:1:2101:1151:2236 :N:0:CAGCGGTA
+TAGCGGTA
++
+########
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAACATT.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAACATT.1.fastq
new file mode 100644
index 0000000..8305d35
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAACATT.1.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1083:2193 1:Y:0:CCAACATT
+TTCTACCTCACCTTAGGGAGAAGAC
++
+@@@DDBDDD>F><C<4CG?EHGHIG
+ at machine1:HiMom:abcdeACXX:1:1101:1175:2197 1:Y:0:CCAACATT
+CCCCTGAGGACACCATCCCACTCCA
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1138:2227 1:N:0:CCAACATT
+GCTGACACAATCTCTTCCGCCTGGT
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1201:1260:2165 1:Y:0:CCAACATT
+GGACACGGACAGGATTGACAGATTG
++
+BCBFFFFFHHHHHHIIJHIIIFHIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1281:2133 1:Y:0:CCAACATT
+NGGAAATCCAGAAAACATAGAAGAT
++
+#1=DDFFFHHHHHIJJJJJJJJIJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1331:2162 1:Y:0:CCAACATT
+ACGCTCGGCTAATTTTTGTATTTTT
++
+ at CCFFFDFHHHHHIJJJJHIJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1186:2093 1:Y:0:CCAACATT
+NCGACCATAAACGATGCCGACCGGC
++
+#4=DFFFFHHHHHJJJJJJJJJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAACATT.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAACATT.2.fastq
new file mode 100644
index 0000000..ab8867f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAACATT.2.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1083:2193 2:Y:0:CCAACATT
+AGGCTNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1175:2197 2:Y:0:CCAACATT
+AAGAGCTGGGGAACATCCAGAAAGG
++
+BC at FFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1138:2227 2:N:0:CCAACATT
+GACAAATATAGGAAATAGAAGCTAT
++
+=1=A=AAA,2?4>7C<<4<A+3<AB
+ at machine1:HiMom:abcdeACXX:1:1201:1260:2165 2:Y:0:CCAACATT
+ATCTGATCTAAGTTGGGGGACGCCG
++
+@@@FFDFFHHHHHJJJIJIIIGIJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1281:2133 2:Y:0:CCAACATT
+GCAACAAAATTTCATATGACTTAGC
++
+CCCFFFFFHHHHHJJIIIHICHIIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1331:2162 2:Y:0:CCAACATT
+TAATCCCAGTACTTTGGGAGGCCAA
++
+CCCFFFFFHHHHHJJJJIJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1186:2093 2:Y:0:CCAACATT
+AATGTTGGGAGGACAATGATGGAAA
++
+#########################
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAACATT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAACATT.barcode_1.fastq
new file mode 100644
index 0000000..576b369
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAACATT.barcode_1.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1083:2193 :Y:0:CCAACATT
+CCAACATT
++
+?@;DD?BD
+ at machine1:HiMom:abcdeACXX:1:1101:1175:2197 :Y:0:CCAACATT
+CCAACATT
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1138:2227 :N:0:CCAACATT
+CCAACATT
++
+########
+ at machine1:HiMom:abcdeACXX:1:1201:1260:2165 :Y:0:CCAACATT
+CCAACATT
++
+C at CFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1281:2133 :Y:0:CCAACATT
+CCAACATT
++
+C at CFFFDF
+ at machine1:HiMom:abcdeACXX:1:1201:1331:2162 :Y:0:CCAACATT
+CCAACATT
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1186:2093 :Y:0:CCAACATT
+CCAACATT
++
+CCCFFFFF
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAGCACC.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAGCACC.1.fastq
new file mode 100644
index 0000000..1f95caa
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAGCACC.1.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1212:2230 1:Y:0:CCAGCACC
+TTTCTATTAGCTCTTAGTAAGATTA
++
+CCCFFFFFHHHHHJJJIJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1204:2228 1:Y:0:CCAGCACC
+CCGATACGCTGAGTGTGGTTTGCGG
++
+CCCFFFFFHHHFHEGGHIHIJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1100:2085 1:Y:0:CCAGCACC
+NCACATGGATGAGGAGAATGAGGAT
++
+#1=DDFFFFHHHHJHIGIHHHIJEH
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAGCACC.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAGCACC.2.fastq
new file mode 100644
index 0000000..d5b31ba
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAGCACC.2.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1212:2230 2:Y:0:CCAGCACC
+TTTTAGCTTTATTGGGGAGGGGGTG
++
+CCCFFFFFHHGHHJJJJGJJJJJDF
+ at machine1:HiMom:abcdeACXX:1:1201:1204:2228 2:Y:0:CCAGCACC
+TCTTCTTGTCGATGAGGAACTTGGT
++
+@?@FFFFFDHHGHJIJJGHIIJJJH
+ at machine1:HiMom:abcdeACXX:1:2101:1100:2085 2:Y:0:CCAGCACC
+ATCTTGATCTCCTCCTTCTTGGCCT
++
+@@@DDDDDHHFHFEIIIIHHBAHBG
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAGCACC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAGCACC.barcode_1.fastq
new file mode 100644
index 0000000..05832a8
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAGCACC.barcode_1.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1212:2230 :Y:0:CCAGCACC
+CCAGCACC
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1204:2228 :Y:0:CCAGCACC
+CCAGCACC
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1100:2085 :Y:0:CCAGCACC
+CCAGCACC
++
+CCCFFFFF
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GGTCCAGA-GGTCCAGA.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCATGCGT.1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GGTCCAGA-GGTCCAGA.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/CCATGCGT.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GTATAACA-GTATAACA-GTATAACA.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCATGCGT.2.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GTATAACA-GTATAACA-GTATAACA.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/CCATGCGT.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GTATAACA-GTATAACA.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CCATGCGT.barcode_1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GTATAACA-GTATAACA.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/CCATGCGT.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCCTTCC.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCCTTCC.1.fastq
new file mode 100644
index 0000000..96daf32
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCCTTCC.1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1122:2227 1:Y:0:CGCCTTCC
+AGAAGACGAGGCTGAGAGTGACATC
++
+@@@FFFFFHHHDHJGHGHCHHJJIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1160:2109 1:Y:0:CGCCTTCC
+NAGAAGCCTTTGCACCCTGGGAGGA
++
+#1=DDDFFHHHHHJJJJJJJJIIJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCCTTCC.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCCTTCC.2.fastq
new file mode 100644
index 0000000..3c26563
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCCTTCC.2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1122:2227 2:Y:0:CGCCTTCC
+GTCATATAAGGCCCAGTCCAAGGAA
++
+@@@FFFFFHHHGGIJIGGIJFIJII
+ at machine1:HiMom:abcdeACXX:1:1201:1160:2109 2:Y:0:CGCCTTCC
+ACATCCTTCCCATGCCACCAACTCG
++
+CCCFFFFFGHHHHJJJJJJJJJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCCTTCC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCCTTCC.barcode_1.fastq
new file mode 100644
index 0000000..a14ab0c
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCCTTCC.barcode_1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1122:2227 :Y:0:CGCCTTCC
+CGCCTTCC
++
+@@@DDFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1160:2109 :Y:0:CGCCTTCC
+CGCCTTCC
++
+C at BFFFFF
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCTATGT.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCTATGT.1.fastq
new file mode 100644
index 0000000..3542f21
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCTATGT.1.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1291:2150 1:Y:0:CGCTATGT
+CGTGGGGAACCTGGCGCTAAACCAT
++
+ at BBFFFFFHHHHHJJJJIJJJJJIJ
+ at machine1:HiMom:abcdeACXX:1:1101:1314:2233 1:Y:0:CGCTATGT
+GTTTATTGGGGCATTCCTTATCCCA
++
+@??DDDDBDHF>FCHGGGBFAAED9
+ at machine1:HiMom:abcdeACXX:1:1101:1441:2148 1:Y:0:CGCTATGT
+ACTTTCACCGCTACACGACCGGGGG
++
+CCCFFFFFHGFFHIIFIHJIGGII>
+ at machine1:HiMom:abcdeACXX:1:1201:1043:2246 1:Y:0:CGCTATGT
+NTTCTCGGCTGTCATGTGCAACATT
++
+#1=DDBDFHHHDFFBHGHGHIIJEH
+ at machine1:HiMom:abcdeACXX:1:1201:1134:2144 1:Y:0:CGCTATGT
+TGCCAGGAAGTGTTTTTTCTGGGTC
++
+ at CCFFEFFHHFFFGIJJJJJJJJGH
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCTATGT.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCTATGT.2.fastq
new file mode 100644
index 0000000..74bd04e
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCTATGT.2.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1291:2150 2:Y:0:CGCTATGT
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CCCFFFFFHHFHHIJJJIIIGIJIJ
+ at machine1:HiMom:abcdeACXX:1:1101:1314:2233 2:Y:0:CGCTATGT
+AGGAAAGTTGGGCTGACCTGACAGA
++
+@@<DDD;=FBFADBCGDEH?F;FCG
+ at machine1:HiMom:abcdeACXX:1:1101:1441:2148 2:Y:0:CGCTATGT
+TTTTGGCTCTAGAGGGGGTAGAGGG
++
+CCCFFFFFHHDFBHIIJJ1?FGHIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1043:2246 2:Y:0:CGCTATGT
+NGCATCATTTCNNGCTTCTCTCTGT
++
+#0;@@??@=@>##22=;@??><@??
+ at machine1:HiMom:abcdeACXX:1:1201:1134:2144 2:Y:0:CGCTATGT
+AGTGTGAGTAATGGTTGAGAGGTGG
++
+B@?DDDFFFHHGHJHHGFIHHIFGI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCTATGT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCTATGT.barcode_1.fastq
new file mode 100644
index 0000000..0a09fe6
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCTATGT.barcode_1.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1291:2150 :Y:0:CGCTATGT
+CGCTATGT
++
+@@@FFFFF
+ at machine1:HiMom:abcdeACXX:1:1101:1314:2233 :Y:0:CGCTATGT
+CGCTATGT
++
+@<@?B@;A
+ at machine1:HiMom:abcdeACXX:1:1101:1441:2148 :Y:0:CGCTATGT
+CGCTATGT
++
+@@BFFDDD
+ at machine1:HiMom:abcdeACXX:1:1201:1043:2246 :Y:0:CGCTATGT
+CGCTATGT
++
+@<?DD:B=
+ at machine1:HiMom:abcdeACXX:1:1201:1134:2144 :Y:0:CGCTATGT
+CGCTATGT
++
+CCCFFFFD
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTAACTCG.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTAACTCG.1.fastq
new file mode 100644
index 0000000..75df3c2
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTAACTCG.1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1363:2138 1:Y:0:CTAACTCG
+NGTCTGGCCTGCACAGACATCCTAC
++
+#1=DDFFFHHHHHJJJIJJIJJJIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1393:2143 1:Y:0:CTAACTCG
+TGGTTGATCCTGCCAGTAGCATATG
++
+@@@ADADDFHFFDBHE?G at HIIIEE
+ at machine1:HiMom:abcdeACXX:1:2101:1273:2119 1:N:0:CTAACTCG
+NAGATAAGAGTCCACACAGTTGAGT
++
+#11AAAAA<A?4=C=7?733<ACA3
+ at machine1:HiMom:abcdeACXX:1:2101:1414:2098 1:Y:0:CTAACTCG
+NAGGACATCGATAAAGGCGAGGTGT
++
+#1=DDFFFHHHHHJJJJJJJJJHHG
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTAACTCG.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTAACTCG.2.fastq
new file mode 100644
index 0000000..edb09e6
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTAACTCG.2.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1363:2138 2:Y:0:CTAACTCG
+GTTCTTAAACCTGTTAGAACTTCTG
++
+C@@FFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1393:2143 2:Y:0:CTAACTCG
+GATAAATGCACGCATCCCCCCCGCG
++
+C at CFFFFFGGHHHHJJJJJJJJJJI
+ at machine1:HiMom:abcdeACXX:1:2101:1273:2119 2:N:0:CTAACTCG
+ATGATGGATCTTCTCTAACTTGTCA
++
+>=><AAAAA+2AA?CB4@@ABB3?A
+ at machine1:HiMom:abcdeACXX:1:2101:1414:2098 2:Y:0:CTAACTCG
+TTGGGGCCGGTGCCGTCGGGCCCAA
++
+CCCFFFFFHHHHGJJIJJJJJJJIJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTAACTCG.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTAACTCG.barcode_1.fastq
new file mode 100644
index 0000000..038b4dc
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTAACTCG.barcode_1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1363:2138 :Y:0:CTAACTCG
+CTAACTCG
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1393:2143 :Y:0:CTAACTCG
+CTAACTCG
++
+@@CFDDFD
+ at machine1:HiMom:abcdeACXX:1:2101:1273:2119 :N:0:CTAACTCG
+CTAACTCG
++
+=++==ADB
+ at machine1:HiMom:abcdeACXX:1:2101:1414:2098 :Y:0:CTAACTCG
+CTAACTCG
++
+CCCFFFFF
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/N-N-N.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGC.1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/N-N-N.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/N-N.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGC.2.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/N-N.sam
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/L001/C1.1/s_1_1.bcl b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGC.barcode_1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaTests/L001/C1.1/s_1_1.bcl
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGT.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGT.1.fastq
new file mode 100644
index 0000000..8f1cd46
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGT.1.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1083:2121 1:Y:0:CTATGCGT
+NAGAACTGGCGCTGCGGGATGAACC
++
+#1=BDFFFHHHHHJJJJJHIJIJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1185:2143 1:Y:0:CTATGCGT
+ATCTGCCTGGTTCGGCCCGCCTGCC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1219:2115 1:Y:0:CTATGCGT
+NTATAGTGGAGGCCGGAGCAGGAAC
++
+#1:DABADHHHFHIIIGGHGIIIII
+ at machine1:HiMom:abcdeACXX:1:1201:1472:2121 1:N:0:CTATGCGT
+NTAAAGTGTGAACAAGGAAGGTCAT
++
+#07>@<9=@################
+ at machine1:HiMom:abcdeACXX:1:2101:1013:2146 1:Y:0:CTATGCGT
+NACACTGCTGCAGATGACAAGCAGC
++
+#4BDFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1231:2208 1:Y:0:CTATGCGT
+ACGCCGCAAGTCAGAGCCCCCCAGA
++
+@@@DDDFFFFB:DBBEBEFDHBDDB
+ at machine1:HiMom:abcdeACXX:1:2101:1233:2133 1:N:0:CTATGCGT
+GAGAGAAGCACTCTTGAGCGGGATA
++
+0;(@((@)2@###############
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGT.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGT.2.fastq
new file mode 100644
index 0000000..e9bc995
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGT.2.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1083:2121 2:Y:0:CTATGCGT
+ACACACAACACCACCGCCCTCCCCC
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1201:1185:2143 2:Y:0:CTATGCGT
+GCTGAAGGCCCGTGGGCCAGAGGTG
++
+ at CCFFFFFHHHHHJJJJJJJJJJHI
+ at machine1:HiMom:abcdeACXX:1:1201:1219:2115 2:Y:0:CTATGCGT
+TGGGAGTAGTTCCCTGCTAAGGGAG
++
+???DBDBDADDDDIEID:AFFD:?8
+ at machine1:HiMom:abcdeACXX:1:1201:1472:2121 2:N:0:CTATGCGT
+GTGTGCTCTTCCGATCTGGAGGATG
++
+=+=??A4A==A at 7A<?#########
+ at machine1:HiMom:abcdeACXX:1:2101:1013:2146 2:Y:0:CTATGCGT
+NNNNCGCTAGAACCAACTTATTCAT
++
+####24=?@@?@?@@?@@@@@@?@@
+ at machine1:HiMom:abcdeACXX:1:2101:1231:2208 2:Y:0:CTATGCGT
+AGCCAGTGTTGGTGTGTTGACTGTT
++
+@@;1ADABCF;BF<AACGCHEBHC<
+ at machine1:HiMom:abcdeACXX:1:2101:1233:2133 2:N:0:CTATGCGT
+TTTTTTTTTTTTTTTTTTTTTTTTT
++
+CCCFFFFFGHHHHJJJFDDDDDDDD
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGT.barcode_1.fastq
new file mode 100644
index 0000000..a776107
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGT.barcode_1.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1083:2121 :Y:0:CTATGCGT
+CTATGCGT
++
+CCCFFFFD
+ at machine1:HiMom:abcdeACXX:1:1201:1185:2143 :Y:0:CTATGCGT
+CTATGCGT
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1219:2115 :Y:0:CTATGCGT
+CCATGCGT
++
+??<DDA?D
+ at machine1:HiMom:abcdeACXX:1:1201:1472:2121 :N:0:CTATGCGT
+CTATGCGC
++
+;?=D####
+ at machine1:HiMom:abcdeACXX:1:2101:1013:2146 :Y:0:CTATGCGT
+CTATGCGT
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1231:2208 :Y:0:CTATGCGT
+CTATGCGT
++
+@<@?D8 at D
+ at machine1:HiMom:abcdeACXX:1:2101:1233:2133 :N:0:CTATGCGT
+CTATGCGT
++
+=??B####
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGCGGAT.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGCGGAT.1.fastq
new file mode 100644
index 0000000..b5fa044
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGCGGAT.1.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:2101:1102:2221 1:Y:0:CTGCGGAT
+TTTCATCTTATTTCATTGGTTTATA
++
+CCCFFFFFHHHHHJIJJJJIJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1126:2082 1:Y:0:CTGCGGAT
+NGTTTTAGGGGTGCGCAGGAGTCAA
++
+#11=A=DD?DF at D@CCGHIEFH at BG
+ at machine1:HiMom:abcdeACXX:1:2101:1216:2172 1:Y:0:CTGCGGAT
+TTTCTTCGCAGGATTTTTCTGAGCC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGCGGAT.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGCGGAT.2.fastq
new file mode 100644
index 0000000..1d02e67
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGCGGAT.2.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:2101:1102:2221 2:Y:0:CTGCGGAT
+ATAACTGACTCTACTCAGTAGATTA
++
+CCCFFFFFHHHHHJJJJJIJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1126:2082 2:Y:0:CTGCGGAT
+TCTCTTTCCACCTTGGTCACCTTCC
++
+ at C@DDDFFHHHHHJEGGIHHIJGIH
+ at machine1:HiMom:abcdeACXX:1:2101:1216:2172 2:Y:0:CTGCGGAT
+GGACTTCTAGGGGATTTAGCGGGGT
++
+CCCFFFFFHHHHHJJJJJJJJJJJD
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGCGGAT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGCGGAT.barcode_1.fastq
new file mode 100644
index 0000000..6e8722b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGCGGAT.barcode_1.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:2101:1102:2221 :Y:0:CTGCGGAT
+CTGCGGAT
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1126:2082 :Y:0:CTGCGGAT
+CTGCGGAT
++
+@@@FFFDA
+ at machine1:HiMom:abcdeACXX:1:2101:1216:2172 :Y:0:CTGCGGAT
+CAGCGGAT
++
+C at CFFFFF
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGTAATC.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGTAATC.1.fastq
new file mode 100644
index 0000000..3e478fc
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGTAATC.1.fastq
@@ -0,0 +1,24 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1403:2194 1:Y:0:CTGTAATC
+CTAAACAGAGAGAAGGTTTCTCTTT
++
+CCCFFFFFHHHHHJJJFHIJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1045:2105 1:N:0:CTGTAATC
+NTAAAGAGAAATCAAGAATACTATT
++
+#-4@?(@)@@###############
+ at machine1:HiMom:abcdeACXX:1:1201:1483:2126 1:N:0:CTGTAATC
+NTGATAAGGTGTTGCTATGTTACCC
++
+#1:D?DDDDA??2:<CC4:AEDF>?
+ at machine1:HiMom:abcdeACXX:1:2101:1011:2102 1:Y:0:CTGTAATC
+NAAACAAAACTGTAGAACTGTGTAT
++
+#1=DDFFFHHHHHJJIJJJIHHHJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1245:2154 1:Y:0:CTGTAATC
+TCGTTAAGTATATTCTTAGGTATTT
++
+CCCFFDFFFHFHHIIJJJJJFJJJI
+ at machine1:HiMom:abcdeACXX:1:2101:1386:2105 1:Y:0:CTGTAATC
+NTACTAAAGAAAAAGTTGAAGAACT
++
+#1=DDDFFHHHHHJJGHIJJJJIJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGTAATC.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGTAATC.2.fastq
new file mode 100644
index 0000000..8398b40
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGTAATC.2.fastq
@@ -0,0 +1,24 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1403:2194 2:Y:0:CTGTAATC
+ACATGGTGAAACCCTGTCTCTACTA
++
+CCCFFFDDHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1045:2105 2:N:0:CTGTAATC
+NTTTTTTTTTTNNTTTTTTTTTTTT
++
+#0;@@@@@@@?##0:????????=<
+ at machine1:HiMom:abcdeACXX:1:1201:1483:2126 2:N:0:CTGTAATC
+GCATGCAGCTGGGTGCTGTGATGCA
++
+@@@DDDBB<DD8F<<CGG?AA?A<F
+ at machine1:HiMom:abcdeACXX:1:2101:1011:2102 2:Y:0:CTGTAATC
+NNNNNTCACACATAATTTTAAAATT
++
+#####22@?@@??@@@@@??@@@@@
+ at machine1:HiMom:abcdeACXX:1:2101:1245:2154 2:Y:0:CTGTAATC
+ACCAATCAGTAGCACCACTATACAC
++
+CCCFFFFFHHHHHJJJJJJIJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1386:2105 2:Y:0:CTGTAATC
+AGGAATTATTCTTCTGCCATAAGGT
++
+B@@DDFFFHGFHHIJJJJJGIGIJH
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGTAATC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGTAATC.barcode_1.fastq
new file mode 100644
index 0000000..8163888
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGTAATC.barcode_1.fastq
@@ -0,0 +1,24 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1403:2194 :Y:0:CTGTAATC
+CTGTAATC
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1045:2105 :N:0:CTGTAATC
+CTGTAATC
++
+1112 at A##
+ at machine1:HiMom:abcdeACXX:1:1201:1483:2126 :N:0:CTGTAATC
+CTGTAATC
++
+ at C<DD:B?
+ at machine1:HiMom:abcdeACXX:1:2101:1011:2102 :Y:0:CTGTAATC
+CTGTAATC
++
+C at CFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1245:2154 :Y:0:CTGTAATC
+CTGTAATC
++
+ at CCFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1386:2105 :Y:0:CTGTAATC
+CTGTAATC
++
+CCCFFFFF
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/L001/C2.1/s_1_1.bcl.gz b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAAAAAA.1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaTests/L001/C2.1/s_1_1.bcl.gz
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAAAAAA.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/L001/C3.1/s_1_1.bcl b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAAAAAA.2.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaTests/L001/C3.1/s_1_1.bcl
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAAAAAA.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/L001/C4.1/s_1_1.bcl b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAAAAAA.barcode_1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaTests/L001/C4.1/s_1_1.bcl
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAAAAAA.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/Matrix/s_3_152_matrix.txt b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GAACGAT..1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaTests/Matrix/s_3_152_matrix.txt
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/GAACGAT..1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/Matrix/s_3_76_matrix.txt b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GAACGAT..2.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaTests/Matrix/s_3_76_matrix.txt
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/GAACGAT..2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/Matrix/s_6_152_matrix.txt b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GAACGAT..barcode_1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaTests/Matrix/s_6_152_matrix.txt
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/GAACGAT..barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAGGAAG.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAGGAAG.1.fastq
new file mode 100644
index 0000000..cb24187
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAGGAAG.1.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1338:2175 1:Y:0:GAAGGAAG
+CCCACCTTCCGGCGGCCGAAGACAC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1028:2202 1:Y:0:GAAGGAAG
+NTCCTGGGAAACGGGGCGCGGCTGG
++
+#4BDDDFFHHHHHIJIIJJJJJJIJ
+ at machine1:HiMom:abcdeACXX:1:2101:1084:2188 1:Y:0:GAAGGAAG
+TTGCTGCATGGGTTAATTGAGAATA
++
+CCCFFFFFHHHHFHHIIJJIJJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAGGAAG.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAGGAAG.2.fastq
new file mode 100644
index 0000000..604d638
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAGGAAG.2.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1338:2175 2:Y:0:GAAGGAAG
+GCTTGTTGGCTTTAACATCCACAAT
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1028:2202 2:Y:0:GAAGGAAG
+NNAAACNCNTNNNNNNNGGNNTGNN
++
+##42@?###################
+ at machine1:HiMom:abcdeACXX:1:2101:1084:2188 2:Y:0:GAAGGAAG
+TACAAGGTCAAAATCAGCAACAAGT
++
+CCCFFFFDHHHHHJJJJJJJJJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAGGAAG.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAGGAAG.barcode_1.fastq
new file mode 100644
index 0000000..7aad7f6
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAGGAAG.barcode_1.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1338:2175 :Y:0:GAAGGAAG
+GAAGGAAG
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1028:2202 :Y:0:GAAGGAAG
+GAAGGAAG
++
+CCCFFDFF
+ at machine1:HiMom:abcdeACXX:1:2101:1084:2188 :Y:0:GAAGGAAG
+GAAGGAAG
++
+ at B@FFFFF
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGA.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGA.1.fastq
new file mode 100644
index 0000000..2f3cd2a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGA.1.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1089:2172 1:Y:0:GACCAGGA
+TTCCAGCATGCGGTTTAAGTAGGAT
++
+ at CCFDFDBDFBF:<CEBHAFHHICH
+ at machine1:HiMom:abcdeACXX:1:1101:1347:2149 1:Y:0:GACCAGGA
+GAGCAGATCGGAAGAGCACAGATCG
++
+@@@FFDDDHHHHHIJJBGGHJIHEG
+ at machine1:HiMom:abcdeACXX:1:1201:1095:2146 1:Y:0:GACCAGGA
+GCTGAGTCATGTAGTAAGCCTGTGC
++
+BB at FDDDFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1123:2161 1:N:0:GACCAGGA
+CACTAACTCCTGACCTCAAATAATC
++
+?7?=DD?DD+CDBE>E at EEF@+<CF
+ at machine1:HiMom:abcdeACXX:1:1201:1439:2156 1:Y:0:GACCAGGA
+AGCCGCGAGGTGCTGGCGGACTTCC
++
+:;1BDDDAA88A<?<E1C:D#####
+ at machine1:HiMom:abcdeACXX:1:2101:1207:2084 1:N:0:GACCAGGA
+NTAGATGACCAAAACTTGCAGGGCA
++
+#1:A<?@A+7A=?CBCCBCCBAAAA
+ at machine1:HiMom:abcdeACXX:1:2101:1312:2105 1:Y:0:GACCAGGA
+NTTCCCTCAGGATAGCTGGCGCTCT
++
+#1=DDFFFGHGHHJJJJJJJJJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGA.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGA.2.fastq
new file mode 100644
index 0000000..759b346
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGA.2.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1089:2172 2:Y:0:GACCAGGA
+TCCGGNNNNNNNNNNNNNNNNNNNN
++
+:<<??####################
+ at machine1:HiMom:abcdeACXX:1:1101:1347:2149 2:Y:0:GACCAGGA
+GCTCTTCCGATCTGTGCTCTTCCGA
++
+CCCFFFFFDFHHFIJDGIGGHGIGH
+ at machine1:HiMom:abcdeACXX:1:1201:1095:2146 2:Y:0:GACCAGGA
+ACTGACAACACCAAATGCTGCTAAG
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1123:2161 2:N:0:GACCAGGA
+CGTGTGCTCTTCCGATCTGCATACA
++
+===AAAA8AAAA<AAA)@CBA9>A#
+ at machine1:HiMom:abcdeACXX:1:1201:1439:2156 2:Y:0:GACCAGGA
+GGAGATTATTTGCCTTGAAGTAAGC
++
+-;(22<>>@>8@>8;@#########
+ at machine1:HiMom:abcdeACXX:1:2101:1207:2084 2:N:0:GACCAGGA
+TCACCACTCTTCTGGGCATCCCCTG
++
+@@@DDEDFHHHHHIJIHHGHGGJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1312:2105 2:Y:0:GACCAGGA
+GTTGAGAATAGGTTGAGATCGTTTC
++
+ at CCFFFDFHHFHDHIJJJJJJJIJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGA.barcode_1.fastq
new file mode 100644
index 0000000..5036139
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGA.barcode_1.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1089:2172 :Y:0:GACCAGGA
+GACCAGGA
++
+?@@FF;=B
+ at machine1:HiMom:abcdeACXX:1:1101:1347:2149 :Y:0:GACCAGGA
+GACCAGGA
++
+CC at DFFFD
+ at machine1:HiMom:abcdeACXX:1:1201:1095:2146 :Y:0:GACCAGGA
+GACCAGGA
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1123:2161 :N:0:GACCAGGA
+GACCAGGA
++
+?;@DFDFF
+ at machine1:HiMom:abcdeACXX:1:1201:1439:2156 :Y:0:GACCAGGA
+GACCAGGC
++
+########
+ at machine1:HiMom:abcdeACXX:1:2101:1207:2084 :N:0:GACCAGGA
+GACCAGGA
++
+@@CDFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1312:2105 :Y:0:GACCAGGA
+GACCAGGA
++
+CCCFFFFF
diff --git a/testdata/net/sf/picard/illumina/s_2_eland_query.txt b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGC.1.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/s_2_eland_query.txt
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/s_5_eland_query.txt b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGC.2.fastq
similarity index 100%
rename from testdata/net/sf/picard/illumina/s_5_eland_query.txt
rename to testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGC.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCGTTG.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCGTTG.1.fastq
new file mode 100644
index 0000000..52b1c2e
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCGTTG.1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1218:2200 1:Y:0:GACCGTTG
+GCACCGGAAGAGCACACAGATCGGA
++
+CCCFFFFDFHGHHJJIJIJJJJJJI
+ at machine1:HiMom:abcdeACXX:1:1101:1257:2223 1:Y:0:GACCGTTG
+TGTATTCGAGAGATCAAAGAGAGAG
++
+@@=DDBDD?FFHHEIDBDFCEDBAF
+ at machine1:HiMom:abcdeACXX:1:1201:1180:2119 1:Y:0:GACCGTTG
+NTGAAAGATTTAGAGAGCTTACAAA
++
+#1=DDDDDHHHGHJJIIJJJJIJJI
+ at machine1:HiMom:abcdeACXX:1:2101:1036:2087 1:Y:0:GACCGTTG
+NTGTAGTTTCTTTAGGCAAATTTGT
++
+#4=BDDDFHHHHHJJJJJJIIJJJI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCGTTG.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCGTTG.2.fastq
new file mode 100644
index 0000000..a634b3b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCGTTG.2.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1218:2200 2:Y:0:GACCGTTG
+GCTCTTCCGATCTATCTGCTCGTCC
++
+(-(=34???3;@#############
+ at machine1:HiMom:abcdeACXX:1:1101:1257:2223 2:Y:0:GACCGTTG
+TGCTCTTCCGATCTTTTAGCAAAGC
++
+:?@DDBDDHFFHDGIGIIJJJGGGI
+ at machine1:HiMom:abcdeACXX:1:1201:1180:2119 2:Y:0:GACCGTTG
+GCTCTAAATTTTGCTTTTCTACAGC
++
+CCCFFFFFHHHHHJJJJIJIJJIJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1036:2087 2:Y:0:GACCGTTG
+NGTCCACTTACGAAGCAAATACTTT
++
+#4=DDFFFHHHHHJJJJJJJJJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCGTTG.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCGTTG.barcode_1.fastq
new file mode 100644
index 0000000..67cede4
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCGTTG.barcode_1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1218:2200 :Y:0:GACCGTTG
+GACCGTTG
++
+ at CCFFDDF
+ at machine1:HiMom:abcdeACXX:1:1101:1257:2223 :Y:0:GACCGTTG
+GACCGTTG
++
+;@@DD=DD
+ at machine1:HiMom:abcdeACXX:1:1201:1180:2119 :Y:0:GACCGTTG
+GACCGTTG
++
+CCCFFDFF
+ at machine1:HiMom:abcdeACXX:1:2101:1036:2087 :Y:0:GACCGTTG
+GACCGTTG
++
+B at CFFDFF
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCTAAC.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCTAAC.1.fastq
new file mode 100644
index 0000000..d7bbf4d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCTAAC.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1302:2244 1:Y:0:GACCTAAC
+GGAAAAGACGGAAAGGTTCTATCTC
++
+ at C@DFFFDFHHHHJIJHHIJJJJJI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCTAAC.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCTAAC.2.fastq
new file mode 100644
index 0000000..8d08e7e
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCTAAC.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1302:2244 2:Y:0:GACCTAAC
+TGAATACATATAACAAATGCAAAAA
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCTAAC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCTAAC.barcode_1.fastq
new file mode 100644
index 0000000..0a1d60f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCTAAC.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1302:2244 :Y:0:GACCTAAC
+GACCTAAC
++
+CCCFFFFF
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GATATCCA.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GATATCCA.1.fastq
new file mode 100644
index 0000000..64c2f2e
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GATATCCA.1.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1460:2176 1:Y:0:GATATCCA
+AGTCCAGGCTGAGCCCAGGGAAGAA
++
+CCCFFFFFHHHHGJIJJIJJHIJJI
+ at machine1:HiMom:abcdeACXX:1:2101:1031:2163 1:Y:0:GATATCCA
+NTTTCCATGGCCGTCACCTTTGGGT
++
+#4=DDFFFHHHHHJJJJJJJJJJJI
+ at machine1:HiMom:abcdeACXX:1:2101:1226:2088 1:Y:0:GATATCCA
+NGATCGGAAGAGCACACGTTTGACT
++
+#4=DAA=DDFHFHIIBFGHHIG>EG
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GATATCCA.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GATATCCA.2.fastq
new file mode 100644
index 0000000..32b29ec
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GATATCCA.2.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1460:2176 2:Y:0:GATATCCA
+AGGAAAAAGACACAACAAGTCCAAC
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1031:2163 2:Y:0:GATATCCA
+NNACATTTGTCACCACTAGCCACCA
++
+##0<@?@@@@@@@@@@?@@@@@@@?
+ at machine1:HiMom:abcdeACXX:1:2101:1226:2088 2:Y:0:GATATCCA
+GCTCTTCCGATCTAGGTAATAGCTA
++
+==?BDFFFDCDDHFFFAFHDHIJGJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GATATCCA.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GATATCCA.barcode_1.fastq
new file mode 100644
index 0000000..9ddb963
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GATATCCA.barcode_1.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1460:2176 :Y:0:GATATCCA
+GATATCCA
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1031:2163 :Y:0:GATATCCA
+GATATCCA
++
+B at BFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1226:2088 :Y:0:GATATCCA
+GATATCCA
++
+@@@:DDDD
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCGTCGA.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCGTCGA.1.fastq
new file mode 100644
index 0000000..bc84fb1
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCGTCGA.1.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1111:2148 1:Y:0:GCCGTCGA
+GTGGAGACCACCTCCGAGGCCTTGT
++
+BBCFFFFFHHHHHJJJIJJJJJJJI
+ at machine1:HiMom:abcdeACXX:1:1101:1221:2143 1:Y:0:GCCGTCGA
+TTTGGTGGAAATTTTTTGTTATGAT
++
+CCCFFBDBHFD?FBFHIIGGIC at EF
+ at machine1:HiMom:abcdeACXX:1:1101:1327:2200 1:N:0:GCCGTCGA
+AGGGGGATCCGCCGGGGGACCACAA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1122:2136 1:Y:0:GCCGTCGA
+GTAGGCGCTCAGCAAATACTTGTCG
++
+@@@DDDD8?<CACEHHBBHDAAFH@
+ at machine1:HiMom:abcdeACXX:1:2101:1459:2083 1:Y:0:GCCGTCGA
+NCACACGCCACACGGAGCACACTTT
++
+#4=DDFFFHHHHHJJJJJJJJIIJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCGTCGA.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCGTCGA.2.fastq
new file mode 100644
index 0000000..37e8e60
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCGTCGA.2.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1111:2148 2:Y:0:GCCGTCGA
+GCGAANANNNNNNNNNNGGACGACN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1221:2143 2:Y:0:GCCGTCGA
+CAATTGAATGTCTGCACAGCCGCTT
++
+@@@FFFFDHHHHHJJJIIIJGHIJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1327:2200 2:N:0:GCCGTCGA
+GTCATCTGGGCTGTCGACAGGTGTC
++
+ at B@FFFFFHHHHGIJJJJJJIFHHI
+ at machine1:HiMom:abcdeACXX:1:2101:1122:2136 2:Y:0:GCCGTCGA
+CTTGCCAGCCTGCAGGCCCCGCGGC
++
+???BBAABDD?DDIID)A:3<EADD
+ at machine1:HiMom:abcdeACXX:1:2101:1459:2083 2:Y:0:GCCGTCGA
+ATTTCACCAAAATAATCAGAAGGCC
++
+CCCFFFFDBHGHHIGGIJFJJGGFH
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCGTCGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCGTCGA.barcode_1.fastq
new file mode 100644
index 0000000..4bed826
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCGTCGA.barcode_1.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1111:2148 :Y:0:GCCGTCGA
+GCCGTCGA
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1101:1221:2143 :Y:0:GCCGTCGA
+GCCGTCGA
++
+@@CDDDDF
+ at machine1:HiMom:abcdeACXX:1:1101:1327:2200 :N:0:GCCGTCGA
+GCCGTCGA
++
+BCCFDFFD
+ at machine1:HiMom:abcdeACXX:1:2101:1122:2136 :Y:0:GCCGTCGA
+GCCGTCGA
++
+?@<DDDD?
+ at machine1:HiMom:abcdeACXX:1:2101:1459:2083 :Y:0:GCCGTCGA
+GCCGTCGA
++
+@@CFDDFD
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCTAGCC.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCTAGCC.1.fastq
new file mode 100644
index 0000000..db6ed91
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCTAGCC.1.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1165:2239 1:Y:0:GCCTAGCC
+GGCGGAGGCAGCATTTCAGCTGTGA
++
+CCCFFDFFHHHHHIJJIGHHHJHHF
+ at machine1:HiMom:abcdeACXX:1:1101:1290:2225 1:Y:0:GCCTAGCC
+CTTGGGCGCATGGTGAGGGAGGGAG
++
+@@@FFDDFHDFH??CBEBHHIGDCD
+ at machine1:HiMom:abcdeACXX:1:1201:1280:2179 1:Y:0:GCCTAGCC
+TTCAAGGAATCGTCCTGCCTCAGCC
++
+BCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1300:2137 1:Y:0:GCCTAGCC
+NTGTAATCCCAGCTCTCAGGGAGGC
++
+#1=ADDDDDDDBBA?@AE?E at FE8;
+ at machine1:HiMom:abcdeACXX:1:2101:1023:2237 1:N:0:GCCTAGCC
+NTAAACAGCTTCTGCACAGCCAAAG
++
+#00@@?>=39>9;<412@?######
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCTAGCC.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCTAGCC.2.fastq
new file mode 100644
index 0000000..1fbef6a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCTAGCC.2.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1165:2239 2:Y:0:GCCTAGCC
+ATGGAAGTCGAGACAGAAGTGAGAA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1290:2225 2:Y:0:GCCTAGCC
+TCAGTTCACTGGCAAAGACAGTCAC
++
+C@@FBEDDFHFHGIIICEHGDHBHE
+ at machine1:HiMom:abcdeACXX:1:1201:1280:2179 2:Y:0:GCCTAGCC
+GAGGACTGCTTGAGTCCAGGAGTTC
++
+@@BFFDEFGHHHHIFGCHIJJJGGI
+ at machine1:HiMom:abcdeACXX:1:1201:1300:2137 2:Y:0:GCCTAGCC
+GCTCTTCCGATCTTTTTTTTAATTT
++
+@@?DDDDDFDHADEHGIGGED3?FD
+ at machine1:HiMom:abcdeACXX:1:2101:1023:2237 2:N:0:GCCTAGCC
+NNTTTGTTTGAGTTCCTTGTAGATT
++
+##0:=@?>?@???@:>?@??>?;?<
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCTAGCC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCTAGCC.barcode_1.fastq
new file mode 100644
index 0000000..ea0f08d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCTAGCC.barcode_1.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1165:2239 :Y:0:GCCTAGCC
+GCCTAGCC
++
+B@@DFFFF
+ at machine1:HiMom:abcdeACXX:1:1101:1290:2225 :Y:0:GCCTAGCC
+GCCTAGCC
++
+?<@DFBBD
+ at machine1:HiMom:abcdeACXX:1:1201:1280:2179 :Y:0:GCCTAGCC
+GCCTAGCC
++
+BCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1300:2137 :Y:0:GCCTAGCC
+GCCTAGCC
++
+8?84B23?
+ at machine1:HiMom:abcdeACXX:1:2101:1023:2237 :N:0:GCCTAGCC
+GCCTAGCC
++
+########
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTAACATC.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTAACATC.1.fastq
new file mode 100644
index 0000000..6fed4dd
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTAACATC.1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1188:2237 1:Y:0:GTAACATC
+TCCCCCTCCCTTTTGCGCACACACC
++
+@?@DDADDHDHBDH<EFHIIHG?HF
+ at machine1:HiMom:abcdeACXX:1:2101:1208:2231 1:N:0:GTAACATC
+TCACTAAACATCCAAACATCACTTT
++
+#########################
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTAACATC.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTAACATC.2.fastq
new file mode 100644
index 0000000..a082c08
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTAACATC.2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1188:2237 2:Y:0:GTAACATC
+GCTTCCTTCAAGACAGAAGTGAGAA
++
+CCCFFDDEFHHFFE at FDHHAIAFHG
+ at machine1:HiMom:abcdeACXX:1:2101:1208:2231 2:N:0:GTAACATC
+CTTTTTTTTTTTTTTTTTTTTTTTT
++
+CCCFFFFFHHHHHJJJHFDDDDDDD
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTAACATC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTAACATC.barcode_1.fastq
new file mode 100644
index 0000000..ae2eaa6
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTAACATC.barcode_1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1188:2237 :Y:0:GTAACATC
+GTAACATC
++
+@@?DFFDF
+ at machine1:HiMom:abcdeACXX:1:2101:1208:2231 :N:0:GTAACATC
+GTAACATC
++
+1+:A1A22
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTCCACAG.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTCCACAG.1.fastq
new file mode 100644
index 0000000..fa99998
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTCCACAG.1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1069:2159 1:Y:0:GTCCACAG
+TCCCTTACCATCAAATCAATTGNCC
++
+CCCFFFFFHHHHHJJJJJJJJJ#3A
+ at machine1:HiMom:abcdeACXX:1:1201:1486:2109 1:Y:0:GTCCACAG
+NCACCTCCTAGCCCCTCACTTCTGT
++
+#1=B;BDDHHHGFIIIIIIIIIGGG
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTCCACAG.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTCCACAG.2.fastq
new file mode 100644
index 0000000..7d3a59e
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTCCACAG.2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1069:2159 2:Y:0:GTCCACAG
+GACGTNNNNNNNNNNNNNNNNNNNN
++
+<<<@?####################
+ at machine1:HiMom:abcdeACXX:1:1201:1486:2109 2:Y:0:GTCCACAG
+ACGTGTGCTCTTCCCGATCTGTATA
++
+CCCFF?DDFBHHHJJIIDHJIJJJH
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTCCACAG.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTCCACAG.barcode_1.fastq
new file mode 100644
index 0000000..6b60259
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/GTCCACAG.barcode_1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1069:2159 :Y:0:GTCCACAG
+GTCCACAG
++
+ at BBFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1486:2109 :Y:0:GTCCACAG
+GTCCACAG
++
+CCCFFFFD
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/N.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/N.1.fastq
new file mode 100644
index 0000000..dea46f1
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/N.1.fastq
@@ -0,0 +1,64 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1031:2224 1:N:0:
+NAATANNNNNNNNNNNNTNNNNNNN
++
+#0;@@####################
+ at machine1:HiMom:abcdeACXX:1:1101:1039:2147 1:N:0:
+NCCAANGNNGGNNNNATGTAANNNN
++
+#4;@@#4##2<####43@@@@####
+ at machine1:HiMom:abcdeACXX:1:1101:1046:2175 1:N:0:
+NTGCCNGNGTTNCGNGGTCTTNNNN
++
+#4;@@####################
+ at machine1:HiMom:abcdeACXX:1:1101:1047:2122 1:N:0:
+NCTAANGNACTNTGNGTGTGCNNNN
++
+#0;@@#4#3@@#3@#2<@@@@####
+ at machine1:HiMom:abcdeACXX:1:1101:1048:2197 1:N:0:
+NCTCCNGNTCANCANGTGGAGNNNN
++
+#0;?@####################
+ at machine1:HiMom:abcdeACXX:1:1101:1065:2193 1:Y:0:
+GAAGTACGCCCTGCCCCTGGTTNGC
++
+?@@DAADAHHFHBEBEGGHG?####
+ at machine1:HiMom:abcdeACXX:1:1101:1162:2207 1:N:0:
+ACCTTGAGGAGAACATAAGAGCAAA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1201:1159:2179 1:N:0:
+GTTAGCACAGATATTGGATGAGTGA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1201:1414:2174 1:N:0:
+GCCAAAAAAAAGAACCAGCCCAAGG
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1040:2208 1:N:0:
+NATGCCCACCTCCCTCCTACGCACC
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1059:2083 1:Y:0:
+NAAGAGGGGTCAAGAGTTAAACTTA
++
+#1=DDFFFHFHHGIGHGHJJJJJJI
+ at machine1:HiMom:abcdeACXX:1:2101:1143:2137 1:Y:0:
+ATGCAGCAGCTGCCACGGAGCACCA
++
+CC at FFDFDFHFHHGIDHEHIGJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1151:2182 1:N:0:
+TTGTTTTGGCTTATAATGACAAGAA
++
+;;8-2).2())(<6=@8;?4??>>?
+ at machine1:HiMom:abcdeACXX:1:2101:1215:2110 1:Y:0:
+NAATATAATTTGGAGACCCTTTGTT
++
+#1=DDDDDEDDDDIDDBB3ABAB##
+ at machine1:HiMom:abcdeACXX:1:2101:1285:2105 1:N:0:
+NGCGGGGAGCCGGGCGTGGAATGCG
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1450:2134 1:Y:0:
+AGCACGCTGCCGCGGGACCTGCCCA
++
+?@@AD at DDHFH?DGIIIIG at FGFBF
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/N.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/N.2.fastq
new file mode 100644
index 0000000..27efd74
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/N.2.fastq
@@ -0,0 +1,64 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1031:2224 2:N:0:
+NNNNNNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1039:2147 2:N:0:
+NNNNNNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1046:2175 2:N:0:
+NNGGANNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1047:2122 2:N:0:
+NNTCANNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1048:2197 2:N:0:
+NNGTGNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1065:2193 2:Y:0:
+NCTTGNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1162:2207 2:N:0:
+TAAAACTGGGGAAGTTAGAGGAATG
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1201:1159:2179 2:N:0:
+TTTTTTTTTATTTTTCTAAATACTT
++
+===AA####################
+ at machine1:HiMom:abcdeACXX:1:1201:1414:2174 2:N:0:
+TTTTTTTTTTTTTTTTTTTTTTTTT
++
+@;@1BDADF????FFEB>B6=BBBB
+ at machine1:HiMom:abcdeACXX:1:2101:1040:2208 2:N:0:
+NCTGATAGTCACTGAAATGAATTCA
++
+#-0=>(2 at .22@@############
+ at machine1:HiMom:abcdeACXX:1:2101:1059:2083 2:Y:0:
+NGAATGTCTTAGAAGGATGCTTCTC
++
+#1=BDDDEHHGHHJJJJJIJJIIJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1143:2137 2:Y:0:
+GCTCTTCAGATCTAGGGGGAACAGC
++
+@@@DD?=DCAFFFHIIDG:EFHIII
+ at machine1:HiMom:abcdeACXX:1:2101:1151:2182 2:N:0:
+TTTTTTTTTTTTTTTTTTTTTTTTA
++
+9<<?@?@;5=?##############
+ at machine1:HiMom:abcdeACXX:1:2101:1215:2110 2:Y:0:
+ATCTTTCCCCCATTAAGAACAGCAA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1285:2105 2:N:0:
+TGTCTATATCAACCAACACCTCTTC
++
+-(0(():94:9:???##########
+ at machine1:HiMom:abcdeACXX:1:2101:1450:2134 2:Y:0:
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CC at FDFDFFDFHFGIIE1CGGHBGE
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/N.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/N.barcode_1.fastq
new file mode 100644
index 0000000..d58da4a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/N.barcode_1.fastq
@@ -0,0 +1,64 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1031:2224 :N:0:
+NNNNNNNN
++
+########
+ at machine1:HiMom:abcdeACXX:1:1101:1039:2147 :N:0:
+NNNNNNNN
++
+########
+ at machine1:HiMom:abcdeACXX:1:1101:1046:2175 :N:0:
+NNNNNNNN
++
+########
+ at machine1:HiMom:abcdeACXX:1:1101:1047:2122 :N:0:
+NNNANNNN
++
+########
+ at machine1:HiMom:abcdeACXX:1:1101:1048:2197 :N:0:
+NNNCNNNN
++
+########
+ at machine1:HiMom:abcdeACXX:1:1101:1065:2193 :Y:0:
+GAACGATN
++
+########
+ at machine1:HiMom:abcdeACXX:1:1101:1162:2207 :N:0:
+ACAAAATT
++
+########
+ at machine1:HiMom:abcdeACXX:1:1201:1159:2179 :N:0:
+AAAAAAAA
++
+########
+ at machine1:HiMom:abcdeACXX:1:1201:1414:2174 :N:0:
+AGAAAAGA
++
+########
+ at machine1:HiMom:abcdeACXX:1:2101:1040:2208 :N:0:
+ACGAAATC
++
+########
+ at machine1:HiMom:abcdeACXX:1:2101:1059:2083 :Y:0:
+TACCGTCT
++
+1:?D####
+ at machine1:HiMom:abcdeACXX:1:2101:1143:2137 :Y:0:
+TCCGTCTA
++
+########
+ at machine1:HiMom:abcdeACXX:1:2101:1151:2182 :N:0:
+GAAAAAAA
++
+########
+ at machine1:HiMom:abcdeACXX:1:2101:1215:2110 :Y:0:
+AAAAGAAG
++
+########
+ at machine1:HiMom:abcdeACXX:1:2101:1285:2105 :N:0:
+TATCTCGG
++
+########
+ at machine1:HiMom:abcdeACXX:1:2101:1450:2134 :Y:0:
+ACCAGTTG
++
+ at C@DDDB?
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TAAGCACA.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TAAGCACA.1.fastq
new file mode 100644
index 0000000..1a5e44a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TAAGCACA.1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1064:2239 1:Y:0:TAAGCACA
+CATGCAGCGCAAGTAGGTCTACAAG
++
+@@;DFAFFHHHHAHEGHFDGGFABG
+ at machine1:HiMom:abcdeACXX:1:2101:1258:2092 1:Y:0:TAAGCACA
+NCACACACACACTCATTCACAGCTT
++
+#1=DDDFFHHHFHJJIJGGGIIGIJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TAAGCACA.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TAAGCACA.2.fastq
new file mode 100644
index 0000000..74cfba7
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TAAGCACA.2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1064:2239 2:Y:0:TAAGCACA
+GGGATGGGAGGGCGATGAGGACTAG
++
+8?@:DDDACC:FHHGIH<EGDDDFH
+ at machine1:HiMom:abcdeACXX:1:2101:1258:2092 2:Y:0:TAAGCACA
+TTAGACAAAACACCAAAATAAAATA
++
+#########################
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TAAGCACA.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TAAGCACA.barcode_1.fastq
new file mode 100644
index 0000000..05f34f1
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TAAGCACA.barcode_1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1064:2239 :Y:0:TAAGCACA
+TAAGCACA
++
+@@@FFADB
+ at machine1:HiMom:abcdeACXX:1:2101:1258:2092 :Y:0:TAAGCACA
+TAAGCACA
++
+@@CDDFFF
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TACCGTCT.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TACCGTCT.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TACCGTCT.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TACCGTCT.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TACCGTCT.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TACCGTCT.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TAGCGGTA.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TAGCGGTA.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TAGCGGTA.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TAGCGGTA.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TAGCGGTA.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TAGCGGTA.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCAGCC.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCAGCC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCAGCC.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCAGCC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCAGCC.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCAGCC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCAGG.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCAGG.1.fastq
new file mode 100644
index 0000000..71e3a4a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCAGG.1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1071:2233 1:Y:0:TATCCAGG
+TTTGACAGTCTCTGAATGAGAANGG
++
+CCCFFFFFHHHHHJIIIJJJIJ#4A
+ at machine1:HiMom:abcdeACXX:1:1201:1140:2125 1:Y:0:TATCCAGG
+NTTTCAGTTCAGAGAACTGCAGAAT
++
+#1=DBDFDHHHHGJIJJJJJIIIJI
+ at machine1:HiMom:abcdeACXX:1:1201:1236:2187 1:Y:0:TATCCAGG
+TTTAAATGGGTAAGAAGCCCGGCTC
++
+ at BCDDFEFHHDHHJJJJJIJJIJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1133:2239 1:Y:0:TATCCAGG
+AGACAGAAGTACGGGAAGGCGAAGA
++
+@@@FFFFEHFHHHJJCGDHIIECD@
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCAGG.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCAGG.2.fastq
new file mode 100644
index 0000000..3751abf
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCAGG.2.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1071:2233 2:Y:0:TATCCAGG
+GTTTGNNNNNNNNNNNNNNNNNNNN
++
+<<<@@####################
+ at machine1:HiMom:abcdeACXX:1:1201:1140:2125 2:Y:0:TATCCAGG
+TTCATAAATTGGTCTTAGATGTTGC
++
+CC at FFFFFHHHHFGIJIIIJIJIJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1236:2187 2:Y:0:TATCCAGG
+CTCCTTAGCGGATTCCGACTTCCAT
++
+CCCFFFFDHHHHGIJJIGIGIJJGG
+ at machine1:HiMom:abcdeACXX:1:2101:1133:2239 2:Y:0:TATCCAGG
+AGCTTTTTGTTTCCTAGCTTGTCTT
++
+?@?DDFFFHHHHF4ACFHIJHHHGH
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCAGG.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCAGG.barcode_1.fastq
new file mode 100644
index 0000000..177b1dd
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCAGG.barcode_1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1071:2233 :Y:0:TATCCAGG
+TATCCAGG
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1140:2125 :Y:0:TATCCAGG
+TATCCAGG
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1236:2187 :Y:0:TATCCAGG
+TATCCAGG
++
+@@BFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1133:2239 :Y:0:TATCCAGG
+TATCCATG
++
+@@@BDDDF
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCATG.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCATG.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCATG.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCATG.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCATG.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCATG.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTCGG.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTCGG.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTCGG.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTCGG.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTCGG.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTCGG.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTGCC.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTGCC.1.fastq
new file mode 100644
index 0000000..7b209b1
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTGCC.1.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1267:2209 1:Y:0:TATCTGCC
+GAGACGGAGGCCAACGGGGGCCTGG
++
+@@CFFFFD8FDHFHIGIBG?@BCDG
+ at machine1:HiMom:abcdeACXX:1:1101:1353:2226 1:Y:0:TATCTGCC
+TTGCTTGTCTGTAAAGTATTTTATT
++
+ at C@DDFFDHHFHFHHIBGG>IHHII
+ at machine1:HiMom:abcdeACXX:1:1101:1435:2194 1:Y:0:TATCTGCC
+GAGAAAGAACATGACTACAGAGATG
++
+CCCFFFFFHHHHHJJJJJJJJJHJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1084:2204 1:Y:0:TATCTGCC
+GGCCCGTGGACGCCGCCGAAGAAGC
++
+CCCFFFFFHHHHHJJJJJIJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1142:2242 1:Y:0:TATCTGCC
+TGTTGATAGTCCTTCTTATCTTAGT
++
+???DB?==CC2<AC:CC<CFEF<FF
+ at machine1:HiMom:abcdeACXX:1:1201:1187:2100 1:Y:0:TATCTGCC
+NGCGGTAATTCCAGCTCCAATAGCG
++
+#1:BB2 at DHHFHHIIIIHHIIGHGG
+ at machine1:HiMom:abcdeACXX:1:1201:1392:2109 1:Y:0:TATCTGCC
+NCTGAAGAGGCCAAAGCGCCCTCCA
++
+#1=DDFFFHHHHHJJJJJJJJJJJI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTGCC.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTGCC.2.fastq
new file mode 100644
index 0000000..3e6c54a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTGCC.2.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1267:2209 2:Y:0:TATCTGCC
+GGCAGAGTCTCCAACAGCCCCGTAC
++
+=;?DDDD?CCFHAIIIGGIIGE at EG
+ at machine1:HiMom:abcdeACXX:1:1101:1353:2226 2:Y:0:TATCTGCC
+GTGCTCTTCCGATCTTCAGGTTACC
++
+BBBFFFFFHHHHHJJJJJJJIJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1435:2194 2:Y:0:TATCTGCC
+TTTTGTTTTCTTTTACTGAAGTGTA
++
+CCCFFDFFHHHHHJJJJIHIJHHHJ
+ at machine1:HiMom:abcdeACXX:1:1201:1084:2204 2:Y:0:TATCTGCC
+TGGCTCCTCAGGCTCTCATCAGTTG
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1142:2242 2:Y:0:TATCTGCC
+GTAAAATGTAAAATAATAAAAAATG
++
+?=?DDDD;AF<DF<FFFFIIIFF@<
+ at machine1:HiMom:abcdeACXX:1:1201:1187:2100 2:Y:0:TATCTGCC
+AAAAAAGAGCCCGCATTGCCGAGAC
++
+=<=;AA###################
+ at machine1:HiMom:abcdeACXX:1:1201:1392:2109 2:Y:0:TATCTGCC
+GTCAGACAGGGGGATTTGGGCTGTG
++
+BBCFFFFFHHHHHHJJJHIJIJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTGCC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTGCC.barcode_1.fastq
new file mode 100644
index 0000000..4d597f4
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTGCC.barcode_1.fastq
@@ -0,0 +1,28 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1267:2209 :Y:0:TATCTGCC
+TATCAGCC
++
+?@@D;ADD
+ at machine1:HiMom:abcdeACXX:1:1101:1353:2226 :Y:0:TATCTGCC
+TATCTGCC
++
+ at B@FFEFF
+ at machine1:HiMom:abcdeACXX:1:1101:1435:2194 :Y:0:TATCTGCC
+TATCTGCC
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1084:2204 :Y:0:TATCTGCC
+TATCTGCC
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1142:2242 :Y:0:TATCTGCC
+TATCTGCC
++
+??<D?D83
+ at machine1:HiMom:abcdeACXX:1:1201:1187:2100 :Y:0:TATCTGCC
+TATCTGCC
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1392:2109 :Y:0:TATCTGCC
+TATCTGCC
++
+CCCDF?DD
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCCGTCTA.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TCCGTCTA.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCCGTCTA.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TCCGTCTA.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCCGTCTA.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B25T/fastq/TCCGTCTA.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCGCTAGA.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCGCTAGA.1.fastq
new file mode 100644
index 0000000..4613164
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCGCTAGA.1.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1143:2192 1:Y:0:TCGCTAGA
+GGAGCGAGTCTGGGTCTCAGCCCCG
++
+CCCFFFFFHHHHHJGHIIIHJJJJI
+ at machine1:HiMom:abcdeACXX:1:1101:1479:2221 1:Y:0:TCGCTAGA
+TGTAAAGTATGCTGGCTCAGTGTAT
++
+BBBFDFFEHHHHHJJJJJJJIJHJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1312:2112 1:Y:0:TCGCTAGA
+NTCCCAGCGAACCCGCGTGCAACCT
++
+#1=DFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1416:2128 1:Y:0:TCGCTAGA
+NACAGGCGTGGAGGAGGCGGCGGCC
++
+#4=DDDFFHHHHHJIGJHFHHFFED
+ at machine1:HiMom:abcdeACXX:1:2101:1064:2242 1:Y:0:TCGCTAGA
+ATGAACAAAGGAAGAATTATGCACG
++
+?;?D;DDDF?;:+<<CFFCHE433A
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCGCTAGA.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCGCTAGA.2.fastq
new file mode 100644
index 0000000..9f0f4fc
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCGCTAGA.2.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1143:2192 2:Y:0:TCGCTAGA
+CGACAAGTCTGGCTTATCACTCATC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1479:2221 2:Y:0:TCGCTAGA
+GGGGAAATCTATTTTTATGTAAAAA
++
+ at CCFFFFFHHHHHJIGIJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1312:2112 2:Y:0:TCGCTAGA
+ATTTGCAGGAGCCGGCGCAGGTGCA
++
+CCCFFFFFHHHHHJJJIJJJJGHIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1416:2128 2:Y:0:TCGCTAGA
+TTGGTGTGGAGGCGGTGGCGGGATC
++
+@@@DDDDDHHFHHII:?GGHIIB6?
+ at machine1:HiMom:abcdeACXX:1:2101:1064:2242 2:Y:0:TCGCTAGA
+NGGAAAAAGGTTGTCAAGCGTTAAA
++
+#########################
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCGCTAGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCGCTAGA.barcode_1.fastq
new file mode 100644
index 0000000..e148256
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCGCTAGA.barcode_1.fastq
@@ -0,0 +1,20 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1143:2192 :Y:0:TCGCTAGA
+TCGCTAGA
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1101:1479:2221 :Y:0:TCGCTAGA
+TCGCTAGA
++
+ at BCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1312:2112 :Y:0:TCGCTAGA
+TCGCTAGA
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1416:2128 :Y:0:TCGCTAGA
+TCGCTAGA
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1064:2242 :Y:0:TCGCTAGA
+TCGCTAGA
++
+;@<:AA at A
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCTGCAAG.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCTGCAAG.1.fastq
new file mode 100644
index 0000000..a34f51d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCTGCAAG.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1042:2174 1:Y:0:TCTGCAAG
+NGTTGGTGTCTTCATTTTATGTATA
++
+#1=DDFDFHHHHHJIJJJHIJHIJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCTGCAAG.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCTGCAAG.2.fastq
new file mode 100644
index 0000000..4fda3b0
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCTGCAAG.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1042:2174 2:Y:0:TCTGCAAG
+NTCAGGAAGGCNNCAAAAAAAGAAA
++
+#0;@@@?@?<@##3<@@?@@?????
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCTGCAAG.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCTGCAAG.barcode_1.fastq
new file mode 100644
index 0000000..5237cc1
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TCTGCAAG.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1042:2174 :Y:0:TCTGCAAG
+TCTGCAAG
++
+CCCFFFFF
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCAAGTA.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCAAGTA.1.fastq
new file mode 100644
index 0000000..105fefa
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCAAGTA.1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1242:2170 1:Y:0:TGCAAGTA
+ATGGCAGGGCAGAGTTCTGATGAGT
++
+CCCFFFFFHHGGGIFHEIIGIIII?
+ at machine1:HiMom:abcdeACXX:1:2101:1163:2222 1:Y:0:TGCAAGTA
+GAGCAGGCAAGGAGGACTTCTTGTT
++
+CCCFFFFFGHHHHJJHHIJJJJJIJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCAAGTA.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCAAGTA.2.fastq
new file mode 100644
index 0000000..4e7ea3b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCAAGTA.2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1242:2170 2:Y:0:TGCAAGTA
+GGAAGGAAAAGAAGCACAAGTACAT
++
+@@@DFDFFHHHGHHGIIGJJEHHIG
+ at machine1:HiMom:abcdeACXX:1:2101:1163:2222 2:Y:0:TGCAAGTA
+GAGCGATAATGGTTCTTTTCCTCAC
++
+@@@DFFFFHHHHHJJJJJJJIJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCAAGTA.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCAAGTA.barcode_1.fastq
new file mode 100644
index 0000000..ffe1705
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCAAGTA.barcode_1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1242:2170 :Y:0:TGCAAGTA
+TGCAAGTA
++
+@@CFFF?D
+ at machine1:HiMom:abcdeACXX:1:2101:1163:2222 :Y:0:TGCAAGTA
+TGCAAGTA
++
+CCCFFFEF
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCTGCTG.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCTGCTG.1.fastq
new file mode 100644
index 0000000..8210bc4
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCTGCTG.1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1084:2136 1:Y:0:TGCTGCTG
+NTCTCACTGTGAATTTGTGGTGGGC
++
+#1=DDFFFHHHHHJJJJGIJIJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1285:2100 1:Y:0:TGCTGCTG
+NAATGACATGTTTAAAGATGGACTC
++
+#1:BDDFFHHFHHGIJIJIIIIGII
+ at machine1:HiMom:abcdeACXX:1:2101:1162:2139 1:Y:0:TGCTGCTG
+AGAGGTGAAATTCTTGGACCGGCGC
++
+@@@DDDDDHFHHHDB:EFHHCAG?D
+ at machine1:HiMom:abcdeACXX:1:2101:1195:2150 1:Y:0:TGCTGCTG
+CCGAGAGAGTGAGAGCGCTCCTGGG
++
+CCCFFFFFHFHHHJJJJIJJJJIJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCTGCTG.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCTGCTG.2.fastq
new file mode 100644
index 0000000..33f1fbc
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCTGCTG.2.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1084:2136 2:Y:0:TGCTGCTG
+TTTCTNNNNNNNNNNNNNNNNNNNN
++
+<<<@@####################
+ at machine1:HiMom:abcdeACXX:1:1201:1285:2100 2:Y:0:TGCTGCTG
+GATCTTTTTTGCTTTGTAGTTATAG
++
+@@@DFFFFHHHHHIIGIABCFFHBF
+ at machine1:HiMom:abcdeACXX:1:2101:1162:2139 2:Y:0:TGCTGCTG
+ATCGTTTATGGTCGGAACTACGACG
++
+BCCFFFFFHHHHHIJJJJJJJIJJI
+ at machine1:HiMom:abcdeACXX:1:2101:1195:2150 2:Y:0:TGCTGCTG
+AATTGAACTTCACCACCCAGAGGAA
++
+CCCFFFFFHHHHHJJJJJJIJJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCTGCTG.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCTGCTG.barcode_1.fastq
new file mode 100644
index 0000000..af4fe61
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCTGCTG.barcode_1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1084:2136 :Y:0:TGCTGCTG
+TGCTGCTG
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1285:2100 :Y:0:TGCTGCTG
+TGCTGCTG
++
+@@@FFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1162:2139 :Y:0:TGCTGCTG
+TGCTGCTG
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:2101:1195:2150 :Y:0:TGCTGCTG
+TGCTGCTG
++
+CCCFFFFF
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAACTC.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAACTC.1.fastq
new file mode 100644
index 0000000..4b08426
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAACTC.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1421:2154 1:Y:0:TGTAACTC
+TGTGTGTGTGGGTGTGTGTATATAT
++
+?@?DDFFFFFHH at GEFCCCHGIGJI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAACTC.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAACTC.2.fastq
new file mode 100644
index 0000000..af29dc5
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAACTC.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1421:2154 2:Y:0:TGTAACTC
+TGTGCTCTTCCGATCTTGTGCTCTT
++
+BC at DFFFFHHHHHJJJJFHIHHIJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAACTC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAACTC.barcode_1.fastq
new file mode 100644
index 0000000..c1a6dc0
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAACTC.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1201:1421:2154 :Y:0:TGTAACTC
+TGTAACTC
++
+@@@FFFFF
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAATCA.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAATCA.1.fastq
new file mode 100644
index 0000000..b22ab5d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAATCA.1.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1419:2119 1:Y:0:TGTAATCA
+NATGACTATGGTAACTGAAAGAAAA
++
+#1:A1BDADBFFDFIIIEEHECACF
+ at machine1:HiMom:abcdeACXX:1:1201:1208:2132 1:Y:0:TGTAATCA
+NCCTCAATGAGCGGCACTATGGGGG
++
+#1=DDFFFHHHHGJJIJJGHIJGIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1344:2147 1:Y:0:TGTAATCA
+TATCCTCCCTACTATGCCTAGAAGG
++
+=?@DADEFHBHDFG>EFGDHGFGHD
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAATCA.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAATCA.2.fastq
new file mode 100644
index 0000000..4332332
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAATCA.2.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1419:2119 2:Y:0:TGTAATCA
+ACTTTCCTTTTTTGTTTTACTTTAA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1201:1208:2132 2:Y:0:TGTAATCA
+CTGTAGAAAGGATGGTCGGGCTCCA
++
+@@CDFFFFGHFHHJIJJGJIBHJJG
+ at machine1:HiMom:abcdeACXX:1:1201:1344:2147 2:Y:0:TGTAATCA
+ACGATTAGTTTTAGCATTGGAGTAG
++
+@<??DDDDFHHHFGGHHIIIGGAGH
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAATCA.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAATCA.barcode_1.fastq
new file mode 100644
index 0000000..aba2eaa
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAATCA.barcode_1.fastq
@@ -0,0 +1,12 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1419:2119 :Y:0:TGTAATCA
+TGTAATCA
++
+@@@DFDFD
+ at machine1:HiMom:abcdeACXX:1:1201:1208:2132 :Y:0:TGTAATCA
+TGTAATCA
++
+CC at FFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1344:2147 :Y:0:TGTAATCA
+TGTAATCA
++
+=?1AA:=D
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TTGTCTAT.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TTGTCTAT.1.fastq
new file mode 100644
index 0000000..9c4229b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TTGTCTAT.1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1219:2164 1:Y:0:TTGTCTAT
+TCAAGCAGGAGCAGCTAAGTCCTAA
++
+CCCFFFFFHHHHHJJJJJJHIJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1103:2184 1:Y:0:TTGTCTAT
+GTAAGAACTACCCTGGGTCCCCGTG
++
+@@BFFFFFHHHHHJJJJGIJJJJHI
+ at machine1:HiMom:abcdeACXX:1:1201:1107:2109 1:Y:0:TTGTCTAT
+NGGGAACCTGGCGCTAAACCATTCG
++
+#1=DFFFFHHHHHJJJJJJJJJIJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1252:2141 1:Y:0:TTGTCTAT
+NTTCCCCCCATGTAATTATTGTGAA
++
+#1=DDFFFHHHHHJJJJJJJJIJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TTGTCTAT.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TTGTCTAT.2.fastq
new file mode 100644
index 0000000..1507d9d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TTGTCTAT.2.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1219:2164 2:Y:0:TTGTCTAT
+ATCTTATCCACTCCTTCCACTTTGG
++
+CCCFFFFFHHHHHJJIJJJJJJJIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1103:2184 2:Y:0:TTGTCTAT
+AGAAGTTTCAGAATTGTGGCCCCAT
++
+B at BFFDEFHHHHHJJJGHIJJJJJI
+ at machine1:HiMom:abcdeACXX:1:1201:1107:2109 2:Y:0:TTGTCTAT
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CCCFFFFFHHGHHJJJJIIJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1252:2141 2:Y:0:TTGTCTAT
+AGTTATTTTGCCTATGTCCAACAAG
++
+BCBFFFFFGHHHHJIJJJJJJJJJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/TTGTCTAT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TTGTCTAT.barcode_1.fastq
new file mode 100644
index 0000000..f81053d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/TTGTCTAT.barcode_1.fastq
@@ -0,0 +1,16 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1219:2164 :Y:0:TTGTCTAT
+TTGTCTAT
++
+CCCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1103:2184 :Y:0:TTGTCTAT
+TTGTCTAT
++
+ at CCFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1107:2109 :Y:0:TTGTCTAT
+TTGTCTAT
++
+B at CFFFFF
+ at machine1:HiMom:abcdeACXX:1:1201:1252:2141 :Y:0:TTGTCTAT
+TTGTCTAT
++
+CCCFFFFF
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/barcode.params b/testdata/net/sf/picard/illumina/25T8B25T/fastq/barcode.params
new file mode 100644
index 0000000..8046f3b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/barcode.params
@@ -0,0 +1,63 @@
+BARCODE SAMPLE_ALIAS LIBRARY_NAME
+AAAAAAAA SA_AAAAAAAA LN_AAAAAAAA
+AAAAGAAG SA_AAAAGAAG LN_AAAAGAAG
+AACAATGG SA_AACAATGG LN_AACAATGG
+AACGCATT SA_AACGCATT LN_AACGCATT
+ACAAAATT SA_ACAAAATT LN_ACAAAATT
+ACAGGTAT SA_ACAGGTAT LN_ACAGGTAT
+ACAGTTGA SA_ACAGTTGA LN_ACAGTTGA
+ACCAGTTG SA_ACCAGTTG LN_ACCAGTTG
+ACGAAATC SA_ACGAAATC LN_ACGAAATC
+ACTAAGAC SA_ACTAAGAC LN_ACTAAGAC
+ACTGTACC SA_ACTGTACC LN_ACTGTACC
+ACTGTATC SA_ACTGTATC LN_ACTGTATC
+AGAAAAGA SA_AGAAAAGA LN_AGAAAAGA
+AGCATGGA SA_AGCATGGA LN_AGCATGGA
+AGGTAAGG SA_AGGTAAGG LN_AGGTAAGG
+AGGTCGCA SA_AGGTCGCA LN_AGGTCGCA
+ATTATCAA SA_ATTATCAA LN_ATTATCAA
+ATTCCTCT SA_ATTCCTCT LN_ATTCCTCT
+CAACTCTC SA_CAACTCTC LN_CAACTCTC
+CAATAGAC SA_CAATAGAC LN_CAATAGAC
+CAATAGTC SA_CAATAGTC LN_CAATAGTC
+CAGCGGAT SA_CAGCGGAT LN_CAGCGGAT
+CAGCGGTA SA_CAGCGGTA LN_CAGCGGTA
+CCAACATT SA_CCAACATT LN_CCAACATT
+CCAGCACC SA_CCAGCACC LN_CCAGCACC
+CCATGCGT SA_CCATGCGT LN_CCATGCGT
+CGCCTTCC SA_CGCCTTCC LN_CGCCTTCC
+CGCTATGT SA_CGCTATGT LN_CGCTATGT
+CTAACTCG SA_CTAACTCG LN_CTAACTCG
+CTATGCGC SA_CTATGCGC LN_CTATGCGC
+CTATGCGT SA_CTATGCGT LN_CTATGCGT
+CTGCGGAT SA_CTGCGGAT LN_CTGCGGAT
+CTGTAATC SA_CTGTAATC LN_CTGTAATC
+GAAAAAAA SA_GAAAAAAA LN_GAAAAAAA
+GAACGAT. SA_GAACGAT. LN_GAACGAT.
+GAAGGAAG SA_GAAGGAAG LN_GAAGGAAG
+GACCAGGA SA_GACCAGGA LN_GACCAGGA
+GACCAGGC SA_GACCAGGC LN_GACCAGGC
+GACCGTTG SA_GACCGTTG LN_GACCGTTG
+GACCTAAC SA_GACCTAAC LN_GACCTAAC
+GATATCCA SA_GATATCCA LN_GATATCCA
+GCCGTCGA SA_GCCGTCGA LN_GCCGTCGA
+GCCTAGCC SA_GCCTAGCC LN_GCCTAGCC
+GTAACATC SA_GTAACATC LN_GTAACATC
+GTCCACAG SA_GTCCACAG LN_GTCCACAG
+TAAGCACA SA_TAAGCACA LN_TAAGCACA
+TACCGTCT SA_TACCGTCT LN_TACCGTCT
+TAGCGGTA SA_TAGCGGTA LN_TAGCGGTA
+TATCAGCC SA_TATCAGCC LN_TATCAGCC
+TATCCAGG SA_TATCCAGG LN_TATCCAGG
+TATCCATG SA_TATCCATG LN_TATCCATG
+TATCTCGG SA_TATCTCGG LN_TATCTCGG
+TATCTGCC SA_TATCTGCC LN_TATCTGCC
+TCCGTCTA SA_TCCGTCTA LN_TCCGTCTA
+TCGCTAGA SA_TCGCTAGA LN_TCGCTAGA
+TCTGCAAG SA_TCTGCAAG LN_TCTGCAAG
+TGCAAGTA SA_TGCAAGTA LN_TGCAAGTA
+TGCTGCTG SA_TGCTGCTG LN_TGCTGCTG
+TGTAACTC SA_TGTAACTC LN_TGTAACTC
+TGTAATCA SA_TGTAATCA LN_TGTAATCA
+TTGTCTAT SA_TTGTCTAT LN_TTGTCTAT
+N SA_N LN_N
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/mp_barcode.params b/testdata/net/sf/picard/illumina/25T8B25T/fastq/mp_barcode.params
new file mode 100644
index 0000000..f56b403
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/mp_barcode.params
@@ -0,0 +1,63 @@
+BARCODE_1 SAMPLE_ALIAS LIBRARY_NAME
+AAAAAAAA SA_AAAAAAAA LN_AAAAAAAA
+AAAAGAAG SA_AAAAGAAG LN_AAAAGAAG
+AACAATGG SA_AACAATGG LN_AACAATGG
+AACGCATT SA_AACGCATT LN_AACGCATT
+ACAAAATT SA_ACAAAATT LN_ACAAAATT
+ACAGGTAT SA_ACAGGTAT LN_ACAGGTAT
+ACAGTTGA SA_ACAGTTGA LN_ACAGTTGA
+ACCAGTTG SA_ACCAGTTG LN_ACCAGTTG
+ACGAAATC SA_ACGAAATC LN_ACGAAATC
+ACTAAGAC SA_ACTAAGAC LN_ACTAAGAC
+ACTGTACC SA_ACTGTACC LN_ACTGTACC
+ACTGTATC SA_ACTGTATC LN_ACTGTATC
+AGAAAAGA SA_AGAAAAGA LN_AGAAAAGA
+AGCATGGA SA_AGCATGGA LN_AGCATGGA
+AGGTAAGG SA_AGGTAAGG LN_AGGTAAGG
+AGGTCGCA SA_AGGTCGCA LN_AGGTCGCA
+ATTATCAA SA_ATTATCAA LN_ATTATCAA
+ATTCCTCT SA_ATTCCTCT LN_ATTCCTCT
+CAACTCTC SA_CAACTCTC LN_CAACTCTC
+CAATAGAC SA_CAATAGAC LN_CAATAGAC
+CAATAGTC SA_CAATAGTC LN_CAATAGTC
+CAGCGGAT SA_CAGCGGAT LN_CAGCGGAT
+CAGCGGTA SA_CAGCGGTA LN_CAGCGGTA
+CCAACATT SA_CCAACATT LN_CCAACATT
+CCAGCACC SA_CCAGCACC LN_CCAGCACC
+CCATGCGT SA_CCATGCGT LN_CCATGCGT
+CGCCTTCC SA_CGCCTTCC LN_CGCCTTCC
+CGCTATGT SA_CGCTATGT LN_CGCTATGT
+CTAACTCG SA_CTAACTCG LN_CTAACTCG
+CTATGCGC SA_CTATGCGC LN_CTATGCGC
+CTATGCGT SA_CTATGCGT LN_CTATGCGT
+CTGCGGAT SA_CTGCGGAT LN_CTGCGGAT
+CTGTAATC SA_CTGTAATC LN_CTGTAATC
+GAAAAAAA SA_GAAAAAAA LN_GAAAAAAA
+GAACGAT. SA_GAACGAT. LN_GAACGAT.
+GAAGGAAG SA_GAAGGAAG LN_GAAGGAAG
+GACCAGGA SA_GACCAGGA LN_GACCAGGA
+GACCAGGC SA_GACCAGGC LN_GACCAGGC
+GACCGTTG SA_GACCGTTG LN_GACCGTTG
+GACCTAAC SA_GACCTAAC LN_GACCTAAC
+GATATCCA SA_GATATCCA LN_GATATCCA
+GCCGTCGA SA_GCCGTCGA LN_GCCGTCGA
+GCCTAGCC SA_GCCTAGCC LN_GCCTAGCC
+GTAACATC SA_GTAACATC LN_GTAACATC
+GTCCACAG SA_GTCCACAG LN_GTCCACAG
+TAAGCACA SA_TAAGCACA LN_TAAGCACA
+TACCGTCT SA_TACCGTCT LN_TACCGTCT
+TAGCGGTA SA_TAGCGGTA LN_TAGCGGTA
+TATCAGCC SA_TATCAGCC LN_TATCAGCC
+TATCCAGG SA_TATCCAGG LN_TATCCAGG
+TATCCATG SA_TATCCATG LN_TATCCATG
+TATCTCGG SA_TATCTCGG LN_TATCTCGG
+TATCTGCC SA_TATCTGCC LN_TATCTGCC
+TCCGTCTA SA_TCCGTCTA LN_TCCGTCTA
+TCGCTAGA SA_TCGCTAGA LN_TCGCTAGA
+TCTGCAAG SA_TCTGCAAG LN_TCTGCAAG
+TGCAAGTA SA_TGCAAGTA LN_TGCAAGTA
+TGCTGCTG SA_TGCTGCTG LN_TGCTGCTG
+TGTAACTC SA_TGTAACTC LN_TGTAACTC
+TGTAATCA SA_TGTAATCA LN_TGTAATCA
+TTGTCTAT SA_TTGTCTAT LN_TTGTCTAT
+N SA_N LN_N
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/nonBarcoded.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/nonBarcoded.1.fastq
new file mode 100644
index 0000000..9588f4b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/nonBarcoded.1.fastq
@@ -0,0 +1,720 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1031:2224 1:N:0:
+NAATANNNNNNNNNNNNTNNNNNNN
++
+#0;@@####################
+ at machine1:HiMom:abcdeACXX:1:1101:1039:2147 1:N:0:
+NCCAANGNNGGNNNNATGTAANNNN
++
+#4;@@#4##2<####43@@@@####
+ at machine1:HiMom:abcdeACXX:1:1101:1046:2175 1:N:0:
+NTGCCNGNGTTNCGNGGTCTTNNNN
++
+#4;@@####################
+ at machine1:HiMom:abcdeACXX:1:1101:1047:2122 1:N:0:
+NCTAANGNACTNTGNGTGTGCNNNN
++
+#0;@@#4#3@@#3@#2<@@@@####
+ at machine1:HiMom:abcdeACXX:1:1101:1048:2197 1:N:0:
+NCTCCNGNTCANCANGTGGAGNNNN
++
+#0;?@####################
+ at machine1:HiMom:abcdeACXX:1:1101:1065:2193 1:Y:0:
+GAAGTACGCCCTGCCCCTGGTTNGC
++
+?@@DAADAHHFHBEBEGGHG?####
+ at machine1:HiMom:abcdeACXX:1:1101:1069:2159 1:Y:0:
+TCCCTTACCATCAAATCAATTGNCC
++
+CCCFFFFFHHHHHJJJJJJJJJ#3A
+ at machine1:HiMom:abcdeACXX:1:1101:1071:2233 1:Y:0:
+TTTGACAGTCTCTGAATGAGAANGG
++
+CCCFFFFFHHHHHJIIIJJJIJ#4A
+ at machine1:HiMom:abcdeACXX:1:1101:1083:2193 1:Y:0:
+TTCTACCTCACCTTAGGGAGAAGAC
++
+@@@DDBDDD>F><C<4CG?EHGHIG
+ at machine1:HiMom:abcdeACXX:1:1101:1084:2136 1:Y:0:
+NTCTCACTGTGAATTTGTGGTGGGC
++
+#1=DDFFFHHHHHJJJJGIJIJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1089:2172 1:Y:0:
+TTCCAGCATGCGGTTTAAGTAGGAT
++
+ at CCFDFDBDFBF:<CEBHAFHHICH
+ at machine1:HiMom:abcdeACXX:1:1101:1100:2207 1:Y:0:
+ACGACAGACGTTCTTTCTTTGCTGC
++
+CCCFFFFFHHFHHJIJJJJJHIJJH
+ at machine1:HiMom:abcdeACXX:1:1101:1111:2148 1:Y:0:
+GTGGAGACCACCTCCGAGGCCTTGT
++
+BBCFFFFFHHHHHJJJIJJJJJJJI
+ at machine1:HiMom:abcdeACXX:1:1101:1138:2141 1:Y:0:
+NTTACCAAGGTTTTCTGTTTAGTGA
++
+#1=DDFFFHHFHHJJJIHJIJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1140:2120 1:Y:0:
+NCCCCAACATTCTAATTATGCCTCA
++
+#1:BDFFDHFFDFIJJJIIJIIIII
+ at machine1:HiMom:abcdeACXX:1:1101:1143:2192 1:Y:0:
+GGAGCGAGTCTGGGTCTCAGCCCCG
++
+CCCFFFFFHHHHHJGHIIIHJJJJI
+ at machine1:HiMom:abcdeACXX:1:1101:1150:2228 1:Y:0:
+GCTACTCAGTAGACAGTCCCACCCT
++
+@@CADDDDFCFHHIIIIGGIIGGGI
+ at machine1:HiMom:abcdeACXX:1:1101:1157:2135 1:Y:0:
+NGGACATTGTAATCATTTCTTACAA
++
+#1=DD?DDHHHHHGGHIIIIIIIII
+ at machine1:HiMom:abcdeACXX:1:1101:1162:2207 1:N:0:
+ACCTTGAGGAGAACATAAGAGCAAA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1165:2239 1:Y:0:
+GGCGGAGGCAGCATTTCAGCTGTGA
++
+CCCFFDFFHHHHHIJJIGHHHJHHF
+ at machine1:HiMom:abcdeACXX:1:1101:1175:2197 1:Y:0:
+CCCCTGAGGACACCATCCCACTCCA
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1188:2237 1:Y:0:
+TCCCCCTCCCTTTTGCGCACACACC
++
+@?@DDADDHDHBDH<EFHIIHG?HF
+ at machine1:HiMom:abcdeACXX:1:1101:1197:2200 1:Y:0:
+GGGCGCCCCGTGAGGACCCAGTCCT
++
+ at C@FFADDFFCFCEHIIJIJJIEFC
+ at machine1:HiMom:abcdeACXX:1:1101:1206:2126 1:Y:0:
+NATTCTGCCATATTGGTCCGACAGT
++
+#1=DDFFFHHHHHJJJJJJJJJIJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1212:2230 1:Y:0:
+TTTCTATTAGCTCTTAGTAAGATTA
++
+CCCFFFFFHHHHHJJJIJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1218:2200 1:Y:0:
+GCACCGGAAGAGCACACAGATCGGA
++
+CCCFFFFDFHGHHJJIJIJJJJJJI
+ at machine1:HiMom:abcdeACXX:1:1101:1219:2164 1:Y:0:
+TCAAGCAGGAGCAGCTAAGTCCTAA
++
+CCCFFFFFHHHHHJJJJJJHIJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1221:2143 1:Y:0:
+TTTGGTGGAAATTTTTTGTTATGAT
++
+CCCFFBDBHFD?FBFHIIGGIC at EF
+ at machine1:HiMom:abcdeACXX:1:1101:1236:2121 1:Y:0:
+NGGTGCTTCATATCCCTCTAGAGGA
++
+#1=BDDFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1242:2170 1:Y:0:
+ATGGCAGGGCAGAGTTCTGATGAGT
++
+CCCFFFFFHHGGGIFHEIIGIIII?
+ at machine1:HiMom:abcdeACXX:1:1101:1257:2223 1:Y:0:
+TGTATTCGAGAGATCAAAGAGAGAG
++
+@@=DDBDD?FFHHEIDBDFCEDBAF
+ at machine1:HiMom:abcdeACXX:1:1101:1259:2152 1:Y:0:
+CACCTATAATCCCAGCTACTCCAGA
++
+CCCFFFFFHHHHHJJJJJJIJJJIJ
+ at machine1:HiMom:abcdeACXX:1:1101:1261:2127 1:N:0:
+NTGAAATCTGGATAGGCTGGAGTTA
++
+#0-@@@###################
+ at machine1:HiMom:abcdeACXX:1:1101:1263:2236 1:N:0:
+CTTTGAAGACATTGTGAGATCTGTA
++
+<==A<42 at C+A4A?,2A@=4 at 7A??
+ at machine1:HiMom:abcdeACXX:1:1101:1267:2209 1:Y:0:
+GAGACGGAGGCCAACGGGGGCCTGG
++
+@@CFFFFD8FDHFHIGIBG?@BCDG
+ at machine1:HiMom:abcdeACXX:1:1101:1269:2170 1:Y:0:
+ACAGTGTGGGAGGCAGACGAAGAGA
++
+@@@DDDDDFA:C at EGA?FD<FFHII
+ at machine1:HiMom:abcdeACXX:1:1101:1290:2225 1:Y:0:
+CTTGGGCGCATGGTGAGGGAGGGAG
++
+@@@FFDDFHDFH??CBEBHHIGDCD
+ at machine1:HiMom:abcdeACXX:1:1101:1291:2150 1:Y:0:
+CGTGGGGAACCTGGCGCTAAACCAT
++
+ at BBFFFFFHHHHHJJJJIJJJJJIJ
+ at machine1:HiMom:abcdeACXX:1:1101:1302:2244 1:Y:0:
+GGAAAAGACGGAAAGGTTCTATCTC
++
+ at C@DFFFDFHHHHJIJHHIJJJJJI
+ at machine1:HiMom:abcdeACXX:1:1101:1308:2153 1:N:0:
+TTTTGGAAGAGACCTCAATTACTGT
++
+???DDDDD?:22AE:A2<3,AF?3A
+ at machine1:HiMom:abcdeACXX:1:1101:1309:2210 1:Y:0:
+ACACCAACCACCCAACTATCTATAA
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1314:2233 1:Y:0:
+GTTTATTGGGGCATTCCTTATCCCA
++
+@??DDDDBDHF>FCHGGGBFAAED9
+ at machine1:HiMom:abcdeACXX:1:1101:1316:2126 1:Y:0:
+NAAAAAAAAAAAAAAAAAAAAAAAA
++
+#1BDFFFFHHHHHJJJJFDDDDDDD
+ at machine1:HiMom:abcdeACXX:1:1101:1327:2200 1:N:0:
+AGGGGGATCCGCCGGGGGACCACAA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1328:2225 1:Y:0:
+GAAATGCATCTGTCTTAGAAACTGG
++
+??@=BDDDFDD<<,<2:C<F:FFEA
+ at machine1:HiMom:abcdeACXX:1:1101:1338:2175 1:Y:0:
+CCCACCTTCCGGCGGCCGAAGACAC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1347:2149 1:Y:0:
+GAGCAGATCGGAAGAGCACAGATCG
++
+@@@FFDDDHHHHHIJJBGGHJIHEG
+ at machine1:HiMom:abcdeACXX:1:1101:1353:2226 1:Y:0:
+TTGCTTGTCTGTAAAGTATTTTATT
++
+ at C@DDFFDHHFHFHHIBGG>IHHII
+ at machine1:HiMom:abcdeACXX:1:1101:1363:2138 1:Y:0:
+NGTCTGGCCTGCACAGACATCCTAC
++
+#1=DDFFFHHHHHJJJIJJIJJJIJ
+ at machine1:HiMom:abcdeACXX:1:1101:1399:2128 1:Y:0:
+NTGCCCTTCGTCCTGGGAAACGGGG
++
+#1BDFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1403:2194 1:Y:0:
+CTAAACAGAGAGAAGGTTTCTCTTT
++
+CCCFFFFFHHHHHJJJFHIJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1406:2222 1:Y:0:
+CTCCCCCCGGGCTGAACCAGGGTAC
++
+CCCFFDDDDHDFHIIIIIIIII9DG
+ at machine1:HiMom:abcdeACXX:1:1101:1419:2119 1:Y:0:
+NATGACTATGGTAACTGAAAGAAAA
++
+#1:A1BDADBFFDFIIIEEHECACF
+ at machine1:HiMom:abcdeACXX:1:1101:1420:2213 1:Y:0:
+TACCTGGTTGATCCTGCCAGTAGCA
++
+@@CFFFFDDHHGHJGGHIJJIHGBH
+ at machine1:HiMom:abcdeACXX:1:1101:1435:2194 1:Y:0:
+GAGAAAGAACATGACTACAGAGATG
++
+CCCFFFFFHHHHHJJJJJJJJJHJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1441:2148 1:Y:0:
+ACTTTCACCGCTACACGACCGGGGG
++
+CCCFFFFFHGFFHIIFIHJIGGII>
+ at machine1:HiMom:abcdeACXX:1:1101:1452:2132 1:Y:0:
+NCGTCCTGGAAAACGGGGCGCGGCT
++
+#1=BDBDDFHHHHF at FHDHIGIIII
+ at machine1:HiMom:abcdeACXX:1:1101:1460:2176 1:Y:0:
+AGTCCAGGCTGAGCCCAGGGAAGAA
++
+CCCFFFFFHHHHGJIJJIJJHIJJI
+ at machine1:HiMom:abcdeACXX:1:1101:1479:2221 1:Y:0:
+TGTAAAGTATGCTGGCTCAGTGTAT
++
+BBBFDFFEHHHHHJJJJJJJIJHJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1491:2120 1:Y:0:
+NGGCAGGTGCCCCCACTTGACTCTC
++
+#1?DFFFFGHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1018:2133 1:Y:0:
+NAAAACTTGAGGATGCTATGCAAGC
++
+#1:B:ADDDDDDDEEAEBF9FFEBF
+ at machine1:HiMom:abcdeACXX:1:1201:1018:2217 1:N:0:
+NTTTCTCTGGGCGCAAAGATGTTCA
++
+#07;8=8<<99(:=@@/@7>>6=?>
+ at machine1:HiMom:abcdeACXX:1:1201:1028:2202 1:Y:0:
+NTCCTGGGAAACGGGGCGCGGCTGG
++
+#4BDDDFFHHHHHIJIIJJJJJJIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1042:2174 1:Y:0:
+NGTTGGTGTCTTCATTTTATGTATA
++
+#1=DDFDFHHHHHJIJJJHIJHIJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1043:2246 1:Y:0:
+NTTCTCGGCTGTCATGTGCAACATT
++
+#1=DDBDFHHHDFFBHGHGHIIJEH
+ at machine1:HiMom:abcdeACXX:1:1201:1045:2105 1:N:0:
+NTAAAGAGAAATCAAGAATACTATT
++
+#-4@?(@)@@###############
+ at machine1:HiMom:abcdeACXX:1:1201:1054:2151 1:Y:0:
+NTAGTGCTGGGCACTAAGTAATACC
++
+#4=DDDFFHHHHHJJJJJHIJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1064:2239 1:Y:0:
+CATGCAGCGCAAGTAGGTCTACAAG
++
+@@;DFAFFHHHHAHEGHFDGGFABG
+ at machine1:HiMom:abcdeACXX:1:1201:1073:2225 1:Y:0:
+GGGGCTGAGACCTTTGCTGATGGTG
++
+@@@FFFFFHHHGHJJJJJIIIGICH
+ at machine1:HiMom:abcdeACXX:1:1201:1083:2121 1:Y:0:
+NAGAACTGGCGCTGCGGGATGAACC
++
+#1=BDFFFHHHHHJJJJJHIJIJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1084:2204 1:Y:0:
+GGCCCGTGGACGCCGCCGAAGAAGC
++
+CCCFFFFFHHHHHJJJJJIJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1095:2146 1:Y:0:
+GCTGAGTCATGTAGTAAGCCTGTGC
++
+BB at FDDDFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1103:2184 1:Y:0:
+GTAAGAACTACCCTGGGTCCCCGTG
++
+@@BFFFFFHHHHHJJJJGIJJJJHI
+ at machine1:HiMom:abcdeACXX:1:1201:1107:2109 1:Y:0:
+NGGGAACCTGGCGCTAAACCATTCG
++
+#1=DFFFFHHHHHJJJJJJJJJIJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1118:2198 1:Y:0:
+CAAGTGTACAGGATTAGACTGGGTT
++
+BCCFDEBDHHHHHIJJJGIIIJJGH
+ at machine1:HiMom:abcdeACXX:1:1201:1122:2227 1:Y:0:
+AGAAGACGAGGCTGAGAGTGACATC
++
+@@@FFFFFHHHDHJGHGHCHHJJIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1123:2161 1:N:0:
+CACTAACTCCTGACCTCAAATAATC
++
+?7?=DD?DD+CDBE>E at EEF@+<CF
+ at machine1:HiMom:abcdeACXX:1:1201:1127:2112 1:N:0:
+NGTCAAGGATGTTCGTCGTGGCAAC
++
+#1=BDDDDDDDDDID<AE?@<CEEE
+ at machine1:HiMom:abcdeACXX:1:1201:1134:2144 1:Y:0:
+TGCCAGGAAGTGTTTTTTCTGGGTC
++
+ at CCFFEFFHHFFFGIJJJJJJJJGH
+ at machine1:HiMom:abcdeACXX:1:1201:1138:2227 1:N:0:
+GCTGACACAATCTCTTCCGCCTGGT
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1201:1140:2125 1:Y:0:
+NTTTCAGTTCAGAGAACTGCAGAAT
++
+#1=DBDFDHHHHGJIJJJJJIIIJI
+ at machine1:HiMom:abcdeACXX:1:1201:1142:2242 1:Y:0:
+TGTTGATAGTCCTTCTTATCTTAGT
++
+???DB?==CC2<AC:CC<CFEF<FF
+ at machine1:HiMom:abcdeACXX:1:1201:1150:2161 1:Y:0:
+AAGTCACCTAATATCTTTTTTTTTT
++
+@@<??;?D?CFD,A4CDDHFBIIID
+ at machine1:HiMom:abcdeACXX:1:1201:1159:2179 1:N:0:
+GTTAGCACAGATATTGGATGAGTGA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1201:1160:2109 1:Y:0:
+NAGAAGCCTTTGCACCCTGGGAGGA
++
+#1=DDDFFHHHHHJJJJJJJJIIJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1180:2119 1:Y:0:
+NTGAAAGATTTAGAGAGCTTACAAA
++
+#1=DDDDDHHHGHJJIIJJJJIJJI
+ at machine1:HiMom:abcdeACXX:1:1201:1185:2143 1:Y:0:
+ATCTGCCTGGTTCGGCCCGCCTGCC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1187:2100 1:Y:0:
+NGCGGTAATTCCAGCTCCAATAGCG
++
+#1:BB2 at DHHFHHIIIIHHIIGHGG
+ at machine1:HiMom:abcdeACXX:1:1201:1190:2194 1:Y:0:
+AACCTGGCGCTAAACCATTCGTAGA
++
+CCCFFFFFHHHHHJJJJJJJJIJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1204:2228 1:Y:0:
+CCGATACGCTGAGTGTGGTTTGCGG
++
+CCCFFFFFHHHFHEGGHIHIJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1208:2132 1:Y:0:
+NCCTCAATGAGCGGCACTATGGGGG
++
+#1=DDFFFHHHHGJJIJJGHIJGIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1219:2115 1:Y:0:
+NTATAGTGGAGGCCGGAGCAGGAAC
++
+#1:DABADHHHFHIIIGGHGIIIII
+ at machine1:HiMom:abcdeACXX:1:1201:1236:2187 1:Y:0:
+TTTAAATGGGTAAGAAGCCCGGCTC
++
+ at BCDDFEFHHDHHJJJJJIJJIJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1242:2207 1:Y:0:
+ATGGCAAAGTGGTGTCTGAGACCAA
++
+BCCFFFFFGHHHHHIIIJFHIJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1252:2141 1:Y:0:
+NTTCCCCCCATGTAATTATTGTGAA
++
+#1=DDFFFHHHHHJJJJJJJJIJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1260:2165 1:Y:0:
+GGACACGGACAGGATTGACAGATTG
++
+BCBFFFFFHHHHHHIIJHIIIFHIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1280:2179 1:Y:0:
+TTCAAGGAATCGTCCTGCCTCAGCC
++
+BCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1281:2133 1:Y:0:
+NGGAAATCCAGAAAACATAGAAGAT
++
+#1=DDFFFHHHHHIJJJJJJJJIJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1285:2100 1:Y:0:
+NAATGACATGTTTAAAGATGGACTC
++
+#1:BDDFFHHFHHGIJIJIIIIGII
+ at machine1:HiMom:abcdeACXX:1:1201:1291:2158 1:Y:0:
+AGAAGGGGAAAGCCTTCATCTTGGC
++
+BCBFFFFFHHHHHJJJJJIIFIJIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1300:2137 1:Y:0:
+NTGTAATCCCAGCTCTCAGGGAGGC
++
+#1=ADDDDDDDBBA?@AE?E at FE8;
+ at machine1:HiMom:abcdeACXX:1:1201:1312:2112 1:Y:0:
+NTCCCAGCGAACCCGCGTGCAACCT
++
+#1=DFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1331:2162 1:Y:0:
+ACGCTCGGCTAATTTTTGTATTTTT
++
+ at CCFFFDFHHHHHIJJJJHIJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1341:2116 1:Y:0:
+NAGAAGCCCCAGGAGGAAGACAGTC
++
+#1=DDFFFHHHHHHHJIIJJJJJGI
+ at machine1:HiMom:abcdeACXX:1:1201:1344:2147 1:Y:0:
+TATCCTCCCTACTATGCCTAGAAGG
++
+=?@DADEFHBHDFG>EFGDHGFGHD
+ at machine1:HiMom:abcdeACXX:1:1201:1345:2181 1:Y:0:
+GGATAATCCTATTTATTACCTCAGA
++
+BBBDDFFFHHHHHJJJJJJJJJIJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1364:2113 1:Y:0:
+NCACTCATTTTCTTATGTGGGATAT
++
+#1=DDFDFHHHHHIJJIFHIIHHHI
+ at machine1:HiMom:abcdeACXX:1:1201:1392:2109 1:Y:0:
+NCTGAAGAGGCCAAAGCGCCCTCCA
++
+#1=DDFFFHHHHHJJJJJJJJJJJI
+ at machine1:HiMom:abcdeACXX:1:1201:1392:2184 1:Y:0:
+TTTCAGATTGGTCATTGTTAGTGTA
++
+??@BDDDEHBHADHHIIEHDHFHFF
+ at machine1:HiMom:abcdeACXX:1:1201:1393:2143 1:Y:0:
+TGGTTGATCCTGCCAGTAGCATATG
++
+@@@ADADDFHFFDBHE?G at HIIIEE
+ at machine1:HiMom:abcdeACXX:1:1201:1414:2174 1:N:0:
+GCCAAAAAAAAGAACCAGCCCAAGG
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1201:1416:2128 1:Y:0:
+NACAGGCGTGGAGGAGGCGGCGGCC
++
+#4=DDDFFHHHHHJIGJHFHHFFED
+ at machine1:HiMom:abcdeACXX:1:1201:1421:2154 1:Y:0:
+TGTGTGTGTGGGTGTGTGTATATAT
++
+?@?DDFFFFFHH at GEFCCCHGIGJI
+ at machine1:HiMom:abcdeACXX:1:1201:1439:2156 1:Y:0:
+AGCCGCGAGGTGCTGGCGGACTTCC
++
+:;1BDDDAA88A<?<E1C:D#####
+ at machine1:HiMom:abcdeACXX:1:1201:1452:2143 1:Y:0:
+TATCCCCTCTAAGACGGACCTGGGT
++
+CCCFFFFFHHHHHJJIIIJJJJJJG
+ at machine1:HiMom:abcdeACXX:1:1201:1458:2109 1:Y:0:
+NGAGACCATAGAGCGGATGCTTTCA
++
+#1=DDDFFHHGHGIJJIGIIJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1472:2121 1:N:0:
+NTAAAGTGTGAACAAGGAAGGTCAT
++
+#07>@<9=@################
+ at machine1:HiMom:abcdeACXX:1:1201:1483:2126 1:N:0:
+NTGATAAGGTGTTGCTATGTTACCC
++
+#1:D?DDDDA??2:<CC4:AEDF>?
+ at machine1:HiMom:abcdeACXX:1:1201:1486:2109 1:Y:0:
+NCACCTCCTAGCCCCTCACTTCTGT
++
+#1=B;BDDHHHGFIIIIIIIIIGGG
+ at machine1:HiMom:abcdeACXX:1:1201:1486:2146 1:N:0:
+GTTCTCTGTCCCCAGGTCCTGTCTC
++
+===A7<7222<<=C=?+<7>@?ACB
+ at machine1:HiMom:abcdeACXX:1:2101:1011:2102 1:Y:0:
+NAAACAAAACTGTAGAACTGTGTAT
++
+#1=DDFFFHHHHHJJIJJJIHHHJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1013:2146 1:Y:0:
+NACACTGCTGCAGATGACAAGCAGC
++
+#4BDFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1021:2209 1:Y:0:
+NGGCCCCACCCTCCTCCAGCACGTC
++
+#1=DDFFFHHHHHJJJJJJHIIHFH
+ at machine1:HiMom:abcdeACXX:1:2101:1023:2237 1:N:0:
+NTAAACAGCTTCTGCACAGCCAAAG
++
+#00@@?>=39>9;<412@?######
+ at machine1:HiMom:abcdeACXX:1:2101:1031:2163 1:Y:0:
+NTTTCCATGGCCGTCACCTTTGGGT
++
+#4=DDFFFHHHHHJJJJJJJJJJJI
+ at machine1:HiMom:abcdeACXX:1:2101:1036:2087 1:Y:0:
+NTGTAGTTTCTTTAGGCAAATTTGT
++
+#4=BDDDFHHHHHJJJJJJIIJJJI
+ at machine1:HiMom:abcdeACXX:1:2101:1040:2208 1:N:0:
+NATGCCCACCTCCCTCCTACGCACC
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1048:2238 1:Y:0:
+NCTGCCGTGTCCTGACTTCTGGAAT
++
+#1:B?ADDACF<DCG;EG<FHH at CE
+ at machine1:HiMom:abcdeACXX:1:2101:1054:2162 1:Y:0:
+NCCAGGTGTCTTCCCGGGCCCTGCC
++
+#1=DDFBDFHHHHJJJJJIJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1059:2083 1:Y:0:
+NAAGAGGGGTCAAGAGTTAAACTTA
++
+#1=DDFFFHFHHGIGHGHJJJJJJI
+ at machine1:HiMom:abcdeACXX:1:2101:1063:2206 1:Y:0:
+TCCTATTCGCCTACACAATTCTCCG
++
+CCCFFFFFHHHHHJJJJJJJHJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1064:2242 1:Y:0:
+ATGAACAAAGGAAGAATTATGCACG
++
+?;?D;DDDF?;:+<<CFFCHE433A
+ at machine1:HiMom:abcdeACXX:1:2101:1072:2170 1:Y:0:
+ATCACCGCACTCATTTCCCGCTTCC
++
+CCCFFFFFHHHACEEGHIIBHIIII
+ at machine1:HiMom:abcdeACXX:1:2101:1077:2139 1:Y:0:
+CACAGGCTTCCACGGACTTAACGTC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1084:2188 1:Y:0:
+TTGCTGCATGGGTTAATTGAGAATA
++
+CCCFFFFFHHHHFHHIIJJIJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1100:2085 1:Y:0:
+NCACATGGATGAGGAGAATGAGGAT
++
+#1=DDFFFFHHHHJHIGIHHHIJEH
+ at machine1:HiMom:abcdeACXX:1:2101:1102:2221 1:Y:0:
+TTTCATCTTATTTCATTGGTTTATA
++
+CCCFFFFFHHHHHJIJJJJIJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1105:2131 1:Y:0:
+TTGGAACACAGCGGGAATCACAGCA
++
+CCCFFFFFHHHHHJIJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1112:2245 1:Y:0:
+TGCCATCTGCTCTGGGAAGCACCAG
++
+1:=DDDDDFBC:DEFIFFFIEF at BE
+ at machine1:HiMom:abcdeACXX:1:2101:1122:2136 1:Y:0:
+GTAGGCGCTCAGCAAATACTTGTCG
++
+@@@DDDD8?<CACEHHBBHDAAFH@
+ at machine1:HiMom:abcdeACXX:1:2101:1123:2095 1:Y:0:
+NTGGACAACATGTTCGAGAGCTACA
++
+#1=BBDDDFFFFDGFGIG?F;HHFI
+ at machine1:HiMom:abcdeACXX:1:2101:1126:2082 1:Y:0:
+NGTTTTAGGGGTGCGCAGGAGTCAA
++
+#11=A=DD?DF at D@CCGHIEFH at BG
+ at machine1:HiMom:abcdeACXX:1:2101:1133:2239 1:Y:0:
+AGACAGAAGTACGGGAAGGCGAAGA
++
+@@@FFFFEHFHHHJJCGDHIIECD@
+ at machine1:HiMom:abcdeACXX:1:2101:1143:2137 1:Y:0:
+ATGCAGCAGCTGCCACGGAGCACCA
++
+CC at FFDFDFHFHHGIDHEHIGJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1151:2182 1:N:0:
+TTGTTTTGGCTTATAATGACAAGAA
++
+;;8-2).2())(<6=@8;?4??>>?
+ at machine1:HiMom:abcdeACXX:1:2101:1151:2236 1:N:0:
+TTAAAGAGGTTCAGGGATGCAGAGT
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1162:2139 1:Y:0:
+AGAGGTGAAATTCTTGGACCGGCGC
++
+@@@DDDDDHFHHHDB:EFHHCAG?D
+ at machine1:HiMom:abcdeACXX:1:2101:1163:2203 1:Y:0:
+TCTCCATGTGAAACAAGCAAAAAGA
++
+CCCFFFFFHHHHGJJJIJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1163:2222 1:Y:0:
+GAGCAGGCAAGGAGGACTTCTTGTT
++
+CCCFFFFFGHHHHJJHHIJJJJJIJ
+ at machine1:HiMom:abcdeACXX:1:2101:1172:2152 1:N:0:
+AACACGGACAAAGGAGTCTAACACG
++
+<<<??8@@#################
+ at machine1:HiMom:abcdeACXX:1:2101:1186:2093 1:Y:0:
+NCGACCATAAACGATGCCGACCGGC
++
+#4=DFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1188:2195 1:Y:0:
+TTAGACCGTCGTGAGACAGGTTAGT
++
+ at CCFFFFFHHHHHJJJJJIIEHIJH
+ at machine1:HiMom:abcdeACXX:1:2101:1195:2150 1:Y:0:
+CCGAGAGAGTGAGAGCGCTCCTGGG
++
+CCCFFFFFHFHHHJJJJIJJJJIJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1207:2084 1:N:0:
+NTAGATGACCAAAACTTGCAGGGCA
++
+#1:A<?@A+7A=?CBCCBCCBAAAA
+ at machine1:HiMom:abcdeACXX:1:2101:1208:2231 1:N:0:
+TCACTAAACATCCAAACATCACTTT
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1215:2110 1:Y:0:
+NAATATAATTTGGAGACCCTTTGTT
++
+#1=DDDDDEDDDDIDDBB3ABAB##
+ at machine1:HiMom:abcdeACXX:1:2101:1216:2172 1:Y:0:
+TTTCTTCGCAGGATTTTTCTGAGCC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1216:2193 1:Y:0:
+TTTTCTTGGCCTCTGTTTTTTTTTT
++
+BCCFDFFFHHFFHJIGIJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1226:2088 1:Y:0:
+NGATCGGAAGAGCACACGTTTGACT
++
+#4=DAA=DDFHFHIIBFGHHIG>EG
+ at machine1:HiMom:abcdeACXX:1:2101:1231:2208 1:Y:0:
+ACGCCGCAAGTCAGAGCCCCCCAGA
++
+@@@DDDFFFFB:DBBEBEFDHBDDB
+ at machine1:HiMom:abcdeACXX:1:2101:1233:2133 1:N:0:
+GAGAGAAGCACTCTTGAGCGGGATA
++
+0;(@((@)2@###############
+ at machine1:HiMom:abcdeACXX:1:2101:1240:2197 1:N:0:
+ATAAAACATAGCAATATTTTCCTAT
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1245:2154 1:Y:0:
+TCGTTAAGTATATTCTTAGGTATTT
++
+CCCFFDFFFHFHHIIJJJJJFJJJI
+ at machine1:HiMom:abcdeACXX:1:2101:1249:2231 1:Y:0:
+GTTATTGATAGGATACTGTACAAAC
++
+ at BCFFFFDHHHHFIJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1258:2092 1:Y:0:
+NCACACACACACTCATTCACAGCTT
++
+#1=DDDFFHHHFHJJIJGGGIIGIJ
+ at machine1:HiMom:abcdeACXX:1:2101:1262:2128 1:N:0:
+AGCAGAAGGGCAAAAGCTGGCTTGA
++
+9;<@:@###################
+ at machine1:HiMom:abcdeACXX:1:2101:1273:2119 1:N:0:
+NAGATAAGAGTCCACACAGTTGAGT
++
+#11AAAAA<A?4=C=7?733<ACA3
+ at machine1:HiMom:abcdeACXX:1:2101:1285:2105 1:N:0:
+NGCGGGGAGCCGGGCGTGGAATGCG
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1312:2105 1:Y:0:
+NTTCCCTCAGGATAGCTGGCGCTCT
++
+#1=DDFFFGHGHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1325:2083 1:Y:0:
+NCAGAAGAAAGGGCCTTGTCGGAGG
++
+#1=DDDDDHHFHDGI at EEHG:?FA8
+ at machine1:HiMom:abcdeACXX:1:2101:1336:2109 1:Y:0:
+NACTATCAGGATCGTGGCTATTTTG
++
+#1BDDFFFHHHHHJIJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1349:2084 1:Y:0:
+NCAAGTAGCAGTGTCACGCCTTAGC
++
+#1=DDBDDADFDDBEH at HC=CEGG@
+ at machine1:HiMom:abcdeACXX:1:2101:1365:2094 1:Y:0:
+NAAGGTGAAGGCCGGCGCGCTCGCC
++
+#1=BDDDFFHHHHJGGGIGFIHIIJ
+ at machine1:HiMom:abcdeACXX:1:2101:1370:2116 1:Y:0:
+NTGGTGGTCCATAGAGATTTGAAAC
++
+#1:4BD7DACF?FCA:4+<ACHIIH
+ at machine1:HiMom:abcdeACXX:1:2101:1386:2105 1:Y:0:
+NTACTAAAGAAAAAGTTGAAGAACT
++
+#1=DDDFFHHHHHJJGHIJJJJIJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1414:2098 1:Y:0:
+NAGGACATCGATAAAGGCGAGGTGT
++
+#1=DDFFFHHHHHJJJJJJJJJHHG
+ at machine1:HiMom:abcdeACXX:1:2101:1427:2081 1:Y:0:
+NCGAGTGCCTAGTGGGCCACTTTTG
++
+#4=DDBDFHHHHFHIJJJJIJJJJI
+ at machine1:HiMom:abcdeACXX:1:2101:1450:2134 1:Y:0:
+AGCACGCTGCCGCGGGACCTGCCCA
++
+?@@AD at DDHFH?DGIIIIG at FGFBF
+ at machine1:HiMom:abcdeACXX:1:2101:1459:2083 1:Y:0:
+NCACACGCCACACGGAGCACACTTT
++
+#4=DDFFFHHHHHJJJJJJJJIIJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1491:2093 1:Y:0:
+NCTATGCCGATCGGGTGTCCGCACT
++
+#1=DDDDDHHFHHIIEHHHBGHGII
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/nonBarcoded.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/nonBarcoded.2.fastq
new file mode 100644
index 0000000..3bb2e7f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/nonBarcoded.2.fastq
@@ -0,0 +1,720 @@
+ at machine1:HiMom:abcdeACXX:1:1101:1031:2224 2:N:0:
+NNNNNNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1039:2147 2:N:0:
+NNNNNNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1046:2175 2:N:0:
+NNGGANNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1047:2122 2:N:0:
+NNTCANNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1048:2197 2:N:0:
+NNGTGNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1065:2193 2:Y:0:
+NCTTGNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1069:2159 2:Y:0:
+GACGTNNNNNNNNNNNNNNNNNNNN
++
+<<<@?####################
+ at machine1:HiMom:abcdeACXX:1:1101:1071:2233 2:Y:0:
+GTTTGNNNNNNNNNNNNNNNNNNNN
++
+<<<@@####################
+ at machine1:HiMom:abcdeACXX:1:1101:1083:2193 2:Y:0:
+AGGCTNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1084:2136 2:Y:0:
+TTTCTNNNNNNNNNNNNNNNNNNNN
++
+<<<@@####################
+ at machine1:HiMom:abcdeACXX:1:1101:1089:2172 2:Y:0:
+TCCGGNNNNNNNNNNNNNNNNNNNN
++
+:<<??####################
+ at machine1:HiMom:abcdeACXX:1:1101:1100:2207 2:Y:0:
+AGGCTNNNNNNNNNNNNGNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1111:2148 2:Y:0:
+GCGAANANNNNNNNNNNGGACGACN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1138:2141 2:Y:0:
+TCCGATCTGCTTCAGGTCGATCAGA
++
+CCCFFFFFHGHHHJJIGHIJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1140:2120 2:Y:0:
+TTTTTTTTTTTTTAACTTTGCAAAT
++
+@@@DDDDDHHHHFB at 9FHI@BFH@@
+ at machine1:HiMom:abcdeACXX:1:1101:1143:2192 2:Y:0:
+CGACAAGTCTGGCTTATCACTCATC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1150:2228 2:Y:0:
+ATGGGAGGCGATTCCTAGGGGGTTG
++
+8?=DD8;@BH6DHD<FGGGEIGHIG
+ at machine1:HiMom:abcdeACXX:1:1101:1157:2135 2:Y:0:
+TTTAAAGTCTTAATCAAAGATGATA
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1162:2207 2:N:0:
+TAAAACTGGGGAAGTTAGAGGAATG
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1165:2239 2:Y:0:
+ATGGAAGTCGAGACAGAAGTGAGAA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1175:2197 2:Y:0:
+AAGAGCTGGGGAACATCCAGAAAGG
++
+BC at FFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1188:2237 2:Y:0:
+GCTTCCTTCAAGACAGAAGTGAGAA
++
+CCCFFDDEFHHFFE at FDHHAIAFHG
+ at machine1:HiMom:abcdeACXX:1:1101:1197:2200 2:Y:0:
+ATATTCCACTGGAACCACAGAACCC
++
+@@@FFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1206:2126 2:Y:0:
+ATCTGTCCAGTGGTGCACTGAATGT
++
+CCCFFFFFHHHHHHIIJJJJIJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1212:2230 2:Y:0:
+TTTTAGCTTTATTGGGGAGGGGGTG
++
+CCCFFFFFHHGHHJJJJGJJJJJDF
+ at machine1:HiMom:abcdeACXX:1:1101:1218:2200 2:Y:0:
+GCTCTTCCGATCTATCTGCTCGTCC
++
+(-(=34???3;@#############
+ at machine1:HiMom:abcdeACXX:1:1101:1219:2164 2:Y:0:
+ATCTTATCCACTCCTTCCACTTTGG
++
+CCCFFFFFHHHHHJJIJJJJJJJIJ
+ at machine1:HiMom:abcdeACXX:1:1101:1221:2143 2:Y:0:
+CAATTGAATGTCTGCACAGCCGCTT
++
+@@@FFFFDHHHHHJJJIIIJGHIJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1236:2121 2:Y:0:
+TTGCGCTTACTTTGTAGCCTTCATC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1242:2170 2:Y:0:
+GGAAGGAAAAGAAGCACAAGTACAT
++
+@@@DFDFFHHHGHHGIIGJJEHHIG
+ at machine1:HiMom:abcdeACXX:1:1101:1257:2223 2:Y:0:
+TGCTCTTCCGATCTTTTAGCAAAGC
++
+:?@DDBDDHFFHDGIGIIJJJGGGI
+ at machine1:HiMom:abcdeACXX:1:1101:1259:2152 2:Y:0:
+ATTTTTATATTTTTTTAGACATAGG
++
+CCCFFFFFGHHHHJJJJIGIIJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1261:2127 2:N:0:
+TTTTTTTTTTTTTTTTTTTTTTTTT
++
+CCCFFFFFHGHHHJJIFDDDDDDDD
+ at machine1:HiMom:abcdeACXX:1:1101:1263:2236 2:N:0:
+AGTTCTTCAGTAATTTTAGTACTGC
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1267:2209 2:Y:0:
+GGCAGAGTCTCCAACAGCCCCGTAC
++
+=;?DDDD?CCFHAIIIGGIIGE at EG
+ at machine1:HiMom:abcdeACXX:1:1101:1269:2170 2:Y:0:
+TTCCAAGCCTGTGCTTTAAGGAAAA
++
+@@<ADBDBDF8DDCFH at GIE@@GGH
+ at machine1:HiMom:abcdeACXX:1:1101:1290:2225 2:Y:0:
+TCAGTTCACTGGCAAAGACAGTCAC
++
+C@@FBEDDFHFHGIIICEHGDHBHE
+ at machine1:HiMom:abcdeACXX:1:1101:1291:2150 2:Y:0:
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CCCFFFFFHHFHHIJJJIIIGIJIJ
+ at machine1:HiMom:abcdeACXX:1:1101:1302:2244 2:Y:0:
+TGAATACATATAACAAATGCAAAAA
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1308:2153 2:N:0:
+TCTGTAAGGTAATCCCCGCATGTGT
++
+1?1=4===AFFDFFGFDGFB at CFB:
+ at machine1:HiMom:abcdeACXX:1:1101:1309:2210 2:Y:0:
+AGTGGGCTAGGGCATTTTTAATCTT
++
+@@?DFFDFHHHDFHJIJJIJGIIIJ
+ at machine1:HiMom:abcdeACXX:1:1101:1314:2233 2:Y:0:
+AGGAAAGTTGGGCTGACCTGACAGA
++
+@@<DDD;=FBFADBCGDEH?F;FCG
+ at machine1:HiMom:abcdeACXX:1:1101:1316:2126 2:Y:0:
+TCTTTTTTTTTTTTTTTTTTTTTTT
++
+CCCFFFFFHHHHHJJJJHFDDDDDD
+ at machine1:HiMom:abcdeACXX:1:1101:1327:2200 2:N:0:
+GTCATCTGGGCTGTCGACAGGTGTC
++
+ at B@FFFFFHHHHGIJJJJJJIFHHI
+ at machine1:HiMom:abcdeACXX:1:1101:1328:2225 2:Y:0:
+AGGAAATTAGGACTTACCTGACATA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1338:2175 2:Y:0:
+GCTTGTTGGCTTTAACATCCACAAT
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1347:2149 2:Y:0:
+GCTCTTCCGATCTGTGCTCTTCCGA
++
+CCCFFFFFDFHHFIJDGIGGHGIGH
+ at machine1:HiMom:abcdeACXX:1:1101:1353:2226 2:Y:0:
+GTGCTCTTCCGATCTTCAGGTTACC
++
+BBBFFFFFHHHHHJJJJJJJIJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1363:2138 2:Y:0:
+GTTCTTAAACCTGTTAGAACTTCTG
++
+C@@FFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1399:2128 2:Y:0:
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CCCFFFFFHHHHHIJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1403:2194 2:Y:0:
+ACATGGTGAAACCCTGTCTCTACTA
++
+CCCFFFDDHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1406:2222 2:Y:0:
+GGCTGGACTCCCCTGGTTCTGGGCA
++
+;?@DDDBD?FHDFGIIIGIGHHIII
+ at machine1:HiMom:abcdeACXX:1:1101:1419:2119 2:Y:0:
+ACTTTCCTTTTTTGTTTTACTTTAA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1420:2213 2:Y:0:
+TTCACTGTACCGGCCGTGCGTACTT
++
+ at CCFFFFDHHHFGIJJJJJJGHIGG
+ at machine1:HiMom:abcdeACXX:1:1101:1435:2194 2:Y:0:
+TTTTGTTTTCTTTTACTGAAGTGTA
++
+CCCFFDFFHHHHHJJJJIHIJHHHJ
+ at machine1:HiMom:abcdeACXX:1:1101:1441:2148 2:Y:0:
+TTTTGGCTCTAGAGGGGGTAGAGGG
++
+CCCFFFFFHHDFBHIIJJ1?FGHIJ
+ at machine1:HiMom:abcdeACXX:1:1101:1452:2132 2:Y:0:
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CCCFFFFFHHHHHJJJJJJJIJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1460:2176 2:Y:0:
+AGGAAAAAGACACAACAAGTCCAAC
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:1479:2221 2:Y:0:
+GGGGAAATCTATTTTTATGTAAAAA
++
+ at CCFFFFFHHHHHJIGIJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1101:1491:2120 2:Y:0:
+GGCCAGGCTGAACTTCTGAGCTGCT
++
+CCCFFFFFHHHGHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1018:2133 2:Y:0:
+NNNNNNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1201:1018:2217 2:N:0:
+NNNNNNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1201:1028:2202 2:Y:0:
+NNAAACNCNTNNNNNNNGGNNTGNN
++
+##42@?###################
+ at machine1:HiMom:abcdeACXX:1:1201:1042:2174 2:Y:0:
+NTCAGGAAGGCNNCAAAAAAAGAAA
++
+#0;@@@?@?<@##3<@@?@@?????
+ at machine1:HiMom:abcdeACXX:1:1201:1043:2246 2:Y:0:
+NGCATCATTTCNNGCTTCTCTCTGT
++
+#0;@@??@=@>##22=;@??><@??
+ at machine1:HiMom:abcdeACXX:1:1201:1045:2105 2:N:0:
+NTTTTTTTTTTNNTTTTTTTTTTTT
++
+#0;@@@@@@@?##0:????????=<
+ at machine1:HiMom:abcdeACXX:1:1201:1054:2151 2:Y:0:
+GTCAGGCACTGAGAATATATGGGTG
++
+CBCFFFFFHHHHHJJJJJJJJJJEG
+ at machine1:HiMom:abcdeACXX:1:1201:1064:2239 2:Y:0:
+GGGATGGGAGGGCGATGAGGACTAG
++
+8?@:DDDACC:FHHGIH<EGDDDFH
+ at machine1:HiMom:abcdeACXX:1:1201:1073:2225 2:Y:0:
+CGTGTGCTCTTCCGATCTGGAGGGT
++
+ at BBDFFFFHHHHHJJJJJJJJJJJ:
+ at machine1:HiMom:abcdeACXX:1:1201:1083:2121 2:Y:0:
+ACACACAACACCACCGCCCTCCCCC
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1201:1084:2204 2:Y:0:
+TGGCTCCTCAGGCTCTCATCAGTTG
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1095:2146 2:Y:0:
+ACTGACAACACCAAATGCTGCTAAG
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1103:2184 2:Y:0:
+AGAAGTTTCAGAATTGTGGCCCCAT
++
+B at BFFDEFHHHHHJJJGHIJJJJJI
+ at machine1:HiMom:abcdeACXX:1:1201:1107:2109 2:Y:0:
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CCCFFFFFHHGHHJJJJIIJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1118:2198 2:Y:0:
+AATAAACTTTATTAAAGCAGTTAAA
++
+C at CFFFFFHDHHHGIIIJJJIJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1122:2227 2:Y:0:
+GTCATATAAGGCCCAGTCCAAGGAA
++
+@@@FFFFFHHHGGIJIGGIJFIJII
+ at machine1:HiMom:abcdeACXX:1:1201:1123:2161 2:N:0:
+CGTGTGCTCTTCCGATCTGCATACA
++
+===AAAA8AAAA<AAA)@CBA9>A#
+ at machine1:HiMom:abcdeACXX:1:1201:1127:2112 2:N:0:
+TAATCACCTGAGCAGTGAAGCCAGC
++
+@<@?BDDDHD?FDBHI?AHGGGDFH
+ at machine1:HiMom:abcdeACXX:1:1201:1134:2144 2:Y:0:
+AGTGTGAGTAATGGTTGAGAGGTGG
++
+B@?DDDFFFHHGHJHHGFIHHIFGI
+ at machine1:HiMom:abcdeACXX:1:1201:1138:2227 2:N:0:
+GACAAATATAGGAAATAGAAGCTAT
++
+=1=A=AAA,2?4>7C<<4<A+3<AB
+ at machine1:HiMom:abcdeACXX:1:1201:1140:2125 2:Y:0:
+TTCATAAATTGGTCTTAGATGTTGC
++
+CC at FFFFFHHHHFGIJIIIJIJIJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1142:2242 2:Y:0:
+GTAAAATGTAAAATAATAAAAAATG
++
+?=?DDDD;AF<DF<FFFFIIIFF@<
+ at machine1:HiMom:abcdeACXX:1:1201:1150:2161 2:Y:0:
+TTCTCACTACTGTGATTGTGCCACT
++
+ at C@FFFFFGHHHHGIIIICEHCFGH
+ at machine1:HiMom:abcdeACXX:1:1201:1159:2179 2:N:0:
+TTTTTTTTTATTTTTCTAAATACTT
++
+===AA####################
+ at machine1:HiMom:abcdeACXX:1:1201:1160:2109 2:Y:0:
+ACATCCTTCCCATGCCACCAACTCG
++
+CCCFFFFFGHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1180:2119 2:Y:0:
+GCTCTAAATTTTGCTTTTCTACAGC
++
+CCCFFFFFHHHHHJJJJIJIJJIJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1185:2143 2:Y:0:
+GCTGAAGGCCCGTGGGCCAGAGGTG
++
+ at CCFFFFFHHHHHJJJJJJJJJJHI
+ at machine1:HiMom:abcdeACXX:1:1201:1187:2100 2:Y:0:
+AAAAAAGAGCCCGCATTGCCGAGAC
++
+=<=;AA###################
+ at machine1:HiMom:abcdeACXX:1:1201:1190:2194 2:Y:0:
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1204:2228 2:Y:0:
+TCTTCTTGTCGATGAGGAACTTGGT
++
+@?@FFFFFDHHGHJIJJGHIIJJJH
+ at machine1:HiMom:abcdeACXX:1:1201:1208:2132 2:Y:0:
+CTGTAGAAAGGATGGTCGGGCTCCA
++
+@@CDFFFFGHFHHJIJJGJIBHJJG
+ at machine1:HiMom:abcdeACXX:1:1201:1219:2115 2:Y:0:
+TGGGAGTAGTTCCCTGCTAAGGGAG
++
+???DBDBDADDDDIEID:AFFD:?8
+ at machine1:HiMom:abcdeACXX:1:1201:1236:2187 2:Y:0:
+CTCCTTAGCGGATTCCGACTTCCAT
++
+CCCFFFFDHHHHGIJJIGIGIJJGG
+ at machine1:HiMom:abcdeACXX:1:1201:1242:2207 2:Y:0:
+ATCTTTTATTGGCCTCCTGCTCCCC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1252:2141 2:Y:0:
+AGTTATTTTGCCTATGTCCAACAAG
++
+BCBFFFFFGHHHHJIJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1260:2165 2:Y:0:
+ATCTGATCTAAGTTGGGGGACGCCG
++
+@@@FFDFFHHHHHJJJIJIIIGIJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1280:2179 2:Y:0:
+GAGGACTGCTTGAGTCCAGGAGTTC
++
+@@BFFDEFGHHHHIFGCHIJJJGGI
+ at machine1:HiMom:abcdeACXX:1:1201:1281:2133 2:Y:0:
+GCAACAAAATTTCATATGACTTAGC
++
+CCCFFFFFHHHHHJJIIIHICHIIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1285:2100 2:Y:0:
+GATCTTTTTTGCTTTGTAGTTATAG
++
+@@@DFFFFHHHHHIIGIABCFFHBF
+ at machine1:HiMom:abcdeACXX:1:1201:1291:2158 2:Y:0:
+CGTGTGCTCTTCCGATCTGATGGGC
++
+ at CCFFFDD?FHHFGEHHIIDHIIII
+ at machine1:HiMom:abcdeACXX:1:1201:1300:2137 2:Y:0:
+GCTCTTCCGATCTTTTTTTTAATTT
++
+@@?DDDDDFDHADEHGIGGED3?FD
+ at machine1:HiMom:abcdeACXX:1:1201:1312:2112 2:Y:0:
+ATTTGCAGGAGCCGGCGCAGGTGCA
++
+CCCFFFFFHHHHHJJJIJJJJGHIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1331:2162 2:Y:0:
+TAATCCCAGTACTTTGGGAGGCCAA
++
+CCCFFFFFHHHHHJJJJIJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1341:2116 2:Y:0:
+ATAACAGCGAGACTGGCAACTTAAA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1201:1344:2147 2:Y:0:
+ACGATTAGTTTTAGCATTGGAGTAG
++
+@<??DDDDFHHHFGGHHIIIGGAGH
+ at machine1:HiMom:abcdeACXX:1:1201:1345:2181 2:Y:0:
+ATACGGATGTGTTTAGGAGTGGGAC
++
+CCCFFFFFHHHHHIIJJHJFHIJIJ
+ at machine1:HiMom:abcdeACXX:1:1201:1364:2113 2:Y:0:
+TAAAGAGAGCCAGTGGAGTTACGAC
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1201:1392:2109 2:Y:0:
+GTCAGACAGGGGGATTTGGGCTGTG
++
+BBCFFFFFHHHHHHJJJHIJIJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1392:2184 2:Y:0:
+ATCTTTATTCATTTGTATGATCTTA
++
+@@BFFFFFHFFHFHIHIIJIJJJJI
+ at machine1:HiMom:abcdeACXX:1:1201:1393:2143 2:Y:0:
+GATAAATGCACGCATCCCCCCCGCG
++
+C at CFFFFFGGHHHHJJJJJJJJJJI
+ at machine1:HiMom:abcdeACXX:1:1201:1414:2174 2:N:0:
+TTTTTTTTTTTTTTTTTTTTTTTTT
++
+@;@1BDADF????FFEB>B6=BBBB
+ at machine1:HiMom:abcdeACXX:1:1201:1416:2128 2:Y:0:
+TTGGTGTGGAGGCGGTGGCGGGATC
++
+@@@DDDDDHHFHHII:?GGHIIB6?
+ at machine1:HiMom:abcdeACXX:1:1201:1421:2154 2:Y:0:
+TGTGCTCTTCCGATCTTGTGCTCTT
++
+BC at DFFFFHHHHHJJJJFHIHHIJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1439:2156 2:Y:0:
+GGAGATTATTTGCCTTGAAGTAAGC
++
+-;(22<>>@>8@>8;@#########
+ at machine1:HiMom:abcdeACXX:1:1201:1452:2143 2:Y:0:
+TTTTAGTCTTAGCATTTACTTTCCC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:1201:1458:2109 2:Y:0:
+GATACGAACACACAAGAACTTTTTT
++
+CCCFFFFFHHHHHJJJJJJJJJJJI
+ at machine1:HiMom:abcdeACXX:1:1201:1472:2121 2:N:0:
+GTGTGCTCTTCCGATCTGGAGGATG
++
+=+=??A4A==A at 7A<?#########
+ at machine1:HiMom:abcdeACXX:1:1201:1483:2126 2:N:0:
+GCATGCAGCTGGGTGCTGTGATGCA
++
+@@@DDDBB<DD8F<<CGG?AA?A<F
+ at machine1:HiMom:abcdeACXX:1:1201:1486:2109 2:Y:0:
+ACGTGTGCTCTTCCCGATCTGTATA
++
+CCCFF?DDFBHHHJJIIDHJIJJJH
+ at machine1:HiMom:abcdeACXX:1:1201:1486:2146 2:N:0:
+TTTTTTTTTTTTTTTTTTTTTGGGC
++
+<<<@??@??@???????########
+ at machine1:HiMom:abcdeACXX:1:2101:1011:2102 2:Y:0:
+NNNNNTCACACATAATTTTAAAATT
++
+#####22@?@@??@@@@@??@@@@@
+ at machine1:HiMom:abcdeACXX:1:2101:1013:2146 2:Y:0:
+NNNNCGCTAGAACCAACTTATTCAT
++
+####24=?@@?@?@@?@@@@@@?@@
+ at machine1:HiMom:abcdeACXX:1:2101:1021:2209 2:Y:0:
+NNGGAAGGCTGCTAGCTGGCCAGAG
++
+##08@>??@@??@?????????>?@
+ at machine1:HiMom:abcdeACXX:1:2101:1023:2237 2:N:0:
+NNTTTGTTTGAGTTCCTTGTAGATT
++
+##0:=@?>?@???@:>?@??>?;?<
+ at machine1:HiMom:abcdeACXX:1:2101:1031:2163 2:Y:0:
+NNACATTTGTCACCACTAGCCACCA
++
+##0<@?@@@@@@@@@@?@@@@@@@?
+ at machine1:HiMom:abcdeACXX:1:2101:1036:2087 2:Y:0:
+NGTCCACTTACGAAGCAAATACTTT
++
+#4=DDFFFHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1040:2208 2:N:0:
+NCTGATAGTCACTGAAATGAATTCA
++
+#-0=>(2 at .22@@############
+ at machine1:HiMom:abcdeACXX:1:2101:1048:2238 2:Y:0:
+NGTCACATCGTTGAAGCACTGGATC
++
+#11ADDDB<CFFHCHGDBHGIIIII
+ at machine1:HiMom:abcdeACXX:1:2101:1054:2162 2:Y:0:
+NGGACAGGGAAGGGAAGGAAGGGTG
++
+#4=DDFDFHHHHHJIJIIDHHGICG
+ at machine1:HiMom:abcdeACXX:1:2101:1059:2083 2:Y:0:
+NGAATGTCTTAGAAGGATGCTTCTC
++
+#1=BDDDEHHGHHJJJJJIJJIIJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1063:2206 2:Y:0:
+NTGCTAGGATGAGGATGGATAGTAA
++
+#1=DDDFFHHHHHJHIIJHIIIHHJ
+ at machine1:HiMom:abcdeACXX:1:2101:1064:2242 2:Y:0:
+NGGAAAAAGGTTGTCAAGCGTTAAA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1072:2170 2:Y:0:
+NGGGGAGACAGAGAGGATCAGAAGT
++
+#4=BDDFDHHDFHEGFEGGIJIIIG
+ at machine1:HiMom:abcdeACXX:1:2101:1077:2139 2:Y:0:
+NATTAGTTGGCGGATGAAGCAGATA
++
+#4=DFFFFHHHHHJJJJJJJJJIJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1084:2188 2:Y:0:
+TACAAGGTCAAAATCAGCAACAAGT
++
+CCCFFFFDHHHHHJJJJJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1100:2085 2:Y:0:
+ATCTTGATCTCCTCCTTCTTGGCCT
++
+@@@DDDDDHHFHFEIIIIHHBAHBG
+ at machine1:HiMom:abcdeACXX:1:2101:1102:2221 2:Y:0:
+ATAACTGACTCTACTCAGTAGATTA
++
+CCCFFFFFHHHHHJJJJJIJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1105:2131 2:Y:0:
+CAGCAGCAGCAACAGCAGAAACATG
++
+CCCFFFFFHHHHHJJJJJIJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1112:2245 2:Y:0:
+TCGTAGTGTTGTAATTTCGTCTTCT
++
+?8?DBDDDCCFCAACGGFFCBFFAE
+ at machine1:HiMom:abcdeACXX:1:2101:1122:2136 2:Y:0:
+CTTGCCAGCCTGCAGGCCCCGCGGC
++
+???BBAABDD?DDIID)A:3<EADD
+ at machine1:HiMom:abcdeACXX:1:2101:1123:2095 2:Y:0:
+TCCGCCTCCAGCTTCAGCTTCTCCT
++
+@@@FDDFFHHHHHJHGGJIJJJEHH
+ at machine1:HiMom:abcdeACXX:1:2101:1126:2082 2:Y:0:
+TCTCTTTCCACCTTGGTCACCTTCC
++
+ at C@DDDFFHHHHHJEGGIHHIJGIH
+ at machine1:HiMom:abcdeACXX:1:2101:1133:2239 2:Y:0:
+AGCTTTTTGTTTCCTAGCTTGTCTT
++
+?@?DDFFFHHHHF4ACFHIJHHHGH
+ at machine1:HiMom:abcdeACXX:1:2101:1143:2137 2:Y:0:
+GCTCTTCAGATCTAGGGGGAACAGC
++
+@@@DD?=DCAFFFHIIDG:EFHIII
+ at machine1:HiMom:abcdeACXX:1:2101:1151:2182 2:N:0:
+TTTTTTTTTTTTTTTTTTTTTTTTA
++
+9<<?@?@;5=?##############
+ at machine1:HiMom:abcdeACXX:1:2101:1151:2236 2:N:0:
+TTTGAAGCCTCTTTATCCTTGGCAT
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1162:2139 2:Y:0:
+ATCGTTTATGGTCGGAACTACGACG
++
+BCCFFFFFHHHHHIJJJJJJJIJJI
+ at machine1:HiMom:abcdeACXX:1:2101:1163:2203 2:Y:0:
+TTGGTTCACTTATGTATTTATGAAT
++
+ at CCFDFFFHHHHHJHIIJJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1163:2222 2:Y:0:
+GAGCGATAATGGTTCTTTTCCTCAC
++
+@@@DFFFFHHHHHJJJJJJJIJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1172:2152 2:N:0:
+ATCGTTTCTGGGGACTAGTGAGGCG
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1186:2093 2:Y:0:
+AATGTTGGGAGGACAATGATGGAAA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1188:2195 2:Y:0:
+GCACATACACCAAATGTCTGAACCT
++
+CCCFFFFFHHHHHJJJHIJJJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1195:2150 2:Y:0:
+AATTGAACTTCACCACCCAGAGGAA
++
+CCCFFFFFHHHHHJJJJJJIJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1207:2084 2:N:0:
+TCACCACTCTTCTGGGCATCCCCTG
++
+@@@DDEDFHHHHHIJIHHGHGGJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1208:2231 2:N:0:
+CTTTTTTTTTTTTTTTTTTTTTTTT
++
+CCCFFFFFHHHHHJJJHFDDDDDDD
+ at machine1:HiMom:abcdeACXX:1:2101:1215:2110 2:Y:0:
+ATCTTTCCCCCATTAAGAACAGCAA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1216:2172 2:Y:0:
+GGACTTCTAGGGGATTTAGCGGGGT
++
+CCCFFFFFHHHHHJJJJJJJJJJJD
+ at machine1:HiMom:abcdeACXX:1:2101:1216:2193 2:Y:0:
+AGGCATGACACTGCATTTTAAATAC
++
+@@@DDDDDHFFHHGGDFHFHIIHGG
+ at machine1:HiMom:abcdeACXX:1:2101:1226:2088 2:Y:0:
+GCTCTTCCGATCTAGGTAATAGCTA
++
+==?BDFFFDCDDHFFFAFHDHIJGJ
+ at machine1:HiMom:abcdeACXX:1:2101:1231:2208 2:Y:0:
+AGCCAGTGTTGGTGTGTTGACTGTT
++
+@@;1ADABCF;BF<AACGCHEBHC<
+ at machine1:HiMom:abcdeACXX:1:2101:1233:2133 2:N:0:
+TTTTTTTTTTTTTTTTTTTTTTTTT
++
+CCCFFFFFGHHHHJJJFDDDDDDDD
+ at machine1:HiMom:abcdeACXX:1:2101:1240:2197 2:N:0:
+ACTGGAGATCCTTGTTACATGCCCA
++
+??+++A:DD?:ADEE@::C4:C<E:
+ at machine1:HiMom:abcdeACXX:1:2101:1245:2154 2:Y:0:
+ACCAATCAGTAGCACCACTATACAC
++
+CCCFFFFFHHHHHJJJJJJIJJJJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1249:2231 2:Y:0:
+TCTCTCGGCCTTCCACTCTAGCATA
++
+@@@FFFFFFHHGHIJJJGJIIJHIJ
+ at machine1:HiMom:abcdeACXX:1:2101:1258:2092 2:Y:0:
+TTAGACAAAACACCAAAATAAAATA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1262:2128 2:N:0:
+TCTTGTGGTAACTTTTCTGACACCT
++
+-(---9@;@?:8>?4:>?@######
+ at machine1:HiMom:abcdeACXX:1:2101:1273:2119 2:N:0:
+ATGATGGATCTTCTCTAACTTGTCA
++
+>=><AAAAA+2AA?CB4@@ABB3?A
+ at machine1:HiMom:abcdeACXX:1:2101:1285:2105 2:N:0:
+TGTCTATATCAACCAACACCTCTTC
++
+-(0(():94:9:???##########
+ at machine1:HiMom:abcdeACXX:1:2101:1312:2105 2:Y:0:
+GTTGAGAATAGGTTGAGATCGTTTC
++
+ at CCFFFDFHHFHDHIJJJJJJJIJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1325:2083 2:Y:0:
+TGTGCTCTTCCGATCTGGAGAAAAA
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:2101:1336:2109 2:Y:0:
+AGACCAGAACAGCTCCAGGTGCTCC
++
+CCCFFFFFHHHHHJJJJJJCGHIJJ
+ at machine1:HiMom:abcdeACXX:1:2101:1349:2084 2:Y:0:
+AGTCTGAATCATTGGTGTCTGAAGA
++
+<5;??=>=>>?##############
+ at machine1:HiMom:abcdeACXX:1:2101:1365:2094 2:Y:0:
+GCTCTTCCGATCTTGTGCTCTTCCG
++
+CCCFFFFDHFHHGJJIIJIJJIHII
+ at machine1:HiMom:abcdeACXX:1:2101:1370:2116 2:Y:0:
+CACCATCTGACATCATGTTTGAAAG
++
+@@@DFFFDFFHDHIGBHHII<HEDB
+ at machine1:HiMom:abcdeACXX:1:2101:1386:2105 2:Y:0:
+AGGAATTATTCTTCTGCCATAAGGT
++
+B@@DDFFFHGFHHIJJJJJGIGIJH
+ at machine1:HiMom:abcdeACXX:1:2101:1414:2098 2:Y:0:
+TTGGGGCCGGTGCCGTCGGGCCCAA
++
+CCCFFFFFHHHHGJJIJJJJJJJIJ
+ at machine1:HiMom:abcdeACXX:1:2101:1427:2081 2:Y:0:
+CCGACTTCCATGGCCACCGTCCTGC
++
+CCCFFFFFHHHHHJJJIIGFIIJJI
+ at machine1:HiMom:abcdeACXX:1:2101:1450:2134 2:Y:0:
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CC at FDFDFFDFHFGIIE1CGGHBGE
+ at machine1:HiMom:abcdeACXX:1:2101:1459:2083 2:Y:0:
+ATTTCACCAAAATAATCAGAAGGCC
++
+CCCFFFFDBHGHHIGGIJFJJGGFH
+ at machine1:HiMom:abcdeACXX:1:2101:1491:2093 2:Y:0:
+AGAGACGGGGTCTCGCTATGTTGCC
++
+BCCDFFFFHHHHHJIIJJJJIJIJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplex.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplex.1.fastq
new file mode 100644
index 0000000..11bcfd4
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplex.1.fastq
@@ -0,0 +1,720 @@
+ at HiMom:1:1101:1031:2224
+NAATANNNNNNNNNNNNTNNNNNNNNNNNN
++
+#0;@@#########################
+ at HiMom:1:1101:1039:2147
+NCCAANGNNGGNNNNATGTAANNNNNNNNN
++
+#4;@@#4##2<####43@@@@#########
+ at HiMom:1:1101:1046:2175
+NTGCCNGNGTTNCGNGGTCTTNNNNNNNNN
++
+#4;@@#########################
+ at HiMom:1:1101:1047:2122
+NCTAANGNACTNTGNGTGTGCNNNNNNNAN
++
+#0;@@#4#3@@#3@#2<@@@@#########
+ at HiMom:1:1101:1048:2197
+NCTCCNGNTCANCANGTGGAGNNNNNNNCN
++
+#0;?@#########################
+ at HiMom:1:1101:1065:2193
+GAAGTACGCCCTGCCCCTGGTTNGCGAACG
++
+?@@DAADAHHFHBEBEGGHG?#########
+ at HiMom:1:1101:1069:2159
+TCCCTTACCATCAAATCAATTGNCCGTCCA
++
+CCCFFFFFHHHHHJJJJJJJJJ#3A at BBFF
+ at HiMom:1:1101:1071:2233
+TTTGACAGTCTCTGAATGAGAANGGTATCC
++
+CCCFFFFFHHHHHJIIIJJJIJ#4ACCCFF
+ at HiMom:1:1101:1083:2193
+TTCTACCTCACCTTAGGGAGAAGACCCAAC
++
+@@@DDBDDD>F><C<4CG?EHGHIG?@;DD
+ at HiMom:1:1101:1084:2136
+NTCTCACTGTGAATTTGTGGTGGGCTGCTG
++
+#1=DDFFFHHHHHJJJJGIJIJJJJCCCFF
+ at HiMom:1:1101:1089:2172
+TTCCAGCATGCGGTTTAAGTAGGATGACCA
++
+ at CCFDFDBDFBF:<CEBHAFHHICH?@@FF
+ at HiMom:1:1101:1100:2207
+ACGACAGACGTTCTTTCTTTGCTGCATTAT
++
+CCCFFFFFHHFHHJIJJJJJHIJJHCCCFF
+ at HiMom:1:1101:1111:2148
+GTGGAGACCACCTCCGAGGCCTTGTGCCGT
++
+BBCFFFFFHHHHHJJJIJJJJJJJICCCFF
+ at HiMom:1:1101:1138:2141
+NTTACCAAGGTTTTCTGTTTAGTGAAACAA
++
+#1=DDFFFHHFHHJJJIHJIJJJJJCCCFF
+ at HiMom:1:1101:1140:2120
+NCCCCAACATTCTAATTATGCCTCACAACT
++
+#1:BDFFDHFFDFIJJJIIJIIIII@@@DD
+ at HiMom:1:1101:1143:2192
+GGAGCGAGTCTGGGTCTCAGCCCCGTCGCT
++
+CCCFFFFFHHHHHJGHIIIHJJJJICCCFF
+ at HiMom:1:1101:1150:2228
+GCTACTCAGTAGACAGTCCCACCCTAGGTC
++
+@@CADDDDFCFHHIIIIGGIIGGGI@@@DD
+ at HiMom:1:1101:1157:2135
+NGGACATTGTAATCATTTCTTACAAATTAT
++
+#1=DD?DDHHHHHGGHIIIIIIIIIC at CFF
+ at HiMom:1:1101:1162:2207
+ACCTTGAGGAGAACATAAGAGCAAAACAAA
++
+##############################
+ at HiMom:1:1101:1165:2239
+GGCGGAGGCAGCATTTCAGCTGTGAGCCTA
++
+CCCFFDFFHHHHHIJJIGHHHJHHFB@@DF
+ at HiMom:1:1101:1175:2197
+CCCCTGAGGACACCATCCCACTCCACCAAC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJCCCFF
+ at HiMom:1:1101:1188:2237
+TCCCCCTCCCTTTTGCGCACACACCGTAAC
++
+@?@DDADDHDHBDH<EFHIIHG?HF@@?DF
+ at HiMom:1:1101:1197:2200
+GGGCGCCCCGTGAGGACCCAGTCCTAACGC
++
+ at C@FFADDFFCFCEHIIJIJJIEFC at CCFD
+ at HiMom:1:1101:1206:2126
+NATTCTGCCATATTGGTCCGACAGTAACAA
++
+#1=DDFFFHHHHHJJJJJJJJJIJJCCCFF
+ at HiMom:1:1101:1212:2230
+TTTCTATTAGCTCTTAGTAAGATTACCAGC
++
+CCCFFFFFHHHHHJJJIJJJJJJJJCCCFF
+ at HiMom:1:1101:1218:2200
+GCACCGGAAGAGCACACAGATCGGAGACCG
++
+CCCFFFFDFHGHHJJIJIJJJJJJI at CCFF
+ at HiMom:1:1101:1219:2164
+TCAAGCAGGAGCAGCTAAGTCCTAATTGTC
++
+CCCFFFFFHHHHHJJJJJJHIJJJJCCCFF
+ at HiMom:1:1101:1221:2143
+TTTGGTGGAAATTTTTTGTTATGATGCCGT
++
+CCCFFBDBHFD?FBFHIIGGIC at EF@@CDD
+ at HiMom:1:1101:1236:2121
+NGGTGCTTCATATCCCTCTAGAGGAACAGG
++
+#1=BDDFFHHHHHJJJJJJJJJJJJCCCFF
+ at HiMom:1:1101:1242:2170
+ATGGCAGGGCAGAGTTCTGATGAGTTGCAA
++
+CCCFFFFFHHGGGIFHEIIGIIII?@@CFF
+ at HiMom:1:1101:1257:2223
+TGTATTCGAGAGATCAAAGAGAGAGGACCG
++
+@@=DDBDD?FFHHEIDBDFCEDBAF;@@DD
+ at HiMom:1:1101:1259:2152
+CACCTATAATCCCAGCTACTCCAGAACTAA
++
+CCCFFFFFHHHHHJJJJJJIJJJIJCCCFF
+ at HiMom:1:1101:1261:2127
+NTGAAATCTGGATAGGCTGGAGTTAACTAA
++
+#0-@@@########################
+ at HiMom:1:1101:1263:2236
+CTTTGAAGACATTGTGAGATCTGTAAGGTA
++
+<==A<42 at C+A4A?,2A@=4 at 7A??#####
+ at HiMom:1:1101:1267:2209
+GAGACGGAGGCCAACGGGGGCCTGGTATCA
++
+@@CFFFFD8FDHFHIGIBG?@BCDG?@@D;
+ at HiMom:1:1101:1269:2170
+ACAGTGTGGGAGGCAGACGAAGAGAATTAT
++
+@@@DDDDDFA:C at EGA?FD<FFHII@@@DD
+ at HiMom:1:1101:1290:2225
+CTTGGGCGCATGGTGAGGGAGGGAGGCCTA
++
+@@@FFDDFHDFH??CBEBHHIGDCD?<@DF
+ at HiMom:1:1101:1291:2150
+CGTGGGGAACCTGGCGCTAAACCATCGCTA
++
+ at BBFFFFFHHHHHJJJJIJJJJJIJ@@@FF
+ at HiMom:1:1101:1302:2244
+GGAAAAGACGGAAAGGTTCTATCTCGACCT
++
+ at C@DFFFDFHHHHJIJHHIJJJJJICCCFF
+ at HiMom:1:1101:1308:2153
+TTTTGGAAGAGACCTCAATTACTGTAACGC
++
+???DDDDD?:22AE:A2<3,AF?3A:?@B?
+ at HiMom:1:1101:1309:2210
+ACACCAACCACCCAACTATCTATAAATTCC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ?@@AD
+ at HiMom:1:1101:1314:2233
+GTTTATTGGGGCATTCCTTATCCCACGCTA
++
+@??DDDDBDHF>FCHGGGBFAAED9@<@?B
+ at HiMom:1:1101:1316:2126
+NAAAAAAAAAAAAAAAAAAAAAAAACAATA
++
+#1BDFFFFHHHHHJJJJFDDDDDDD1>>7A
+ at HiMom:1:1101:1327:2200
+AGGGGGATCCGCCGGGGGACCACAAGCCGT
++
+##############################
+ at HiMom:1:1101:1328:2225
+GAAATGCATCTGTCTTAGAAACTGGCAACT
++
+??@=BDDDFDD<<,<2:C<F:FFEA??;=A
+ at HiMom:1:1101:1338:2175
+CCCACCTTCCGGCGGCCGAAGACACGAAGG
++
+CCCFFFFFHHHHHJJJJJJJJJJJJCCCFF
+ at HiMom:1:1101:1347:2149
+GAGCAGATCGGAAGAGCACAGATCGGACCA
++
+@@@FFDDDHHHHHIJJBGGHJIHEGCC at DF
+ at HiMom:1:1101:1353:2226
+TTGCTTGTCTGTAAAGTATTTTATTTATCT
++
+ at C@DDFFDHHFHFHHIBGG>IHHII at B@FF
+ at HiMom:1:1101:1363:2138
+NGTCTGGCCTGCACAGACATCCTACCTAAC
++
+#1=DDFFFHHHHHJJJIJJIJJJIJCCCFF
+ at HiMom:1:1101:1399:2128
+NTGCCCTTCGTCCTGGGAAACGGGGCAATA
++
+#1BDFFFFHHHHHJJJJJJJJJJJJCCCFF
+ at HiMom:1:1101:1403:2194
+CTAAACAGAGAGAAGGTTTCTCTTTCTGTA
++
+CCCFFFFFHHHHHJJJFHIJJJJJJCCCFF
+ at HiMom:1:1101:1406:2222
+CTCCCCCCGGGCTGAACCAGGGTACAGCAT
++
+CCCFFDDDDHDFHIIIIIIIII9DGC@@DB
+ at HiMom:1:1101:1419:2119
+NATGACTATGGTAACTGAAAGAAAATGTAA
++
+#1:A1BDADBFFDFIIIEEHECACF@@@DF
+ at HiMom:1:1101:1420:2213
+TACCTGGTTGATCCTGCCAGTAGCACAGCG
++
+@@CFFFFDDHHGHJGGHIJJIHGBH at C@FF
+ at HiMom:1:1101:1435:2194
+GAGAAAGAACATGACTACAGAGATGTATCT
++
+CCCFFFFFHHHHHJJJJJJJJJHJJCCCFF
+ at HiMom:1:1101:1441:2148
+ACTTTCACCGCTACACGACCGGGGGCGCTA
++
+CCCFFFFFHGFFHIIFIHJIGGII>@@BFF
+ at HiMom:1:1101:1452:2132
+NCGTCCTGGAAAACGGGGCGCGGCTAACGC
++
+#1=BDBDDFHHHHF at FHDHIGIIII@CCFF
+ at HiMom:1:1101:1460:2176
+AGTCCAGGCTGAGCCCAGGGAAGAAGATAT
++
+CCCFFFFFHHHHGJIJJIJJHIJJICCCFF
+ at HiMom:1:1101:1479:2221
+TGTAAAGTATGCTGGCTCAGTGTATTCGCT
++
+BBBFDFFEHHHHHJJJJJJJIJHJJ at BCFF
+ at HiMom:1:1101:1491:2120
+NGGCAGGTGCCCCCACTTGACTCTCAGGTC
++
+#1?DFFFFGHHHHJJJJJJJJJJJJBCCDF
+ at HiMom:1:1201:1018:2133
+NAAAACTTGAGGATGCTATGCAAGCATTCC
++
+#1:B:ADDDDDDDEEAEBF9FFEBF8??=B
+ at HiMom:1:1201:1018:2217
+NTTTCTCTGGGCGCAAAGATGTTCAATTAT
++
+#07;8=8<<99(:=@@/@7>>6=?>;<;:B
+ at HiMom:1:1201:1028:2202
+NTCCTGGGAAACGGGGCGCGGCTGGGAAGG
++
+#4BDDDFFHHHHHIJIIJJJJJJIJCCCFF
+ at HiMom:1:1201:1042:2174
+NGTTGGTGTCTTCATTTTATGTATATCTGC
++
+#1=DDFDFHHHHHJIJJJHIJHIJJCCCFF
+ at HiMom:1:1201:1043:2246
+NTTCTCGGCTGTCATGTGCAACATTCGCTA
++
+#1=DDBDFHHHDFFBHGHGHIIJEH@<?DD
+ at HiMom:1:1201:1045:2105
+NTAAAGAGAAATCAAGAATACTATTCTGTA
++
+#-4@?(@)@@####################
+ at HiMom:1:1201:1054:2151
+NTAGTGCTGGGCACTAAGTAATACCCAATA
++
+#4=DDDFFHHHHHJJJJJHIJJJJJCCCFF
+ at HiMom:1:1201:1064:2239
+CATGCAGCGCAAGTAGGTCTACAAGTAAGC
++
+@@;DFAFFHHHHAHEGHFDGGFABG@@@FF
+ at HiMom:1:1201:1073:2225
+GGGGCTGAGACCTTTGCTGATGGTGATTCC
++
+@@@FFFFFHHHGHJJJJJIIIGICHB@@BD
+ at HiMom:1:1201:1083:2121
+NAGAACTGGCGCTGCGGGATGAACCCTATG
++
+#1=BDFFFHHHHHJJJJJHIJIJJJCCCFF
+ at HiMom:1:1201:1084:2204
+GGCCCGTGGACGCCGCCGAAGAAGCTATCT
++
+CCCFFFFFHHHHHJJJJJIJJJJJJCCCFF
+ at HiMom:1:1201:1095:2146
+GCTGAGTCATGTAGTAAGCCTGTGCGACCA
++
+BB at FDDDFHHHHHJJJJJJJJJJJJCCCFF
+ at HiMom:1:1201:1103:2184
+GTAAGAACTACCCTGGGTCCCCGTGTTGTC
++
+@@BFFFFFHHHHHJJJJGIJJJJHI at CCFF
+ at HiMom:1:1201:1107:2109
+NGGGAACCTGGCGCTAAACCATTCGTTGTC
++
+#1=DFFFFHHHHHJJJJJJJJJIJJB at CFF
+ at HiMom:1:1201:1118:2198
+CAAGTGTACAGGATTAGACTGGGTTATTAT
++
+BCCFDEBDHHHHHIJJJGIIIJJGH@@@DD
+ at HiMom:1:1201:1122:2227
+AGAAGACGAGGCTGAGAGTGACATCCGCCT
++
+@@@FFFFFHHHDHJGHGHCHHJJIJ@@@DD
+ at HiMom:1:1201:1123:2161
+CACTAACTCCTGACCTCAAATAATCGACCA
++
+?7?=DD?DD+CDBE>E at EEF@+<CF?;@DF
+ at HiMom:1:1201:1127:2112
+NGTCAAGGATGTTCGTCGTGGCAACCAACT
++
+#1=BDDDDDDDDDID<AE?@<CEEE=??BA
+ at HiMom:1:1201:1134:2144
+TGCCAGGAAGTGTTTTTTCTGGGTCCGCTA
++
+ at CCFFEFFHHFFFGIJJJJJJJJGHCCCFF
+ at HiMom:1:1201:1138:2227
+GCTGACACAATCTCTTCCGCCTGGTCCAAC
++
+##############################
+ at HiMom:1:1201:1140:2125
+NTTTCAGTTCAGAGAACTGCAGAATTATCC
++
+#1=DBDFDHHHHGJIJJJJJIIIJICCCFF
+ at HiMom:1:1201:1142:2242
+TGTTGATAGTCCTTCTTATCTTAGTTATCT
++
+???DB?==CC2<AC:CC<CFEF<FF??<D?
+ at HiMom:1:1201:1150:2161
+AAGTCACCTAATATCTTTTTTTTTTAACGC
++
+@@<??;?D?CFD,A4CDDHFBIIID@@@FD
+ at HiMom:1:1201:1159:2179
+GTTAGCACAGATATTGGATGAGTGAAAAAA
++
+##############################
+ at HiMom:1:1201:1160:2109
+NAGAAGCCTTTGCACCCTGGGAGGACGCCT
++
+#1=DDDFFHHHHHJJJJJJJJIIJJC at BFF
+ at HiMom:1:1201:1180:2119
+NTGAAAGATTTAGAGAGCTTACAAAGACCG
++
+#1=DDDDDHHHGHJJIIJJJJIJJICCCFF
+ at HiMom:1:1201:1185:2143
+ATCTGCCTGGTTCGGCCCGCCTGCCCTATG
++
+CCCFFFFFHHHHHJJJJJJJJJJJJCCCFF
+ at HiMom:1:1201:1187:2100
+NGCGGTAATTCCAGCTCCAATAGCGTATCT
++
+#1:BB2 at DHHFHHIIIIHHIIGHGGCCCFF
+ at HiMom:1:1201:1190:2194
+AACCTGGCGCTAAACCATTCGTAGAAGGTC
++
+CCCFFFFFHHHHHJJJJJJJJIJJJCCCFF
+ at HiMom:1:1201:1204:2228
+CCGATACGCTGAGTGTGGTTTGCGGCCAGC
++
+CCCFFFFFHHHFHEGGHIHIJJJJJCCCFF
+ at HiMom:1:1201:1208:2132
+NCCTCAATGAGCGGCACTATGGGGGTGTAA
++
+#1=DDFFFHHHHGJJIJJGHIJGIJCC at FF
+ at HiMom:1:1201:1219:2115
+NTATAGTGGAGGCCGGAGCAGGAACCCATG
++
+#1:DABADHHHFHIIIGGHGIIIII??<DD
+ at HiMom:1:1201:1236:2187
+TTTAAATGGGTAAGAAGCCCGGCTCTATCC
++
+ at BCDDFEFHHDHHJJJJJIJJIJJJ@@BFF
+ at HiMom:1:1201:1242:2207
+ATGGCAAAGTGGTGTCTGAGACCAAATTCC
++
+BCCFFFFFGHHHHHIIIJFHIJJJJ?BBDD
+ at HiMom:1:1201:1252:2141
+NTTCCCCCCATGTAATTATTGTGAATTGTC
++
+#1=DDFFFHHHHHJJJJJJJJIJJJCCCFF
+ at HiMom:1:1201:1260:2165
+GGACACGGACAGGATTGACAGATTGCCAAC
++
+BCBFFFFFHHHHHHIIJHIIIFHIJC at CFF
+ at HiMom:1:1201:1280:2179
+TTCAAGGAATCGTCCTGCCTCAGCCGCCTA
++
+BCCFFFFFHHHHHJJJJJJJJJJJJBCCFF
+ at HiMom:1:1201:1281:2133
+NGGAAATCCAGAAAACATAGAAGATCCAAC
++
+#1=DDFFFHHHHHIJJJJJJJJIJJC at CFF
+ at HiMom:1:1201:1285:2100
+NAATGACATGTTTAAAGATGGACTCTGCTG
++
+#1:BDDFFHHFHHGIJIJIIIIGII@@@FF
+ at HiMom:1:1201:1291:2158
+AGAAGGGGAAAGCCTTCATCTTGGCAGCAT
++
+BCBFFFFFHHHHHJJJJJIIFIJIJ at CCFF
+ at HiMom:1:1201:1300:2137
+NTGTAATCCCAGCTCTCAGGGAGGCGCCTA
++
+#1=ADDDDDDDBBA?@AE?E at FE8;8?84B
+ at HiMom:1:1201:1312:2112
+NTCCCAGCGAACCCGCGTGCAACCTTCGCT
++
+#1=DFFFFHHHHHJJJJJJJJJJJJCCCFF
+ at HiMom:1:1201:1331:2162
+ACGCTCGGCTAATTTTTGTATTTTTCCAAC
++
+ at CCFFFDFHHHHHIJJJJHIJJJJJCCCFF
+ at HiMom:1:1201:1341:2116
+NAGAAGCCCCAGGAGGAAGACAGTCACAGG
++
+#1=DDFFFHHHHHHHJIIJJJJJGICCCFF
+ at HiMom:1:1201:1344:2147
+TATCCTCCCTACTATGCCTAGAAGGTGTAA
++
+=?@DADEFHBHDFG>EFGDHGFGHD=?1AA
+ at HiMom:1:1201:1345:2181
+GGATAATCCTATTTATTACCTCAGACAATA
++
+BBBDDFFFHHHHHJJJJJJJJJIJJCCCFF
+ at HiMom:1:1201:1364:2113
+NCACTCATTTTCTTATGTGGGATATCAGCG
++
+#1=DDFDFHHHHHIJJIFHIIHHHIC at CFF
+ at HiMom:1:1201:1392:2109
+NCTGAAGAGGCCAAAGCGCCCTCCATATCT
++
+#1=DDFFFHHHHHJJJJJJJJJJJICCCDF
+ at HiMom:1:1201:1392:2184
+TTTCAGATTGGTCATTGTTAGTGTACAATA
++
+??@BDDDEHBHADHHIIEHDHFHFF at CCFF
+ at HiMom:1:1201:1393:2143
+TGGTTGATCCTGCCAGTAGCATATGCTAAC
++
+@@@ADADDFHFFDBHE?G at HIIIEE@@CFD
+ at HiMom:1:1201:1414:2174
+GCCAAAAAAAAGAACCAGCCCAAGGAGAAA
++
+##############################
+ at HiMom:1:1201:1416:2128
+NACAGGCGTGGAGGAGGCGGCGGCCTCGCT
++
+#4=DDDFFHHHHHJIGJHFHHFFEDCCCFF
+ at HiMom:1:1201:1421:2154
+TGTGTGTGTGGGTGTGTGTATATATTGTAA
++
+?@?DDFFFFFHH at GEFCCCHGIGJI@@@FF
+ at HiMom:1:1201:1439:2156
+AGCCGCGAGGTGCTGGCGGACTTCCGACCA
++
+:;1BDDDAA88A<?<E1C:D##########
+ at HiMom:1:1201:1452:2143
+TATCCCCTCTAAGACGGACCTGGGTCAACT
++
+CCCFFFFFHHHHHJJIIIJJJJJJGBC at DD
+ at HiMom:1:1201:1458:2109
+NGAGACCATAGAGCGGATGCTTTCAACTGT
++
+#1=DDDFFHHGHGIJJIGIIJJJJJCCCFF
+ at HiMom:1:1201:1472:2121
+NTAAAGTGTGAACAAGGAAGGTCATCTATG
++
+#07>@<9=@#####################
+ at HiMom:1:1201:1483:2126
+NTGATAAGGTGTTGCTATGTTACCCCTGTA
++
+#1:D?DDDDA??2:<CC4:AEDF>?@C<DD
+ at HiMom:1:1201:1486:2109
+NCACCTCCTAGCCCCTCACTTCTGTGTCCA
++
+#1=B;BDDHHHGFIIIIIIIIIGGGCCCFF
+ at HiMom:1:1201:1486:2146
+GTTCTCTGTCCCCAGGTCCTGTCTCCAACT
++
+===A7<7222<<=C=?+<7>@?ACB?@@1:
+ at HiMom:1:2101:1011:2102
+NAAACAAAACTGTAGAACTGTGTATCTGTA
++
+#1=DDFFFHHHHHJJIJJJIHHHJJC at CFF
+ at HiMom:1:2101:1013:2146
+NACACTGCTGCAGATGACAAGCAGCCTATG
++
+#4BDFFFFHHHHHJJJJJJJJJJJJCCCFF
+ at HiMom:1:2101:1021:2209
+NGGCCCCACCCTCCTCCAGCACGTCACTAA
++
+#1=DDFFFHHHHHJJJJJJHIIHFH at CCDF
+ at HiMom:1:2101:1023:2237
+NTAAACAGCTTCTGCACAGCCAAAGGCCTA
++
+#00@@?>=39>9;<412@?###########
+ at HiMom:1:2101:1031:2163
+NTTTCCATGGCCGTCACCTTTGGGTGATAT
++
+#4=DDFFFHHHHHJJJJJJJJJJJIB at BFF
+ at HiMom:1:2101:1036:2087
+NTGTAGTTTCTTTAGGCAAATTTGTGACCG
++
+#4=BDDDFHHHHHJJJJJJIIJJJIB at CFF
+ at HiMom:1:2101:1040:2208
+NATGCCCACCTCCCTCCTACGCACCACGAA
++
+##############################
+ at HiMom:1:2101:1048:2238
+NCTGCCGTGTCCTGACTTCTGGAATACAGT
++
+#1:B?ADDACF<DCG;EG<FHH at CE?@7DD
+ at HiMom:1:2101:1054:2162
+NCCAGGTGTCTTCCCGGGCCCTGCCAGGTA
++
+#1=DDFBDFHHHHJJJJJIJJJJJJB at BDD
+ at HiMom:1:2101:1059:2083
+NAAGAGGGGTCAAGAGTTAAACTTATACCG
++
+#1=DDFFFHFHHGIGHGHJJJJJJI1:?D#
+ at HiMom:1:2101:1063:2206
+TCCTATTCGCCTACACAATTCTCCGACAGG
++
+CCCFFFFFHHHHHJJJJJJJHJJJJCCCFF
+ at HiMom:1:2101:1064:2242
+ATGAACAAAGGAAGAATTATGCACGTCGCT
++
+?;?D;DDDF?;:+<<CFFCHE433A;@<:A
+ at HiMom:1:2101:1072:2170
+ATCACCGCACTCATTTCCCGCTTCCCAGCG
++
+CCCFFFFFHHHACEEGHIIBHIIIIB@@DF
+ at HiMom:1:2101:1077:2139
+CACAGGCTTCCACGGACTTAACGTCAACAA
++
+CCCFFFFFHHHHHJJJJJJJJJJJJCCCFF
+ at HiMom:1:2101:1084:2188
+TTGCTGCATGGGTTAATTGAGAATAGAAGG
++
+CCCFFFFFHHHHFHHIIJJIJJJJJ at B@FF
+ at HiMom:1:2101:1100:2085
+NCACATGGATGAGGAGAATGAGGATCCAGC
++
+#1=DDFFFFHHHHJHIGIHHHIJEHCCCFF
+ at HiMom:1:2101:1102:2221
+TTTCATCTTATTTCATTGGTTTATACTGCG
++
+CCCFFFFFHHHHHJIJJJJIJJJJJCCCFF
+ at HiMom:1:2101:1105:2131
+TTGGAACACAGCGGGAATCACAGCAACTGT
++
+CCCFFFFFHHHHHJIJJJJJJJJJJCCCFF
+ at HiMom:1:2101:1112:2245
+TGCCATCTGCTCTGGGAAGCACCAGAACAA
++
+1:=DDDDDFBC:DEFIFFFIEF at BE@@?BB
+ at HiMom:1:2101:1122:2136
+GTAGGCGCTCAGCAAATACTTGTCGGCCGT
++
+@@@DDDD8?<CACEHHBBHDAAFH@?@<DD
+ at HiMom:1:2101:1123:2095
+NTGGACAACATGTTCGAGAGCTACACAGCG
++
+#1=BBDDDFFFFDGFGIG?F;HHFI@?@DD
+ at HiMom:1:2101:1126:2082
+NGTTTTAGGGGTGCGCAGGAGTCAACTGCG
++
+#11=A=DD?DF at D@CCGHIEFH at BG@@@FF
+ at HiMom:1:2101:1133:2239
+AGACAGAAGTACGGGAAGGCGAAGATATCC
++
+@@@FFFFEHFHHHJJCGDHIIECD@@@@BD
+ at HiMom:1:2101:1143:2137
+ATGCAGCAGCTGCCACGGAGCACCATCCGT
++
+CC at FFDFDFHFHHGIDHEHIGJJJJ#####
+ at HiMom:1:2101:1151:2182
+TTGTTTTGGCTTATAATGACAAGAAGAAAA
++
+;;8-2).2())(<6=@8;?4??>>?#####
+ at HiMom:1:2101:1151:2236
+TTAAAGAGGTTCAGGGATGCAGAGTTAGCG
++
+##############################
+ at HiMom:1:2101:1162:2139
+AGAGGTGAAATTCTTGGACCGGCGCTGCTG
++
+@@@DDDDDHFHHHDB:EFHHCAG?DCCCFF
+ at HiMom:1:2101:1163:2203
+TCTCCATGTGAAACAAGCAAAAAGAAGGTA
++
+CCCFFFFFHHHHGJJJIJJJJJJJJCCCFF
+ at HiMom:1:2101:1163:2222
+GAGCAGGCAAGGAGGACTTCTTGTTTGCAA
++
+CCCFFFFFGHHHHJJHHIJJJJJIJCCCFF
+ at HiMom:1:2101:1172:2152
+AACACGGACAAAGGAGTCTAACACGCAATA
++
+<<<??8@@######################
+ at HiMom:1:2101:1186:2093
+NCGACCATAAACGATGCCGACCGGCCCAAC
++
+#4=DFFFFHHHHHJJJJJJJJJJJJCCCFF
+ at HiMom:1:2101:1188:2195
+TTAGACCGTCGTGAGACAGGTTAGTAGGTC
++
+ at CCFFFFFHHHHHJJJJJIIEHIJHBCCDF
+ at HiMom:1:2101:1195:2150
+CCGAGAGAGTGAGAGCGCTCCTGGGTGCTG
++
+CCCFFFFFHFHHHJJJJIJJJJIJJCCCFF
+ at HiMom:1:2101:1207:2084
+NTAGATGACCAAAACTTGCAGGGCAGACCA
++
+#1:A<?@A+7A=?CBCCBCCBAAAA@@CDF
+ at HiMom:1:2101:1208:2231
+TCACTAAACATCCAAACATCACTTTGTAAC
++
+##############################
+ at HiMom:1:2101:1215:2110
+NAATATAATTTGGAGACCCTTTGTTAAAAG
++
+#1=DDDDDEDDDDIDDBB3ABAB#######
+ at HiMom:1:2101:1216:2172
+TTTCTTCGCAGGATTTTTCTGAGCCCAGCG
++
+CCCFFFFFHHHHHJJJJJJJJJJJJC at CFF
+ at HiMom:1:2101:1216:2193
+TTTTCTTGGCCTCTGTTTTTTTTTTACAGT
++
+BCCFDFFFHHFFHJIGIJJJJJJJJCCCFF
+ at HiMom:1:2101:1226:2088
+NGATCGGAAGAGCACACGTTTGACTGATAT
++
+#4=DAA=DDFHFHIIBFGHHIG>EG@@@:D
+ at HiMom:1:2101:1231:2208
+ACGCCGCAAGTCAGAGCCCCCCAGACTATG
++
+@@@DDDFFFFB:DBBEBEFDHBDDB@<@?D
+ at HiMom:1:2101:1233:2133
+GAGAGAAGCACTCTTGAGCGGGATACTATG
++
+0;(@((@)2@####################
+ at HiMom:1:2101:1240:2197
+ATAAAACATAGCAATATTTTCCTATAACGC
++
+##############################
+ at HiMom:1:2101:1245:2154
+TCGTTAAGTATATTCTTAGGTATTTCTGTA
++
+CCCFFDFFFHFHHIIJJJJJFJJJI at CCFF
+ at HiMom:1:2101:1249:2231
+GTTATTGATAGGATACTGTACAAACAGGTA
++
+ at BCFFFFDHHHHFIJJJJJJJJJJJ@@CBD
+ at HiMom:1:2101:1258:2092
+NCACACACACACTCATTCACAGCTTTAAGC
++
+#1=DDDFFHHHFHJJIJGGGIIGIJ@@CDD
+ at HiMom:1:2101:1262:2128
+AGCAGAAGGGCAAAAGCTGGCTTGAACTAA
++
+9;<@:@########################
+ at HiMom:1:2101:1273:2119
+NAGATAAGAGTCCACACAGTTGAGTCTAAC
++
+#11AAAAA<A?4=C=7?733<ACA######
+ at HiMom:1:2101:1285:2105
+NGCGGGGAGCCGGGCGTGGAATGCGTATCT
++
+##############################
+ at HiMom:1:2101:1312:2105
+NTTCCCTCAGGATAGCTGGCGCTCTGACCA
++
+#1=DDFFFGHGHHJJJJJJJJJJJJCCCFF
+ at HiMom:1:2101:1325:2083
+NCAGAAGAAAGGGCCTTGTCGGAGGACAGG
++
+#1=DDDDDHHFHDGI at EEHG:?FA8@@@BD
+ at HiMom:1:2101:1336:2109
+NACTATCAGGATCGTGGCTATTTTGAACGC
++
+#1BDDFFFHHHHHJIJJJJJJJJJJCCCFF
+ at HiMom:1:2101:1349:2084
+NCAAGTAGCAGTGTCACGCCTTAGCACTGT
++
+#1=DDBDDADFDDBEH at HC=CEGG@#####
+ at HiMom:1:2101:1365:2094
+NAAGGTGAAGGCCGGCGCGCTCGCCACTGT
++
+#1=BDDDFFHHHHJGGGIGFIHIIJ#####
+ at HiMom:1:2101:1370:2116
+NTGGTGGTCCATAGAGATTTGAAACAGCAT
++
+#1:4BD7DACF?FCA:4+<ACHIIH?:8A?
+ at HiMom:1:2101:1386:2105
+NTACTAAAGAAAAAGTTGAAGAACTCTGTA
++
+#1=DDDFFHHHHHJJGHIJJJJIJJCCCFF
+ at HiMom:1:2101:1414:2098
+NAGGACATCGATAAAGGCGAGGTGTCTAAC
++
+#1=DDFFFHHHHHJJJJJJJJJHHGCCCFF
+ at HiMom:1:2101:1427:2081
+NCGAGTGCCTAGTGGGCCACTTTTGAACGC
++
+#4=DDBDFHHHHFHIJJJJIJJJJICCCFF
+ at HiMom:1:2101:1450:2134
+AGCACGCTGCCGCGGGACCTGCCCAACCAG
++
+?@@AD at DDHFH?DGIIIIG at FGFBF@C at DD
+ at HiMom:1:2101:1459:2083
+NCACACGCCACACGGAGCACACTTTGCCGT
++
+#4=DDFFFHHHHHJJJJJJJJIIJJ@@CFD
+ at HiMom:1:2101:1491:2093
+NCTATGCCGATCGGGTGTCCGCACTCAATA
++
+#1=DDDDDHHFHHIIEHHHBGHGII@@@FD
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplex.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplex.barcode_1.fastq
new file mode 100644
index 0000000..15796e7
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplex.barcode_1.fastq
@@ -0,0 +1,720 @@
+ at HiMom:1:1101:1031:2224
+NNNNNNNN
++
+########
+ at HiMom:1:1101:1039:2147
+NNNNNNNN
++
+########
+ at HiMom:1:1101:1046:2175
+NNNNNGGA
++
+########
+ at HiMom:1:1101:1047:2122
+NNNNNTCA
++
+########
+ at HiMom:1:1101:1048:2197
+NNNNNGTG
++
+########
+ at HiMom:1:1101:1065:2193
+ATNNCTTG
++
+########
+ at HiMom:1:1101:1069:2159
+CAGGACGT
++
+FFF<<<@?
+ at HiMom:1:1101:1071:2233
+AGGGTTTG
++
+FFF<<<@@
+ at HiMom:1:1101:1083:2193
+ATTAGGCT
++
+?BD#####
+ at HiMom:1:1101:1084:2136
+CTGTTTCT
++
+FFF<<<@@
+ at HiMom:1:1101:1089:2172
+GGATCCGG
++
+;=B:<<??
+ at HiMom:1:1101:1100:2207
+CAAAGGCT
++
+FFF#####
+ at HiMom:1:1101:1111:2148
+CGAGCGAA
++
+FFF#####
+ at HiMom:1:1101:1138:2141
+TGGTCCGA
++
+FFFCCCFF
+ at HiMom:1:1101:1140:2120
+CTCTTTTT
++
+FDF@@@DD
+ at HiMom:1:1101:1143:2192
+AGACGACA
++
+FFFCCCFF
+ at HiMom:1:1101:1150:2228
+GCAATGGG
++
+FFF8?=DD
+ at HiMom:1:1101:1157:2135
+CAATTTAA
++
+FFFCCCFF
+ at HiMom:1:1101:1162:2207
+ATTTAAAA
++
+########
+ at HiMom:1:1101:1165:2239
+GCCATGGA
++
+FFF#####
+ at HiMom:1:1101:1175:2197
+ATTAAGAG
++
+FFFBC at FF
+ at HiMom:1:1101:1188:2237
+ATCGCTTC
++
+FDFCCCFF
+ at HiMom:1:1101:1197:2200
+ATTATATT
++
+FFF@@@FF
+ at HiMom:1:1101:1206:2126
+TGGATCTG
++
+FFFCCCFF
+ at HiMom:1:1101:1212:2230
+ACCTTTTA
++
+FFFCCCFF
+ at HiMom:1:1101:1218:2200
+TTGGCTCT
++
+DDF#####
+ at HiMom:1:1101:1219:2164
+TATATCTT
++
+FFFCCCFF
+ at HiMom:1:1101:1221:2143
+CGACAATT
++
+DDF@@@FF
+ at HiMom:1:1101:1236:2121
+TATTTGCG
++
+DDFCCCFF
+ at HiMom:1:1101:1242:2170
+GTAGGAAG
++
+F?D@@@DF
+ at HiMom:1:1101:1257:2223
+TTGTGCTC
++
+=DD:?@DD
+ at HiMom:1:1101:1259:2152
+GACATTTT
++
+FFFCCCFF
+ at HiMom:1:1101:1261:2127
+GACTTTTT
++
+7A7CCCFF
+ at HiMom:1:1101:1263:2236
+AGGAGTTC
++
+########
+ at HiMom:1:1101:1267:2209
+GCCGGCAG
++
+ADD=;?DD
+ at HiMom:1:1101:1269:2170
+CAATTCCA
++
+DF?@@<AD
+ at HiMom:1:1101:1290:2225
+GCCTCAGT
++
+BBDC@@FB
+ at HiMom:1:1101:1291:2150
+TGTACAAA
++
+FFFCCCFF
+ at HiMom:1:1101:1302:2244
+AACTGAAT
++
+FFFCCCFF
+ at HiMom:1:1101:1308:2153
+ATTTCTGT
++
+ at DD1?1=4
+ at HiMom:1:1101:1309:2210
+TCTAGTGG
++
+EEF@@?DF
+ at HiMom:1:1101:1314:2233
+TGTAGGAA
++
+@;A@@<DD
+ at HiMom:1:1101:1316:2126
+GACTCTTT
++
+7+2CCCFF
+ at HiMom:1:1101:1327:2200
+CGAGTCAT
++
+FFD at B@FF
+ at HiMom:1:1101:1328:2225
+CTCAGGAA
++
+:B######
+ at HiMom:1:1101:1338:2175
+AAGGCTTG
++
+FFFCCCFF
+ at HiMom:1:1101:1347:2149
+GGAGCTCT
++
+FFDCCCFF
+ at HiMom:1:1101:1353:2226
+GCCGTGCT
++
+EFFBBBFF
+ at HiMom:1:1101:1363:2138
+TCGGTTCT
++
+FFFC@@FF
+ at HiMom:1:1101:1399:2128
+GTCACAAA
++
+FFFCCCFF
+ at HiMom:1:1101:1403:2194
+ATCACATG
++
+FFFCCCFF
+ at HiMom:1:1101:1406:2222
+GGAGGCTG
++
+FEF;?@DD
+ at HiMom:1:1101:1419:2119
+TCAACTTT
++
+DFD#####
+ at HiMom:1:1101:1420:2213
+GTATTCAC
++
+FDF at CCFF
+ at HiMom:1:1101:1435:2194
+GCCTTTTG
++
+FFFCCCFF
+ at HiMom:1:1101:1441:2148
+TGTTTTTG
++
+DDDCCCFF
+ at HiMom:1:1101:1452:2132
+ATTACAAA
++
+FFFCCCFF
+ at HiMom:1:1101:1460:2176
+CCAAGGAA
++
+FFF#####
+ at HiMom:1:1101:1479:2221
+AGAGGGGA
++
+FFF at CCFF
+ at HiMom:1:1101:1491:2120
+GCAGGCCA
++
+FFFCCCFF
+ at HiMom:1:1201:1018:2133
+TCTNNNNN
++
+BBA#####
+ at HiMom:1:1201:1018:2217
+CAANNNNN
++
+BDD#####
+ at HiMom:1:1201:1028:2202
+AAGNNAAA
++
+DFF##42@
+ at HiMom:1:1201:1042:2174
+AAGNTCAG
++
+FFF#0;@@
+ at HiMom:1:1201:1043:2246
+TGTNGCAT
++
+:B=#0;@@
+ at HiMom:1:1201:1045:2105
+ATCNTTTT
++
+A,2#0;@@
+ at HiMom:1:1201:1054:2151
+GTCGTCAG
++
+FDFCBCFF
+ at HiMom:1:1201:1064:2239
+ACAGGGAT
++
+ADB8?@:D
+ at HiMom:1:1201:1073:2225
+TCTCGTGT
++
+EFF at BBDF
+ at HiMom:1:1201:1083:2121
+CGTACACA
++
+FFD#####
+ at HiMom:1:1201:1084:2204
+GCCTGGCT
++
+FFFCCCFF
+ at HiMom:1:1201:1095:2146
+GGAACTGA
++
+FFFCCCFF
+ at HiMom:1:1201:1103:2184
+TATAGAAG
++
+FFFB at BFF
+ at HiMom:1:1201:1107:2109
+TATACAAA
++
+FFFCCCFF
+ at HiMom:1:1201:1118:2198
+CAAAATAA
++
+BDDC at CFF
+ at HiMom:1:1201:1122:2227
+TCCGTCAT
++
+FFF@@@FF
+ at HiMom:1:1201:1123:2161
+GGACGTGT
++
+DFF===AA
+ at HiMom:1:1201:1127:2112
+CTCTAATC
++
+?BD@<@?B
+ at HiMom:1:1201:1134:2144
+TGTAGTGT
++
+FFDB@?DD
+ at HiMom:1:1201:1138:2227
+ATTGACAA
++
+++2=1=A=
+ at HiMom:1:1201:1140:2125
+AGGTTCAT
++
+FFFCC at FF
+ at HiMom:1:1201:1142:2242
+GCCGTAAA
++
+D83?=?DD
+ at HiMom:1:1201:1150:2161
+ATTTTCTC
++
+DDD at C@FF
+ at HiMom:1:1201:1159:2179
+AAATTTTT
++
+<0?===AA
+ at HiMom:1:1201:1160:2109
+TCCACATC
++
+FFFCCCFF
+ at HiMom:1:1201:1180:2119
+TTGGCTCT
++
+DFFCCCFF
+ at HiMom:1:1201:1185:2143
+CGTGCTGA
++
+FFF at CCFF
+ at HiMom:1:1201:1187:2100
+GCCAAAAA
++
+FFF=<=;A
+ at HiMom:1:1201:1190:2194
+GCAACAAA
++
+FFFCCCFF
+ at HiMom:1:1201:1204:2228
+ACCTCTTC
++
+FFF@?@FF
+ at HiMom:1:1201:1208:2132
+TCACTGTA
++
+FFF@@CDF
+ at HiMom:1:1201:1219:2115
+CGTTGGGA
++
+A?D???DB
+ at HiMom:1:1201:1236:2187
+AGGCTCCT
++
+FFFCCCFF
+ at HiMom:1:1201:1242:2207
+TCTATCTT
++
+DFFCCCFF
+ at HiMom:1:1201:1252:2141
+TATAGTTA
++
+FFFBCBFF
+ at HiMom:1:1201:1260:2165
+ATTATCTG
++
+FFF@@@FF
+ at HiMom:1:1201:1280:2179
+GCCGAGGA
++
+FFF@@BFF
+ at HiMom:1:1201:1281:2133
+ATTGCAAC
++
+FDFCCCFF
+ at HiMom:1:1201:1285:2100
+CTGGATCT
++
+FFF@@@DF
+ at HiMom:1:1201:1291:2158
+GGACGTGT
++
+FFF at CCFF
+ at HiMom:1:1201:1300:2137
+GCCGCTCT
++
+23?@@?DD
+ at HiMom:1:1201:1312:2112
+AGAATTTG
++
+FFFCCCFF
+ at HiMom:1:1201:1331:2162
+ATTTAATC
++
+FFFCCCFF
+ at HiMom:1:1201:1341:2116
+TATATAAC
++
+BDD#####
+ at HiMom:1:1201:1344:2147
+TCAACGAT
++
+:=D@<??D
+ at HiMom:1:1201:1345:2181
+GTCATACG
++
+FFFCCCFF
+ at HiMom:1:1201:1364:2113
+GTATAAAG
++
+F at D#####
+ at HiMom:1:1201:1392:2109
+GCCGTCAG
++
+?DDBBCFF
+ at HiMom:1:1201:1392:2184
+GTCATCTT
++
+DDE@@BFF
+ at HiMom:1:1201:1393:2143
+TCGGATAA
++
+DFDC at CFF
+ at HiMom:1:1201:1414:2174
+AGATTTTT
++
+>)(@;@1B
+ at HiMom:1:1201:1416:2128
+AGATTGGT
++
+FFF@@@DD
+ at HiMom:1:1201:1421:2154
+CTCTGTGC
++
+FFFBC at DF
+ at HiMom:1:1201:1439:2156
+GGCGGAGA
++
+########
+ at HiMom:1:1201:1452:2143
+CTCTTTTA
++
+FFFCCCFF
+ at HiMom:1:1201:1458:2109
+ATCGATAC
++
+FFFCCCFF
+ at HiMom:1:1201:1472:2121
+CGCGTGTG
++
+:))=+=??
+ at HiMom:1:1201:1483:2126
+ATCGCATG
++
+:B?@@@DD
+ at HiMom:1:1201:1486:2109
+CAGACGTG
++
+FFDCCCFF
+ at HiMom:1:1201:1486:2146
+CTCTTTTT
++
+DBD<<<@?
+ at HiMom:1:2101:1011:2102
+ATCNNNNN
++
+FFF#####
+ at HiMom:1:2101:1013:2146
+CGTNNNNC
++
+FFF#####
+ at HiMom:1:2101:1021:2209
+GACNNGGA
++
+FFF##08@
+ at HiMom:1:2101:1023:2237
+GCCNNTTT
++
+########
+ at HiMom:1:2101:1031:2163
+CCANNACA
++
+FFF##0<@
+ at HiMom:1:2101:1036:2087
+TTGNGTCC
++
+DFF#4=DD
+ at HiMom:1:2101:1040:2208
+ATCNCTGA
++
+########
+ at HiMom:1:2101:1048:2238
+TGANGTCA
++
+DDA#11AD
+ at HiMom:1:2101:1054:2162
+AGGNGGAC
++
+FFF#4=DD
+ at HiMom:1:2101:1059:2083
+TCTNGAAT
++
++02#1=BD
+ at HiMom:1:2101:1063:2206
+TATNTGCT
++
+DFF#1=DD
+ at HiMom:1:2101:1064:2242
+AGANGGAA
++
+A at A#####
+ at HiMom:1:2101:1072:2170
+GTANGGGG
++
+DDF#4=BD
+ at HiMom:1:2101:1077:2139
+TGGNATTA
++
+FFF#4=DF
+ at HiMom:1:2101:1084:2188
+AAGTACAA
++
+FFFCCCFF
+ at HiMom:1:2101:1100:2085
+ACCATCTT
++
+FFF@@@DD
+ at HiMom:1:2101:1102:2221
+GATATAAC
++
+FFFCCCFF
+ at HiMom:1:2101:1105:2131
+ATCCAGCA
++
+FFFCCCFF
+ at HiMom:1:2101:1112:2245
+TGGTCGTA
++
+DDD?8?DB
+ at HiMom:1:2101:1122:2136
+CGACTTGC
++
+DD????BB
+ at HiMom:1:2101:1123:2095
+GTATCCGC
++
+F@@@@@FD
+ at HiMom:1:2101:1126:2082
+GATTCTCT
++
+FDA at C@DD
+ at HiMom:1:2101:1133:2239
+ATGAGCTT
++
+DDF?@?DD
+ at HiMom:1:2101:1143:2137
+CTAGCTCT
++
+=+2@@@DD
+ at HiMom:1:2101:1151:2182
+AAATTTTT
++
+((<9<<?@
+ at HiMom:1:2101:1151:2236
+GTATTTGA
++
+-@######
+ at HiMom:1:2101:1162:2139
+CTGATCGT
++
+FFFBCCFF
+ at HiMom:1:2101:1163:2203
+AGGTTGGT
++
+FFF at CCFD
+ at HiMom:1:2101:1163:2222
+GTAGAGCG
++
+FEF@@@DF
+ at HiMom:1:2101:1172:2152
+GTCATCGT
++
+########
+ at HiMom:1:2101:1186:2093
+ATTAATGT
++
+FFF#####
+ at HiMom:1:2101:1188:2195
+GCAGCACA
++
+FFFCCCFF
+ at HiMom:1:2101:1195:2150
+CTGAATTG
++
+FFFCCCFF
+ at HiMom:1:2101:1207:2084
+GGATCACC
++
+FFF@@@DD
+ at HiMom:1:2101:1208:2231
+ATCCTTTT
++
+A22CCCFF
+ at HiMom:1:2101:1215:2110
+AAGATCTT
++
+########
+ at HiMom:1:2101:1216:2172
+GATGGACT
++
+FFFCCCFF
+ at HiMom:1:2101:1216:2193
+TGAAGGCA
++
+FFF@@@DD
+ at HiMom:1:2101:1226:2088
+CCAGCTCT
++
+DDD==?BD
+ at HiMom:1:2101:1231:2208
+CGTAGCCA
++
+8 at D@@;1A
+ at HiMom:1:2101:1233:2133
+CGTTTTTT
++
+4)2CCCFF
+ at HiMom:1:2101:1240:2197
+ATTACTGG
++
+@?8??###
+ at HiMom:1:2101:1245:2154
+ATCACCAA
++
+FFFCCCFF
+ at HiMom:1:2101:1249:2231
+AGGTCTCT
++
+FFF@@@FF
+ at HiMom:1:2101:1258:2092
+ACATTAGA
++
+FFF#####
+ at HiMom:1:2101:1262:2128
+GACTCTTG
++
+DD######
+ at HiMom:1:2101:1273:2119
+TCGATGAT
++
+ADB>=><A
+ at HiMom:1:2101:1285:2105
+CGGTGTCT
++
+########
+ at HiMom:1:2101:1312:2105
+GGAGTTGA
++
+FFF at CCFF
+ at HiMom:1:2101:1325:2083
+TATTGTGC
++
+=DD#####
+ at HiMom:1:2101:1336:2109
+ATTAGACC
++
+FFFCCCFF
+ at HiMom:1:2101:1349:2084
+ATCAGTCT
++
+2<A<5;??
+ at HiMom:1:2101:1365:2094
+ACCGCTCT
++
+<,2CCCFF
+ at HiMom:1:2101:1370:2116
+GGACACCA
++
+3:B@@@DF
+ at HiMom:1:2101:1386:2105
+ATCAGGAA
++
+FFFB@@DD
+ at HiMom:1:2101:1414:2098
+TCGTTGGG
++
+FFFCCCFF
+ at HiMom:1:2101:1427:2081
+ATTCCGAC
++
+FFFCCCFF
+ at HiMom:1:2101:1450:2134
+TTGACAAA
++
+DB?CC at FD
+ at HiMom:1:2101:1459:2083
+CGAATTTC
++
+DFDCCCFF
+ at HiMom:1:2101:1491:2093
+GTCAGAGA
++
+EBDBCCDF
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplexRH.1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplexRH.1.fastq
new file mode 100644
index 0000000..9976081
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplexRH.1.fastq
@@ -0,0 +1,720 @@
+ at HiMom:1:1101:1031:2224/1
+NAATANNNNNNNNNNNNTNNNNNNN
++
+#0;@@####################
+ at HiMom:1:1101:1039:2147/1
+NCCAANGNNGGNNNNATGTAANNNN
++
+#4;@@#4##2<####43@@@@####
+ at HiMom:1:1101:1046:2175/1
+NTGCCNGNGTTNCGNGGTCTTNNNN
++
+#4;@@####################
+ at HiMom:1:1101:1047:2122/1
+NCTAANGNACTNTGNGTGTGCNNNN
++
+#0;@@#4#3@@#3@#2<@@@@####
+ at HiMom:1:1101:1048:2197/1
+NCTCCNGNTCANCANGTGGAGNNNN
++
+#0;?@####################
+ at HiMom:1:1101:1065:2193/1
+GAAGTACGCCCTGCCCCTGGTTNGC
++
+?@@DAADAHHFHBEBEGGHG?####
+ at HiMom:1:1101:1069:2159/1
+TCCCTTACCATCAAATCAATTGNCC
++
+CCCFFFFFHHHHHJJJJJJJJJ#3A
+ at HiMom:1:1101:1071:2233/1
+TTTGACAGTCTCTGAATGAGAANGG
++
+CCCFFFFFHHHHHJIIIJJJIJ#4A
+ at HiMom:1:1101:1083:2193/1
+TTCTACCTCACCTTAGGGAGAAGAC
++
+@@@DDBDDD>F><C<4CG?EHGHIG
+ at HiMom:1:1101:1084:2136/1
+NTCTCACTGTGAATTTGTGGTGGGC
++
+#1=DDFFFHHHHHJJJJGIJIJJJJ
+ at HiMom:1:1101:1089:2172/1
+TTCCAGCATGCGGTTTAAGTAGGAT
++
+ at CCFDFDBDFBF:<CEBHAFHHICH
+ at HiMom:1:1101:1100:2207/1
+ACGACAGACGTTCTTTCTTTGCTGC
++
+CCCFFFFFHHFHHJIJJJJJHIJJH
+ at HiMom:1:1101:1111:2148/1
+GTGGAGACCACCTCCGAGGCCTTGT
++
+BBCFFFFFHHHHHJJJIJJJJJJJI
+ at HiMom:1:1101:1138:2141/1
+NTTACCAAGGTTTTCTGTTTAGTGA
++
+#1=DDFFFHHFHHJJJIHJIJJJJJ
+ at HiMom:1:1101:1140:2120/1
+NCCCCAACATTCTAATTATGCCTCA
++
+#1:BDFFDHFFDFIJJJIIJIIIII
+ at HiMom:1:1101:1143:2192/1
+GGAGCGAGTCTGGGTCTCAGCCCCG
++
+CCCFFFFFHHHHHJGHIIIHJJJJI
+ at HiMom:1:1101:1150:2228/1
+GCTACTCAGTAGACAGTCCCACCCT
++
+@@CADDDDFCFHHIIIIGGIIGGGI
+ at HiMom:1:1101:1157:2135/1
+NGGACATTGTAATCATTTCTTACAA
++
+#1=DD?DDHHHHHGGHIIIIIIIII
+ at HiMom:1:1101:1162:2207/1
+ACCTTGAGGAGAACATAAGAGCAAA
++
+#########################
+ at HiMom:1:1101:1165:2239/1
+GGCGGAGGCAGCATTTCAGCTGTGA
++
+CCCFFDFFHHHHHIJJIGHHHJHHF
+ at HiMom:1:1101:1175:2197/1
+CCCCTGAGGACACCATCCCACTCCA
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1101:1188:2237/1
+TCCCCCTCCCTTTTGCGCACACACC
++
+@?@DDADDHDHBDH<EFHIIHG?HF
+ at HiMom:1:1101:1197:2200/1
+GGGCGCCCCGTGAGGACCCAGTCCT
++
+ at C@FFADDFFCFCEHIIJIJJIEFC
+ at HiMom:1:1101:1206:2126/1
+NATTCTGCCATATTGGTCCGACAGT
++
+#1=DDFFFHHHHHJJJJJJJJJIJJ
+ at HiMom:1:1101:1212:2230/1
+TTTCTATTAGCTCTTAGTAAGATTA
++
+CCCFFFFFHHHHHJJJIJJJJJJJJ
+ at HiMom:1:1101:1218:2200/1
+GCACCGGAAGAGCACACAGATCGGA
++
+CCCFFFFDFHGHHJJIJIJJJJJJI
+ at HiMom:1:1101:1219:2164/1
+TCAAGCAGGAGCAGCTAAGTCCTAA
++
+CCCFFFFFHHHHHJJJJJJHIJJJJ
+ at HiMom:1:1101:1221:2143/1
+TTTGGTGGAAATTTTTTGTTATGAT
++
+CCCFFBDBHFD?FBFHIIGGIC at EF
+ at HiMom:1:1101:1236:2121/1
+NGGTGCTTCATATCCCTCTAGAGGA
++
+#1=BDDFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1101:1242:2170/1
+ATGGCAGGGCAGAGTTCTGATGAGT
++
+CCCFFFFFHHGGGIFHEIIGIIII?
+ at HiMom:1:1101:1257:2223/1
+TGTATTCGAGAGATCAAAGAGAGAG
++
+@@=DDBDD?FFHHEIDBDFCEDBAF
+ at HiMom:1:1101:1259:2152/1
+CACCTATAATCCCAGCTACTCCAGA
++
+CCCFFFFFHHHHHJJJJJJIJJJIJ
+ at HiMom:1:1101:1261:2127/1
+NTGAAATCTGGATAGGCTGGAGTTA
++
+#0-@@@###################
+ at HiMom:1:1101:1263:2236/1
+CTTTGAAGACATTGTGAGATCTGTA
++
+<==A<42 at C+A4A?,2A@=4 at 7A??
+ at HiMom:1:1101:1267:2209/1
+GAGACGGAGGCCAACGGGGGCCTGG
++
+@@CFFFFD8FDHFHIGIBG?@BCDG
+ at HiMom:1:1101:1269:2170/1
+ACAGTGTGGGAGGCAGACGAAGAGA
++
+@@@DDDDDFA:C at EGA?FD<FFHII
+ at HiMom:1:1101:1290:2225/1
+CTTGGGCGCATGGTGAGGGAGGGAG
++
+@@@FFDDFHDFH??CBEBHHIGDCD
+ at HiMom:1:1101:1291:2150/1
+CGTGGGGAACCTGGCGCTAAACCAT
++
+ at BBFFFFFHHHHHJJJJIJJJJJIJ
+ at HiMom:1:1101:1302:2244/1
+GGAAAAGACGGAAAGGTTCTATCTC
++
+ at C@DFFFDFHHHHJIJHHIJJJJJI
+ at HiMom:1:1101:1308:2153/1
+TTTTGGAAGAGACCTCAATTACTGT
++
+???DDDDD?:22AE:A2<3,AF?3A
+ at HiMom:1:1101:1309:2210/1
+ACACCAACCACCCAACTATCTATAA
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1101:1314:2233/1
+GTTTATTGGGGCATTCCTTATCCCA
++
+@??DDDDBDHF>FCHGGGBFAAED9
+ at HiMom:1:1101:1316:2126/1
+NAAAAAAAAAAAAAAAAAAAAAAAA
++
+#1BDFFFFHHHHHJJJJFDDDDDDD
+ at HiMom:1:1101:1327:2200/1
+AGGGGGATCCGCCGGGGGACCACAA
++
+#########################
+ at HiMom:1:1101:1328:2225/1
+GAAATGCATCTGTCTTAGAAACTGG
++
+??@=BDDDFDD<<,<2:C<F:FFEA
+ at HiMom:1:1101:1338:2175/1
+CCCACCTTCCGGCGGCCGAAGACAC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1101:1347:2149/1
+GAGCAGATCGGAAGAGCACAGATCG
++
+@@@FFDDDHHHHHIJJBGGHJIHEG
+ at HiMom:1:1101:1353:2226/1
+TTGCTTGTCTGTAAAGTATTTTATT
++
+ at C@DDFFDHHFHFHHIBGG>IHHII
+ at HiMom:1:1101:1363:2138/1
+NGTCTGGCCTGCACAGACATCCTAC
++
+#1=DDFFFHHHHHJJJIJJIJJJIJ
+ at HiMom:1:1101:1399:2128/1
+NTGCCCTTCGTCCTGGGAAACGGGG
++
+#1BDFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1101:1403:2194/1
+CTAAACAGAGAGAAGGTTTCTCTTT
++
+CCCFFFFFHHHHHJJJFHIJJJJJJ
+ at HiMom:1:1101:1406:2222/1
+CTCCCCCCGGGCTGAACCAGGGTAC
++
+CCCFFDDDDHDFHIIIIIIIII9DG
+ at HiMom:1:1101:1419:2119/1
+NATGACTATGGTAACTGAAAGAAAA
++
+#1:A1BDADBFFDFIIIEEHECACF
+ at HiMom:1:1101:1420:2213/1
+TACCTGGTTGATCCTGCCAGTAGCA
++
+@@CFFFFDDHHGHJGGHIJJIHGBH
+ at HiMom:1:1101:1435:2194/1
+GAGAAAGAACATGACTACAGAGATG
++
+CCCFFFFFHHHHHJJJJJJJJJHJJ
+ at HiMom:1:1101:1441:2148/1
+ACTTTCACCGCTACACGACCGGGGG
++
+CCCFFFFFHGFFHIIFIHJIGGII>
+ at HiMom:1:1101:1452:2132/1
+NCGTCCTGGAAAACGGGGCGCGGCT
++
+#1=BDBDDFHHHHF at FHDHIGIIII
+ at HiMom:1:1101:1460:2176/1
+AGTCCAGGCTGAGCCCAGGGAAGAA
++
+CCCFFFFFHHHHGJIJJIJJHIJJI
+ at HiMom:1:1101:1479:2221/1
+TGTAAAGTATGCTGGCTCAGTGTAT
++
+BBBFDFFEHHHHHJJJJJJJIJHJJ
+ at HiMom:1:1101:1491:2120/1
+NGGCAGGTGCCCCCACTTGACTCTC
++
+#1?DFFFFGHHHHJJJJJJJJJJJJ
+ at HiMom:1:1201:1018:2133/1
+NAAAACTTGAGGATGCTATGCAAGC
++
+#1:B:ADDDDDDDEEAEBF9FFEBF
+ at HiMom:1:1201:1018:2217/1
+NTTTCTCTGGGCGCAAAGATGTTCA
++
+#07;8=8<<99(:=@@/@7>>6=?>
+ at HiMom:1:1201:1028:2202/1
+NTCCTGGGAAACGGGGCGCGGCTGG
++
+#4BDDDFFHHHHHIJIIJJJJJJIJ
+ at HiMom:1:1201:1042:2174/1
+NGTTGGTGTCTTCATTTTATGTATA
++
+#1=DDFDFHHHHHJIJJJHIJHIJJ
+ at HiMom:1:1201:1043:2246/1
+NTTCTCGGCTGTCATGTGCAACATT
++
+#1=DDBDFHHHDFFBHGHGHIIJEH
+ at HiMom:1:1201:1045:2105/1
+NTAAAGAGAAATCAAGAATACTATT
++
+#-4@?(@)@@###############
+ at HiMom:1:1201:1054:2151/1
+NTAGTGCTGGGCACTAAGTAATACC
++
+#4=DDDFFHHHHHJJJJJHIJJJJJ
+ at HiMom:1:1201:1064:2239/1
+CATGCAGCGCAAGTAGGTCTACAAG
++
+@@;DFAFFHHHHAHEGHFDGGFABG
+ at HiMom:1:1201:1073:2225/1
+GGGGCTGAGACCTTTGCTGATGGTG
++
+@@@FFFFFHHHGHJJJJJIIIGICH
+ at HiMom:1:1201:1083:2121/1
+NAGAACTGGCGCTGCGGGATGAACC
++
+#1=BDFFFHHHHHJJJJJHIJIJJJ
+ at HiMom:1:1201:1084:2204/1
+GGCCCGTGGACGCCGCCGAAGAAGC
++
+CCCFFFFFHHHHHJJJJJIJJJJJJ
+ at HiMom:1:1201:1095:2146/1
+GCTGAGTCATGTAGTAAGCCTGTGC
++
+BB at FDDDFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1201:1103:2184/1
+GTAAGAACTACCCTGGGTCCCCGTG
++
+@@BFFFFFHHHHHJJJJGIJJJJHI
+ at HiMom:1:1201:1107:2109/1
+NGGGAACCTGGCGCTAAACCATTCG
++
+#1=DFFFFHHHHHJJJJJJJJJIJJ
+ at HiMom:1:1201:1118:2198/1
+CAAGTGTACAGGATTAGACTGGGTT
++
+BCCFDEBDHHHHHIJJJGIIIJJGH
+ at HiMom:1:1201:1122:2227/1
+AGAAGACGAGGCTGAGAGTGACATC
++
+@@@FFFFFHHHDHJGHGHCHHJJIJ
+ at HiMom:1:1201:1123:2161/1
+CACTAACTCCTGACCTCAAATAATC
++
+?7?=DD?DD+CDBE>E at EEF@+<CF
+ at HiMom:1:1201:1127:2112/1
+NGTCAAGGATGTTCGTCGTGGCAAC
++
+#1=BDDDDDDDDDID<AE?@<CEEE
+ at HiMom:1:1201:1134:2144/1
+TGCCAGGAAGTGTTTTTTCTGGGTC
++
+ at CCFFEFFHHFFFGIJJJJJJJJGH
+ at HiMom:1:1201:1138:2227/1
+GCTGACACAATCTCTTCCGCCTGGT
++
+#########################
+ at HiMom:1:1201:1140:2125/1
+NTTTCAGTTCAGAGAACTGCAGAAT
++
+#1=DBDFDHHHHGJIJJJJJIIIJI
+ at HiMom:1:1201:1142:2242/1
+TGTTGATAGTCCTTCTTATCTTAGT
++
+???DB?==CC2<AC:CC<CFEF<FF
+ at HiMom:1:1201:1150:2161/1
+AAGTCACCTAATATCTTTTTTTTTT
++
+@@<??;?D?CFD,A4CDDHFBIIID
+ at HiMom:1:1201:1159:2179/1
+GTTAGCACAGATATTGGATGAGTGA
++
+#########################
+ at HiMom:1:1201:1160:2109/1
+NAGAAGCCTTTGCACCCTGGGAGGA
++
+#1=DDDFFHHHHHJJJJJJJJIIJJ
+ at HiMom:1:1201:1180:2119/1
+NTGAAAGATTTAGAGAGCTTACAAA
++
+#1=DDDDDHHHGHJJIIJJJJIJJI
+ at HiMom:1:1201:1185:2143/1
+ATCTGCCTGGTTCGGCCCGCCTGCC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1201:1187:2100/1
+NGCGGTAATTCCAGCTCCAATAGCG
++
+#1:BB2 at DHHFHHIIIIHHIIGHGG
+ at HiMom:1:1201:1190:2194/1
+AACCTGGCGCTAAACCATTCGTAGA
++
+CCCFFFFFHHHHHJJJJJJJJIJJJ
+ at HiMom:1:1201:1204:2228/1
+CCGATACGCTGAGTGTGGTTTGCGG
++
+CCCFFFFFHHHFHEGGHIHIJJJJJ
+ at HiMom:1:1201:1208:2132/1
+NCCTCAATGAGCGGCACTATGGGGG
++
+#1=DDFFFHHHHGJJIJJGHIJGIJ
+ at HiMom:1:1201:1219:2115/1
+NTATAGTGGAGGCCGGAGCAGGAAC
++
+#1:DABADHHHFHIIIGGHGIIIII
+ at HiMom:1:1201:1236:2187/1
+TTTAAATGGGTAAGAAGCCCGGCTC
++
+ at BCDDFEFHHDHHJJJJJIJJIJJJ
+ at HiMom:1:1201:1242:2207/1
+ATGGCAAAGTGGTGTCTGAGACCAA
++
+BCCFFFFFGHHHHHIIIJFHIJJJJ
+ at HiMom:1:1201:1252:2141/1
+NTTCCCCCCATGTAATTATTGTGAA
++
+#1=DDFFFHHHHHJJJJJJJJIJJJ
+ at HiMom:1:1201:1260:2165/1
+GGACACGGACAGGATTGACAGATTG
++
+BCBFFFFFHHHHHHIIJHIIIFHIJ
+ at HiMom:1:1201:1280:2179/1
+TTCAAGGAATCGTCCTGCCTCAGCC
++
+BCCFFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1201:1281:2133/1
+NGGAAATCCAGAAAACATAGAAGAT
++
+#1=DDFFFHHHHHIJJJJJJJJIJJ
+ at HiMom:1:1201:1285:2100/1
+NAATGACATGTTTAAAGATGGACTC
++
+#1:BDDFFHHFHHGIJIJIIIIGII
+ at HiMom:1:1201:1291:2158/1
+AGAAGGGGAAAGCCTTCATCTTGGC
++
+BCBFFFFFHHHHHJJJJJIIFIJIJ
+ at HiMom:1:1201:1300:2137/1
+NTGTAATCCCAGCTCTCAGGGAGGC
++
+#1=ADDDDDDDBBA?@AE?E at FE8;
+ at HiMom:1:1201:1312:2112/1
+NTCCCAGCGAACCCGCGTGCAACCT
++
+#1=DFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1201:1331:2162/1
+ACGCTCGGCTAATTTTTGTATTTTT
++
+ at CCFFFDFHHHHHIJJJJHIJJJJJ
+ at HiMom:1:1201:1341:2116/1
+NAGAAGCCCCAGGAGGAAGACAGTC
++
+#1=DDFFFHHHHHHHJIIJJJJJGI
+ at HiMom:1:1201:1344:2147/1
+TATCCTCCCTACTATGCCTAGAAGG
++
+=?@DADEFHBHDFG>EFGDHGFGHD
+ at HiMom:1:1201:1345:2181/1
+GGATAATCCTATTTATTACCTCAGA
++
+BBBDDFFFHHHHHJJJJJJJJJIJJ
+ at HiMom:1:1201:1364:2113/1
+NCACTCATTTTCTTATGTGGGATAT
++
+#1=DDFDFHHHHHIJJIFHIIHHHI
+ at HiMom:1:1201:1392:2109/1
+NCTGAAGAGGCCAAAGCGCCCTCCA
++
+#1=DDFFFHHHHHJJJJJJJJJJJI
+ at HiMom:1:1201:1392:2184/1
+TTTCAGATTGGTCATTGTTAGTGTA
++
+??@BDDDEHBHADHHIIEHDHFHFF
+ at HiMom:1:1201:1393:2143/1
+TGGTTGATCCTGCCAGTAGCATATG
++
+@@@ADADDFHFFDBHE?G at HIIIEE
+ at HiMom:1:1201:1414:2174/1
+GCCAAAAAAAAGAACCAGCCCAAGG
++
+#########################
+ at HiMom:1:1201:1416:2128/1
+NACAGGCGTGGAGGAGGCGGCGGCC
++
+#4=DDDFFHHHHHJIGJHFHHFFED
+ at HiMom:1:1201:1421:2154/1
+TGTGTGTGTGGGTGTGTGTATATAT
++
+?@?DDFFFFFHH at GEFCCCHGIGJI
+ at HiMom:1:1201:1439:2156/1
+AGCCGCGAGGTGCTGGCGGACTTCC
++
+:;1BDDDAA88A<?<E1C:D#####
+ at HiMom:1:1201:1452:2143/1
+TATCCCCTCTAAGACGGACCTGGGT
++
+CCCFFFFFHHHHHJJIIIJJJJJJG
+ at HiMom:1:1201:1458:2109/1
+NGAGACCATAGAGCGGATGCTTTCA
++
+#1=DDDFFHHGHGIJJIGIIJJJJJ
+ at HiMom:1:1201:1472:2121/1
+NTAAAGTGTGAACAAGGAAGGTCAT
++
+#07>@<9=@################
+ at HiMom:1:1201:1483:2126/1
+NTGATAAGGTGTTGCTATGTTACCC
++
+#1:D?DDDDA??2:<CC4:AEDF>?
+ at HiMom:1:1201:1486:2109/1
+NCACCTCCTAGCCCCTCACTTCTGT
++
+#1=B;BDDHHHGFIIIIIIIIIGGG
+ at HiMom:1:1201:1486:2146/1
+GTTCTCTGTCCCCAGGTCCTGTCTC
++
+===A7<7222<<=C=?+<7>@?ACB
+ at HiMom:1:2101:1011:2102/1
+NAAACAAAACTGTAGAACTGTGTAT
++
+#1=DDFFFHHHHHJJIJJJIHHHJJ
+ at HiMom:1:2101:1013:2146/1
+NACACTGCTGCAGATGACAAGCAGC
++
+#4BDFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:2101:1021:2209/1
+NGGCCCCACCCTCCTCCAGCACGTC
++
+#1=DDFFFHHHHHJJJJJJHIIHFH
+ at HiMom:1:2101:1023:2237/1
+NTAAACAGCTTCTGCACAGCCAAAG
++
+#00@@?>=39>9;<412@?######
+ at HiMom:1:2101:1031:2163/1
+NTTTCCATGGCCGTCACCTTTGGGT
++
+#4=DDFFFHHHHHJJJJJJJJJJJI
+ at HiMom:1:2101:1036:2087/1
+NTGTAGTTTCTTTAGGCAAATTTGT
++
+#4=BDDDFHHHHHJJJJJJIIJJJI
+ at HiMom:1:2101:1040:2208/1
+NATGCCCACCTCCCTCCTACGCACC
++
+#########################
+ at HiMom:1:2101:1048:2238/1
+NCTGCCGTGTCCTGACTTCTGGAAT
++
+#1:B?ADDACF<DCG;EG<FHH at CE
+ at HiMom:1:2101:1054:2162/1
+NCCAGGTGTCTTCCCGGGCCCTGCC
++
+#1=DDFBDFHHHHJJJJJIJJJJJJ
+ at HiMom:1:2101:1059:2083/1
+NAAGAGGGGTCAAGAGTTAAACTTA
++
+#1=DDFFFHFHHGIGHGHJJJJJJI
+ at HiMom:1:2101:1063:2206/1
+TCCTATTCGCCTACACAATTCTCCG
++
+CCCFFFFFHHHHHJJJJJJJHJJJJ
+ at HiMom:1:2101:1064:2242/1
+ATGAACAAAGGAAGAATTATGCACG
++
+?;?D;DDDF?;:+<<CFFCHE433A
+ at HiMom:1:2101:1072:2170/1
+ATCACCGCACTCATTTCCCGCTTCC
++
+CCCFFFFFHHHACEEGHIIBHIIII
+ at HiMom:1:2101:1077:2139/1
+CACAGGCTTCCACGGACTTAACGTC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:2101:1084:2188/1
+TTGCTGCATGGGTTAATTGAGAATA
++
+CCCFFFFFHHHHFHHIIJJIJJJJJ
+ at HiMom:1:2101:1100:2085/1
+NCACATGGATGAGGAGAATGAGGAT
++
+#1=DDFFFFHHHHJHIGIHHHIJEH
+ at HiMom:1:2101:1102:2221/1
+TTTCATCTTATTTCATTGGTTTATA
++
+CCCFFFFFHHHHHJIJJJJIJJJJJ
+ at HiMom:1:2101:1105:2131/1
+TTGGAACACAGCGGGAATCACAGCA
++
+CCCFFFFFHHHHHJIJJJJJJJJJJ
+ at HiMom:1:2101:1112:2245/1
+TGCCATCTGCTCTGGGAAGCACCAG
++
+1:=DDDDDFBC:DEFIFFFIEF at BE
+ at HiMom:1:2101:1122:2136/1
+GTAGGCGCTCAGCAAATACTTGTCG
++
+@@@DDDD8?<CACEHHBBHDAAFH@
+ at HiMom:1:2101:1123:2095/1
+NTGGACAACATGTTCGAGAGCTACA
++
+#1=BBDDDFFFFDGFGIG?F;HHFI
+ at HiMom:1:2101:1126:2082/1
+NGTTTTAGGGGTGCGCAGGAGTCAA
++
+#11=A=DD?DF at D@CCGHIEFH at BG
+ at HiMom:1:2101:1133:2239/1
+AGACAGAAGTACGGGAAGGCGAAGA
++
+@@@FFFFEHFHHHJJCGDHIIECD@
+ at HiMom:1:2101:1143:2137/1
+ATGCAGCAGCTGCCACGGAGCACCA
++
+CC at FFDFDFHFHHGIDHEHIGJJJJ
+ at HiMom:1:2101:1151:2182/1
+TTGTTTTGGCTTATAATGACAAGAA
++
+;;8-2).2())(<6=@8;?4??>>?
+ at HiMom:1:2101:1151:2236/1
+TTAAAGAGGTTCAGGGATGCAGAGT
++
+#########################
+ at HiMom:1:2101:1162:2139/1
+AGAGGTGAAATTCTTGGACCGGCGC
++
+@@@DDDDDHFHHHDB:EFHHCAG?D
+ at HiMom:1:2101:1163:2203/1
+TCTCCATGTGAAACAAGCAAAAAGA
++
+CCCFFFFFHHHHGJJJIJJJJJJJJ
+ at HiMom:1:2101:1163:2222/1
+GAGCAGGCAAGGAGGACTTCTTGTT
++
+CCCFFFFFGHHHHJJHHIJJJJJIJ
+ at HiMom:1:2101:1172:2152/1
+AACACGGACAAAGGAGTCTAACACG
++
+<<<??8@@#################
+ at HiMom:1:2101:1186:2093/1
+NCGACCATAAACGATGCCGACCGGC
++
+#4=DFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:2101:1188:2195/1
+TTAGACCGTCGTGAGACAGGTTAGT
++
+ at CCFFFFFHHHHHJJJJJIIEHIJH
+ at HiMom:1:2101:1195:2150/1
+CCGAGAGAGTGAGAGCGCTCCTGGG
++
+CCCFFFFFHFHHHJJJJIJJJJIJJ
+ at HiMom:1:2101:1207:2084/1
+NTAGATGACCAAAACTTGCAGGGCA
++
+#1:A<?@A+7A=?CBCCBCCBAAAA
+ at HiMom:1:2101:1208:2231/1
+TCACTAAACATCCAAACATCACTTT
++
+#########################
+ at HiMom:1:2101:1215:2110/1
+NAATATAATTTGGAGACCCTTTGTT
++
+#1=DDDDDEDDDDIDDBB3ABAB##
+ at HiMom:1:2101:1216:2172/1
+TTTCTTCGCAGGATTTTTCTGAGCC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:2101:1216:2193/1
+TTTTCTTGGCCTCTGTTTTTTTTTT
++
+BCCFDFFFHHFFHJIGIJJJJJJJJ
+ at HiMom:1:2101:1226:2088/1
+NGATCGGAAGAGCACACGTTTGACT
++
+#4=DAA=DDFHFHIIBFGHHIG>EG
+ at HiMom:1:2101:1231:2208/1
+ACGCCGCAAGTCAGAGCCCCCCAGA
++
+@@@DDDFFFFB:DBBEBEFDHBDDB
+ at HiMom:1:2101:1233:2133/1
+GAGAGAAGCACTCTTGAGCGGGATA
++
+0;(@((@)2@###############
+ at HiMom:1:2101:1240:2197/1
+ATAAAACATAGCAATATTTTCCTAT
++
+#########################
+ at HiMom:1:2101:1245:2154/1
+TCGTTAAGTATATTCTTAGGTATTT
++
+CCCFFDFFFHFHHIIJJJJJFJJJI
+ at HiMom:1:2101:1249:2231/1
+GTTATTGATAGGATACTGTACAAAC
++
+ at BCFFFFDHHHHFIJJJJJJJJJJJ
+ at HiMom:1:2101:1258:2092/1
+NCACACACACACTCATTCACAGCTT
++
+#1=DDDFFHHHFHJJIJGGGIIGIJ
+ at HiMom:1:2101:1262:2128/1
+AGCAGAAGGGCAAAAGCTGGCTTGA
++
+9;<@:@###################
+ at HiMom:1:2101:1273:2119/1
+NAGATAAGAGTCCACACAGTTGAGT
++
+#11AAAAA<A?4=C=7?733<ACA3
+ at HiMom:1:2101:1285:2105/1
+NGCGGGGAGCCGGGCGTGGAATGCG
++
+#########################
+ at HiMom:1:2101:1312:2105/1
+NTTCCCTCAGGATAGCTGGCGCTCT
++
+#1=DDFFFGHGHHJJJJJJJJJJJJ
+ at HiMom:1:2101:1325:2083/1
+NCAGAAGAAAGGGCCTTGTCGGAGG
++
+#1=DDDDDHHFHDGI at EEHG:?FA8
+ at HiMom:1:2101:1336:2109/1
+NACTATCAGGATCGTGGCTATTTTG
++
+#1BDDFFFHHHHHJIJJJJJJJJJJ
+ at HiMom:1:2101:1349:2084/1
+NCAAGTAGCAGTGTCACGCCTTAGC
++
+#1=DDBDDADFDDBEH at HC=CEGG@
+ at HiMom:1:2101:1365:2094/1
+NAAGGTGAAGGCCGGCGCGCTCGCC
++
+#1=BDDDFFHHHHJGGGIGFIHIIJ
+ at HiMom:1:2101:1370:2116/1
+NTGGTGGTCCATAGAGATTTGAAAC
++
+#1:4BD7DACF?FCA:4+<ACHIIH
+ at HiMom:1:2101:1386:2105/1
+NTACTAAAGAAAAAGTTGAAGAACT
++
+#1=DDDFFHHHHHJJGHIJJJJIJJ
+ at HiMom:1:2101:1414:2098/1
+NAGGACATCGATAAAGGCGAGGTGT
++
+#1=DDFFFHHHHHJJJJJJJJJHHG
+ at HiMom:1:2101:1427:2081/1
+NCGAGTGCCTAGTGGGCCACTTTTG
++
+#4=DDBDFHHHHFHIJJJJIJJJJI
+ at HiMom:1:2101:1450:2134/1
+AGCACGCTGCCGCGGGACCTGCCCA
++
+?@@AD at DDHFH?DGIIIIG at FGFBF
+ at HiMom:1:2101:1459:2083/1
+NCACACGCCACACGGAGCACACTTT
++
+#4=DDFFFHHHHHJJJJJJJJIIJJ
+ at HiMom:1:2101:1491:2093/1
+NCTATGCCGATCGGGTGTCCGCACT
++
+#1=DDDDDHHFHHIIEHHHBGHGII
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplexRH.2.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplexRH.2.fastq
new file mode 100644
index 0000000..117a9c0
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplexRH.2.fastq
@@ -0,0 +1,720 @@
+ at HiMom:1:1101:1031:2224/2
+NNNNNNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at HiMom:1:1101:1039:2147/2
+NNNNNNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at HiMom:1:1101:1046:2175/2
+NNGGANNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at HiMom:1:1101:1047:2122/2
+NNTCANNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at HiMom:1:1101:1048:2197/2
+NNGTGNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at HiMom:1:1101:1065:2193/2
+NCTTGNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at HiMom:1:1101:1069:2159/2
+GACGTNNNNNNNNNNNNNNNNNNNN
++
+<<<@?####################
+ at HiMom:1:1101:1071:2233/2
+GTTTGNNNNNNNNNNNNNNNNNNNN
++
+<<<@@####################
+ at HiMom:1:1101:1083:2193/2
+AGGCTNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at HiMom:1:1101:1084:2136/2
+TTTCTNNNNNNNNNNNNNNNNNNNN
++
+<<<@@####################
+ at HiMom:1:1101:1089:2172/2
+TCCGGNNNNNNNNNNNNNNNNNNNN
++
+:<<??####################
+ at HiMom:1:1101:1100:2207/2
+AGGCTNNNNNNNNNNNNGNNNNNNN
++
+#########################
+ at HiMom:1:1101:1111:2148/2
+GCGAANANNNNNNNNNNGGACGACN
++
+#########################
+ at HiMom:1:1101:1138:2141/2
+TCCGATCTGCTTCAGGTCGATCAGA
++
+CCCFFFFFHGHHHJJIGHIJJJJJJ
+ at HiMom:1:1101:1140:2120/2
+TTTTTTTTTTTTTAACTTTGCAAAT
++
+@@@DDDDDHHHHFB at 9FHI@BFH@@
+ at HiMom:1:1101:1143:2192/2
+CGACAAGTCTGGCTTATCACTCATC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1101:1150:2228/2
+ATGGGAGGCGATTCCTAGGGGGTTG
++
+8?=DD8;@BH6DHD<FGGGEIGHIG
+ at HiMom:1:1101:1157:2135/2
+TTTAAAGTCTTAATCAAAGATGATA
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1101:1162:2207/2
+TAAAACTGGGGAAGTTAGAGGAATG
++
+#########################
+ at HiMom:1:1101:1165:2239/2
+ATGGAAGTCGAGACAGAAGTGAGAA
++
+#########################
+ at HiMom:1:1101:1175:2197/2
+AAGAGCTGGGGAACATCCAGAAAGG
++
+BC at FFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1101:1188:2237/2
+GCTTCCTTCAAGACAGAAGTGAGAA
++
+CCCFFDDEFHHFFE at FDHHAIAFHG
+ at HiMom:1:1101:1197:2200/2
+ATATTCCACTGGAACCACAGAACCC
++
+@@@FFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1101:1206:2126/2
+ATCTGTCCAGTGGTGCACTGAATGT
++
+CCCFFFFFHHHHHHIIJJJJIJJJJ
+ at HiMom:1:1101:1212:2230/2
+TTTTAGCTTTATTGGGGAGGGGGTG
++
+CCCFFFFFHHGHHJJJJGJJJJJDF
+ at HiMom:1:1101:1218:2200/2
+GCTCTTCCGATCTATCTGCTCGTCC
++
+(-(=34???3;@#############
+ at HiMom:1:1101:1219:2164/2
+ATCTTATCCACTCCTTCCACTTTGG
++
+CCCFFFFFHHHHHJJIJJJJJJJIJ
+ at HiMom:1:1101:1221:2143/2
+CAATTGAATGTCTGCACAGCCGCTT
++
+@@@FFFFDHHHHHJJJIIIJGHIJJ
+ at HiMom:1:1101:1236:2121/2
+TTGCGCTTACTTTGTAGCCTTCATC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1101:1242:2170/2
+GGAAGGAAAAGAAGCACAAGTACAT
++
+@@@DFDFFHHHGHHGIIGJJEHHIG
+ at HiMom:1:1101:1257:2223/2
+TGCTCTTCCGATCTTTTAGCAAAGC
++
+:?@DDBDDHFFHDGIGIIJJJGGGI
+ at HiMom:1:1101:1259:2152/2
+ATTTTTATATTTTTTTAGACATAGG
++
+CCCFFFFFGHHHHJJJJIGIIJJJJ
+ at HiMom:1:1101:1261:2127/2
+TTTTTTTTTTTTTTTTTTTTTTTTT
++
+CCCFFFFFHGHHHJJIFDDDDDDDD
+ at HiMom:1:1101:1263:2236/2
+AGTTCTTCAGTAATTTTAGTACTGC
++
+#########################
+ at HiMom:1:1101:1267:2209/2
+GGCAGAGTCTCCAACAGCCCCGTAC
++
+=;?DDDD?CCFHAIIIGGIIGE at EG
+ at HiMom:1:1101:1269:2170/2
+TTCCAAGCCTGTGCTTTAAGGAAAA
++
+@@<ADBDBDF8DDCFH at GIE@@GGH
+ at HiMom:1:1101:1290:2225/2
+TCAGTTCACTGGCAAAGACAGTCAC
++
+C@@FBEDDFHFHGIIICEHGDHBHE
+ at HiMom:1:1101:1291:2150/2
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CCCFFFFFHHFHHIJJJIIIGIJIJ
+ at HiMom:1:1101:1302:2244/2
+TGAATACATATAACAAATGCAAAAA
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1101:1308:2153/2
+TCTGTAAGGTAATCCCCGCATGTGT
++
+1?1=4===AFFDFFGFDGFB at CFB:
+ at HiMom:1:1101:1309:2210/2
+AGTGGGCTAGGGCATTTTTAATCTT
++
+@@?DFFDFHHHDFHJIJJIJGIIIJ
+ at HiMom:1:1101:1314:2233/2
+AGGAAAGTTGGGCTGACCTGACAGA
++
+@@<DDD;=FBFADBCGDEH?F;FCG
+ at HiMom:1:1101:1316:2126/2
+TCTTTTTTTTTTTTTTTTTTTTTTT
++
+CCCFFFFFHHHHHJJJJHFDDDDDD
+ at HiMom:1:1101:1327:2200/2
+GTCATCTGGGCTGTCGACAGGTGTC
++
+ at B@FFFFFHHHHGIJJJJJJIFHHI
+ at HiMom:1:1101:1328:2225/2
+AGGAAATTAGGACTTACCTGACATA
++
+#########################
+ at HiMom:1:1101:1338:2175/2
+GCTTGTTGGCTTTAACATCCACAAT
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1101:1347:2149/2
+GCTCTTCCGATCTGTGCTCTTCCGA
++
+CCCFFFFFDFHHFIJDGIGGHGIGH
+ at HiMom:1:1101:1353:2226/2
+GTGCTCTTCCGATCTTCAGGTTACC
++
+BBBFFFFFHHHHHJJJJJJJIJJJJ
+ at HiMom:1:1101:1363:2138/2
+GTTCTTAAACCTGTTAGAACTTCTG
++
+C@@FFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1101:1399:2128/2
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CCCFFFFFHHHHHIJJJJJJJJJJJ
+ at HiMom:1:1101:1403:2194/2
+ACATGGTGAAACCCTGTCTCTACTA
++
+CCCFFFDDHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1101:1406:2222/2
+GGCTGGACTCCCCTGGTTCTGGGCA
++
+;?@DDDBD?FHDFGIIIGIGHHIII
+ at HiMom:1:1101:1419:2119/2
+ACTTTCCTTTTTTGTTTTACTTTAA
++
+#########################
+ at HiMom:1:1101:1420:2213/2
+TTCACTGTACCGGCCGTGCGTACTT
++
+ at CCFFFFDHHHFGIJJJJJJGHIGG
+ at HiMom:1:1101:1435:2194/2
+TTTTGTTTTCTTTTACTGAAGTGTA
++
+CCCFFDFFHHHHHJJJJIHIJHHHJ
+ at HiMom:1:1101:1441:2148/2
+TTTTGGCTCTAGAGGGGGTAGAGGG
++
+CCCFFFFFHHDFBHIIJJ1?FGHIJ
+ at HiMom:1:1101:1452:2132/2
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CCCFFFFFHHHHHJJJJJJJIJJJJ
+ at HiMom:1:1101:1460:2176/2
+AGGAAAAAGACACAACAAGTCCAAC
++
+#########################
+ at HiMom:1:1101:1479:2221/2
+GGGGAAATCTATTTTTATGTAAAAA
++
+ at CCFFFFFHHHHHJIGIJJJJJJJJ
+ at HiMom:1:1101:1491:2120/2
+GGCCAGGCTGAACTTCTGAGCTGCT
++
+CCCFFFFFHHHGHJJJJJJJJJJJJ
+ at HiMom:1:1201:1018:2133/2
+NNNNNNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at HiMom:1:1201:1018:2217/2
+NNNNNNNNNNNNNNNNNNNNNNNNN
++
+#########################
+ at HiMom:1:1201:1028:2202/2
+NNAAACNCNTNNNNNNNGGNNTGNN
++
+##42@?###################
+ at HiMom:1:1201:1042:2174/2
+NTCAGGAAGGCNNCAAAAAAAGAAA
++
+#0;@@@?@?<@##3<@@?@@?????
+ at HiMom:1:1201:1043:2246/2
+NGCATCATTTCNNGCTTCTCTCTGT
++
+#0;@@??@=@>##22=;@??><@??
+ at HiMom:1:1201:1045:2105/2
+NTTTTTTTTTTNNTTTTTTTTTTTT
++
+#0;@@@@@@@?##0:????????=<
+ at HiMom:1:1201:1054:2151/2
+GTCAGGCACTGAGAATATATGGGTG
++
+CBCFFFFFHHHHHJJJJJJJJJJEG
+ at HiMom:1:1201:1064:2239/2
+GGGATGGGAGGGCGATGAGGACTAG
++
+8?@:DDDACC:FHHGIH<EGDDDFH
+ at HiMom:1:1201:1073:2225/2
+CGTGTGCTCTTCCGATCTGGAGGGT
++
+ at BBDFFFFHHHHHJJJJJJJJJJJ:
+ at HiMom:1:1201:1083:2121/2
+ACACACAACACCACCGCCCTCCCCC
++
+#########################
+ at HiMom:1:1201:1084:2204/2
+TGGCTCCTCAGGCTCTCATCAGTTG
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1201:1095:2146/2
+ACTGACAACACCAAATGCTGCTAAG
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1201:1103:2184/2
+AGAAGTTTCAGAATTGTGGCCCCAT
++
+B at BFFDEFHHHHHJJJGHIJJJJJI
+ at HiMom:1:1201:1107:2109/2
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CCCFFFFFHHGHHJJJJIIJJJJJJ
+ at HiMom:1:1201:1118:2198/2
+AATAAACTTTATTAAAGCAGTTAAA
++
+C at CFFFFFHDHHHGIIIJJJIJJJJ
+ at HiMom:1:1201:1122:2227/2
+GTCATATAAGGCCCAGTCCAAGGAA
++
+@@@FFFFFHHHGGIJIGGIJFIJII
+ at HiMom:1:1201:1123:2161/2
+CGTGTGCTCTTCCGATCTGCATACA
++
+===AAAA8AAAA<AAA)@CBA9>A#
+ at HiMom:1:1201:1127:2112/2
+TAATCACCTGAGCAGTGAAGCCAGC
++
+@<@?BDDDHD?FDBHI?AHGGGDFH
+ at HiMom:1:1201:1134:2144/2
+AGTGTGAGTAATGGTTGAGAGGTGG
++
+B@?DDDFFFHHGHJHHGFIHHIFGI
+ at HiMom:1:1201:1138:2227/2
+GACAAATATAGGAAATAGAAGCTAT
++
+=1=A=AAA,2?4>7C<<4<A+3<AB
+ at HiMom:1:1201:1140:2125/2
+TTCATAAATTGGTCTTAGATGTTGC
++
+CC at FFFFFHHHHFGIJIIIJIJIJJ
+ at HiMom:1:1201:1142:2242/2
+GTAAAATGTAAAATAATAAAAAATG
++
+?=?DDDD;AF<DF<FFFFIIIFF@<
+ at HiMom:1:1201:1150:2161/2
+TTCTCACTACTGTGATTGTGCCACT
++
+ at C@FFFFFGHHHHGIIIICEHCFGH
+ at HiMom:1:1201:1159:2179/2
+TTTTTTTTTATTTTTCTAAATACTT
++
+===AA####################
+ at HiMom:1:1201:1160:2109/2
+ACATCCTTCCCATGCCACCAACTCG
++
+CCCFFFFFGHHHHJJJJJJJJJJJJ
+ at HiMom:1:1201:1180:2119/2
+GCTCTAAATTTTGCTTTTCTACAGC
++
+CCCFFFFFHHHHHJJJJIJIJJIJJ
+ at HiMom:1:1201:1185:2143/2
+GCTGAAGGCCCGTGGGCCAGAGGTG
++
+ at CCFFFFFHHHHHJJJJJJJJJJHI
+ at HiMom:1:1201:1187:2100/2
+AAAAAAGAGCCCGCATTGCCGAGAC
++
+=<=;AA###################
+ at HiMom:1:1201:1190:2194/2
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1201:1204:2228/2
+TCTTCTTGTCGATGAGGAACTTGGT
++
+@?@FFFFFDHHGHJIJJGHIIJJJH
+ at HiMom:1:1201:1208:2132/2
+CTGTAGAAAGGATGGTCGGGCTCCA
++
+@@CDFFFFGHFHHJIJJGJIBHJJG
+ at HiMom:1:1201:1219:2115/2
+TGGGAGTAGTTCCCTGCTAAGGGAG
++
+???DBDBDADDDDIEID:AFFD:?8
+ at HiMom:1:1201:1236:2187/2
+CTCCTTAGCGGATTCCGACTTCCAT
++
+CCCFFFFDHHHHGIJJIGIGIJJGG
+ at HiMom:1:1201:1242:2207/2
+ATCTTTTATTGGCCTCCTGCTCCCC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1201:1252:2141/2
+AGTTATTTTGCCTATGTCCAACAAG
++
+BCBFFFFFGHHHHJIJJJJJJJJJJ
+ at HiMom:1:1201:1260:2165/2
+ATCTGATCTAAGTTGGGGGACGCCG
++
+@@@FFDFFHHHHHJJJIJIIIGIJJ
+ at HiMom:1:1201:1280:2179/2
+GAGGACTGCTTGAGTCCAGGAGTTC
++
+@@BFFDEFGHHHHIFGCHIJJJGGI
+ at HiMom:1:1201:1281:2133/2
+GCAACAAAATTTCATATGACTTAGC
++
+CCCFFFFFHHHHHJJIIIHICHIIJ
+ at HiMom:1:1201:1285:2100/2
+GATCTTTTTTGCTTTGTAGTTATAG
++
+@@@DFFFFHHHHHIIGIABCFFHBF
+ at HiMom:1:1201:1291:2158/2
+CGTGTGCTCTTCCGATCTGATGGGC
++
+ at CCFFFDD?FHHFGEHHIIDHIIII
+ at HiMom:1:1201:1300:2137/2
+GCTCTTCCGATCTTTTTTTTAATTT
++
+@@?DDDDDFDHADEHGIGGED3?FD
+ at HiMom:1:1201:1312:2112/2
+ATTTGCAGGAGCCGGCGCAGGTGCA
++
+CCCFFFFFHHHHHJJJIJJJJGHIJ
+ at HiMom:1:1201:1331:2162/2
+TAATCCCAGTACTTTGGGAGGCCAA
++
+CCCFFFFFHHHHHJJJJIJJJJJJJ
+ at HiMom:1:1201:1341:2116/2
+ATAACAGCGAGACTGGCAACTTAAA
++
+#########################
+ at HiMom:1:1201:1344:2147/2
+ACGATTAGTTTTAGCATTGGAGTAG
++
+@<??DDDDFHHHFGGHHIIIGGAGH
+ at HiMom:1:1201:1345:2181/2
+ATACGGATGTGTTTAGGAGTGGGAC
++
+CCCFFFFFHHHHHIIJJHJFHIJIJ
+ at HiMom:1:1201:1364:2113/2
+TAAAGAGAGCCAGTGGAGTTACGAC
++
+#########################
+ at HiMom:1:1201:1392:2109/2
+GTCAGACAGGGGGATTTGGGCTGTG
++
+BBCFFFFFHHHHHHJJJHIJIJJJJ
+ at HiMom:1:1201:1392:2184/2
+ATCTTTATTCATTTGTATGATCTTA
++
+@@BFFFFFHFFHFHIHIIJIJJJJI
+ at HiMom:1:1201:1393:2143/2
+GATAAATGCACGCATCCCCCCCGCG
++
+C at CFFFFFGGHHHHJJJJJJJJJJI
+ at HiMom:1:1201:1414:2174/2
+TTTTTTTTTTTTTTTTTTTTTTTTT
++
+@;@1BDADF????FFEB>B6=BBBB
+ at HiMom:1:1201:1416:2128/2
+TTGGTGTGGAGGCGGTGGCGGGATC
++
+@@@DDDDDHHFHHII:?GGHIIB6?
+ at HiMom:1:1201:1421:2154/2
+TGTGCTCTTCCGATCTTGTGCTCTT
++
+BC at DFFFFHHHHHJJJJFHIHHIJJ
+ at HiMom:1:1201:1439:2156/2
+GGAGATTATTTGCCTTGAAGTAAGC
++
+-;(22<>>@>8@>8;@#########
+ at HiMom:1:1201:1452:2143/2
+TTTTAGTCTTAGCATTTACTTTCCC
++
+CCCFFFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:1201:1458:2109/2
+GATACGAACACACAAGAACTTTTTT
++
+CCCFFFFFHHHHHJJJJJJJJJJJI
+ at HiMom:1:1201:1472:2121/2
+GTGTGCTCTTCCGATCTGGAGGATG
++
+=+=??A4A==A at 7A<?#########
+ at HiMom:1:1201:1483:2126/2
+GCATGCAGCTGGGTGCTGTGATGCA
++
+@@@DDDBB<DD8F<<CGG?AA?A<F
+ at HiMom:1:1201:1486:2109/2
+ACGTGTGCTCTTCCCGATCTGTATA
++
+CCCFF?DDFBHHHJJIIDHJIJJJH
+ at HiMom:1:1201:1486:2146/2
+TTTTTTTTTTTTTTTTTTTTTGGGC
++
+<<<@??@??@???????########
+ at HiMom:1:2101:1011:2102/2
+NNNNNTCACACATAATTTTAAAATT
++
+#####22@?@@??@@@@@??@@@@@
+ at HiMom:1:2101:1013:2146/2
+NNNNCGCTAGAACCAACTTATTCAT
++
+####24=?@@?@?@@?@@@@@@?@@
+ at HiMom:1:2101:1021:2209/2
+NNGGAAGGCTGCTAGCTGGCCAGAG
++
+##08@>??@@??@?????????>?@
+ at HiMom:1:2101:1023:2237/2
+NNTTTGTTTGAGTTCCTTGTAGATT
++
+##0:=@?>?@???@:>?@??>?;?<
+ at HiMom:1:2101:1031:2163/2
+NNACATTTGTCACCACTAGCCACCA
++
+##0<@?@@@@@@@@@@?@@@@@@@?
+ at HiMom:1:2101:1036:2087/2
+NGTCCACTTACGAAGCAAATACTTT
++
+#4=DDFFFHHHHHJJJJJJJJJJJJ
+ at HiMom:1:2101:1040:2208/2
+NCTGATAGTCACTGAAATGAATTCA
++
+#-0=>(2 at .22@@############
+ at HiMom:1:2101:1048:2238/2
+NGTCACATCGTTGAAGCACTGGATC
++
+#11ADDDB<CFFHCHGDBHGIIIII
+ at HiMom:1:2101:1054:2162/2
+NGGACAGGGAAGGGAAGGAAGGGTG
++
+#4=DDFDFHHHHHJIJIIDHHGICG
+ at HiMom:1:2101:1059:2083/2
+NGAATGTCTTAGAAGGATGCTTCTC
++
+#1=BDDDEHHGHHJJJJJIJJIIJJ
+ at HiMom:1:2101:1063:2206/2
+NTGCTAGGATGAGGATGGATAGTAA
++
+#1=DDDFFHHHHHJHIIJHIIIHHJ
+ at HiMom:1:2101:1064:2242/2
+NGGAAAAAGGTTGTCAAGCGTTAAA
++
+#########################
+ at HiMom:1:2101:1072:2170/2
+NGGGGAGACAGAGAGGATCAGAAGT
++
+#4=BDDFDHHDFHEGFEGGIJIIIG
+ at HiMom:1:2101:1077:2139/2
+NATTAGTTGGCGGATGAAGCAGATA
++
+#4=DFFFFHHHHHJJJJJJJJJIJJ
+ at HiMom:1:2101:1084:2188/2
+TACAAGGTCAAAATCAGCAACAAGT
++
+CCCFFFFDHHHHHJJJJJJJJJJJJ
+ at HiMom:1:2101:1100:2085/2
+ATCTTGATCTCCTCCTTCTTGGCCT
++
+@@@DDDDDHHFHFEIIIIHHBAHBG
+ at HiMom:1:2101:1102:2221/2
+ATAACTGACTCTACTCAGTAGATTA
++
+CCCFFFFFHHHHHJJJJJIJJJJJJ
+ at HiMom:1:2101:1105:2131/2
+CAGCAGCAGCAACAGCAGAAACATG
++
+CCCFFFFFHHHHHJJJJJIJJJJJJ
+ at HiMom:1:2101:1112:2245/2
+TCGTAGTGTTGTAATTTCGTCTTCT
++
+?8?DBDDDCCFCAACGGFFCBFFAE
+ at HiMom:1:2101:1122:2136/2
+CTTGCCAGCCTGCAGGCCCCGCGGC
++
+???BBAABDD?DDIID)A:3<EADD
+ at HiMom:1:2101:1123:2095/2
+TCCGCCTCCAGCTTCAGCTTCTCCT
++
+@@@FDDFFHHHHHJHGGJIJJJEHH
+ at HiMom:1:2101:1126:2082/2
+TCTCTTTCCACCTTGGTCACCTTCC
++
+ at C@DDDFFHHHHHJEGGIHHIJGIH
+ at HiMom:1:2101:1133:2239/2
+AGCTTTTTGTTTCCTAGCTTGTCTT
++
+?@?DDFFFHHHHF4ACFHIJHHHGH
+ at HiMom:1:2101:1143:2137/2
+GCTCTTCAGATCTAGGGGGAACAGC
++
+@@@DD?=DCAFFFHIIDG:EFHIII
+ at HiMom:1:2101:1151:2182/2
+TTTTTTTTTTTTTTTTTTTTTTTTA
++
+9<<?@?@;5=?##############
+ at HiMom:1:2101:1151:2236/2
+TTTGAAGCCTCTTTATCCTTGGCAT
++
+#########################
+ at HiMom:1:2101:1162:2139/2
+ATCGTTTATGGTCGGAACTACGACG
++
+BCCFFFFFHHHHHIJJJJJJJIJJI
+ at HiMom:1:2101:1163:2203/2
+TTGGTTCACTTATGTATTTATGAAT
++
+ at CCFDFFFHHHHHJHIIJJJJJJJJ
+ at HiMom:1:2101:1163:2222/2
+GAGCGATAATGGTTCTTTTCCTCAC
++
+@@@DFFFFHHHHHJJJJJJJIJJJJ
+ at HiMom:1:2101:1172:2152/2
+ATCGTTTCTGGGGACTAGTGAGGCG
++
+#########################
+ at HiMom:1:2101:1186:2093/2
+AATGTTGGGAGGACAATGATGGAAA
++
+#########################
+ at HiMom:1:2101:1188:2195/2
+GCACATACACCAAATGTCTGAACCT
++
+CCCFFFFFHHHHHJJJHIJJJJJJJ
+ at HiMom:1:2101:1195:2150/2
+AATTGAACTTCACCACCCAGAGGAA
++
+CCCFFFFFHHHHHJJJJJJIJJJJJ
+ at HiMom:1:2101:1207:2084/2
+TCACCACTCTTCTGGGCATCCCCTG
++
+@@@DDEDFHHHHHIJIHHGHGGJJJ
+ at HiMom:1:2101:1208:2231/2
+CTTTTTTTTTTTTTTTTTTTTTTTT
++
+CCCFFFFFHHHHHJJJHFDDDDDDD
+ at HiMom:1:2101:1215:2110/2
+ATCTTTCCCCCATTAAGAACAGCAA
++
+#########################
+ at HiMom:1:2101:1216:2172/2
+GGACTTCTAGGGGATTTAGCGGGGT
++
+CCCFFFFFHHHHHJJJJJJJJJJJD
+ at HiMom:1:2101:1216:2193/2
+AGGCATGACACTGCATTTTAAATAC
++
+@@@DDDDDHFFHHGGDFHFHIIHGG
+ at HiMom:1:2101:1226:2088/2
+GCTCTTCCGATCTAGGTAATAGCTA
++
+==?BDFFFDCDDHFFFAFHDHIJGJ
+ at HiMom:1:2101:1231:2208/2
+AGCCAGTGTTGGTGTGTTGACTGTT
++
+@@;1ADABCF;BF<AACGCHEBHC<
+ at HiMom:1:2101:1233:2133/2
+TTTTTTTTTTTTTTTTTTTTTTTTT
++
+CCCFFFFFGHHHHJJJFDDDDDDDD
+ at HiMom:1:2101:1240:2197/2
+ACTGGAGATCCTTGTTACATGCCCA
++
+??+++A:DD?:ADEE@::C4:C<E:
+ at HiMom:1:2101:1245:2154/2
+ACCAATCAGTAGCACCACTATACAC
++
+CCCFFFFFHHHHHJJJJJJIJJJJJ
+ at HiMom:1:2101:1249:2231/2
+TCTCTCGGCCTTCCACTCTAGCATA
++
+@@@FFFFFFHHGHIJJJGJIIJHIJ
+ at HiMom:1:2101:1258:2092/2
+TTAGACAAAACACCAAAATAAAATA
++
+#########################
+ at HiMom:1:2101:1262:2128/2
+TCTTGTGGTAACTTTTCTGACACCT
++
+-(---9@;@?:8>?4:>?@######
+ at HiMom:1:2101:1273:2119/2
+ATGATGGATCTTCTCTAACTTGTCA
++
+>=><AAAAA+2AA?CB4@@ABB3?A
+ at HiMom:1:2101:1285:2105/2
+TGTCTATATCAACCAACACCTCTTC
++
+-(0(():94:9:???##########
+ at HiMom:1:2101:1312:2105/2
+GTTGAGAATAGGTTGAGATCGTTTC
++
+ at CCFFFDFHHFHDHIJJJJJJJIJJ
+ at HiMom:1:2101:1325:2083/2
+TGTGCTCTTCCGATCTGGAGAAAAA
++
+#########################
+ at HiMom:1:2101:1336:2109/2
+AGACCAGAACAGCTCCAGGTGCTCC
++
+CCCFFFFFHHHHHJJJJJJCGHIJJ
+ at HiMom:1:2101:1349:2084/2
+AGTCTGAATCATTGGTGTCTGAAGA
++
+<5;??=>=>>?##############
+ at HiMom:1:2101:1365:2094/2
+GCTCTTCCGATCTTGTGCTCTTCCG
++
+CCCFFFFDHFHHGJJIIJIJJIHII
+ at HiMom:1:2101:1370:2116/2
+CACCATCTGACATCATGTTTGAAAG
++
+@@@DFFFDFFHDHIGBHHII<HEDB
+ at HiMom:1:2101:1386:2105/2
+AGGAATTATTCTTCTGCCATAAGGT
++
+B@@DDFFFHGFHHIJJJJJGIGIJH
+ at HiMom:1:2101:1414:2098/2
+TTGGGGCCGGTGCCGTCGGGCCCAA
++
+CCCFFFFFHHHHGJJIJJJJJJJIJ
+ at HiMom:1:2101:1427:2081/2
+CCGACTTCCATGGCCACCGTCCTGC
++
+CCCFFFFFHHHHHJJJIIGFIIJJI
+ at HiMom:1:2101:1450:2134/2
+ACAAACCCTTGTGTCGAGGGCTGAC
++
+CC at FDFDFFDFHFGIIE1CGGHBGE
+ at HiMom:1:2101:1459:2083/2
+ATTTCACCAAAATAATCAGAAGGCC
++
+CCCFFFFDBHGHHIGGIJFJJGGFH
+ at HiMom:1:2101:1491:2093/2
+AGAGACGGGGTCTCGCTATGTTGCC
++
+BCCDFFFFHHHHHJIIJJJJIJIJJ
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplexRH.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplexRH.barcode_1.fastq
new file mode 100644
index 0000000..2c21292
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplexRH.barcode_1.fastq
@@ -0,0 +1,720 @@
+ at HiMom:1:1101:1031:2224
+NNNNNNNN
++
+########
+ at HiMom:1:1101:1039:2147
+NNNNNNNN
++
+########
+ at HiMom:1:1101:1046:2175
+NNNNNNNN
++
+########
+ at HiMom:1:1101:1047:2122
+NNNANNNN
++
+########
+ at HiMom:1:1101:1048:2197
+NNNCNNNN
++
+########
+ at HiMom:1:1101:1065:2193
+GAACGATN
++
+########
+ at HiMom:1:1101:1069:2159
+GTCCACAG
++
+ at BBFFFFF
+ at HiMom:1:1101:1071:2233
+TATCCAGG
++
+CCCFFFFF
+ at HiMom:1:1101:1083:2193
+CCAACATT
++
+?@;DD?BD
+ at HiMom:1:1101:1084:2136
+TGCTGCTG
++
+CCCFFFFF
+ at HiMom:1:1101:1089:2172
+GACCAGGA
++
+?@@FF;=B
+ at HiMom:1:1101:1100:2207
+ATTATCAA
++
+CCCFFFFF
+ at HiMom:1:1101:1111:2148
+GCCGTCGA
++
+CCCFFFFF
+ at HiMom:1:1101:1138:2141
+AACAATGG
++
+CCCFFFFF
+ at HiMom:1:1101:1140:2120
+CAACTCTC
++
+@@@DDFDF
+ at HiMom:1:1101:1143:2192
+TCGCTAGA
++
+CCCFFFFF
+ at HiMom:1:1101:1150:2228
+AGGTCGCA
++
+@@@DDFFF
+ at HiMom:1:1101:1157:2135
+ATTATCAA
++
+C at CFFFFF
+ at HiMom:1:1101:1162:2207
+ACAAAATT
++
+########
+ at HiMom:1:1101:1165:2239
+GCCTAGCC
++
+B@@DFFFF
+ at HiMom:1:1101:1175:2197
+CCAACATT
++
+CCCFFFFF
+ at HiMom:1:1101:1188:2237
+GTAACATC
++
+@@?DFFDF
+ at HiMom:1:1101:1197:2200
+AACGCATT
++
+ at CCFDFFF
+ at HiMom:1:1101:1206:2126
+AACAATGG
++
+CCCFFFFF
+ at HiMom:1:1101:1212:2230
+CCAGCACC
++
+CCCFFFFF
+ at HiMom:1:1101:1218:2200
+GACCGTTG
++
+ at CCFFDDF
+ at HiMom:1:1101:1219:2164
+TTGTCTAT
++
+CCCFFFFF
+ at HiMom:1:1101:1221:2143
+GCCGTCGA
++
+@@CDDDDF
+ at HiMom:1:1101:1236:2121
+ACAGGTAT
++
+CCCFFDDF
+ at HiMom:1:1101:1242:2170
+TGCAAGTA
++
+@@CFFF?D
+ at HiMom:1:1101:1257:2223
+GACCGTTG
++
+;@@DD=DD
+ at HiMom:1:1101:1259:2152
+ACTAAGAC
++
+CCCFFFFF
+ at HiMom:1:1101:1261:2127
+ACTAAGAC
++
+>7+ at A7A7
+ at HiMom:1:1101:1263:2236
+AGGTAAGG
++
+########
+ at HiMom:1:1101:1267:2209
+TATCAGCC
++
+?@@D;ADD
+ at HiMom:1:1101:1269:2170
+ATTATCAA
++
+@@@DDDF?
+ at HiMom:1:1101:1290:2225
+GCCTAGCC
++
+?<@DFBBD
+ at HiMom:1:1101:1291:2150
+CGCTATGT
++
+@@@FFFFF
+ at HiMom:1:1101:1302:2244
+GACCTAAC
++
+CCCFFFFF
+ at HiMom:1:1101:1308:2153
+AACGCATT
++
+:?@B?@DD
+ at HiMom:1:1101:1309:2210
+ATTCCTCT
++
+?@@ADEEF
+ at HiMom:1:1101:1314:2233
+CGCTATGT
++
+@<@?B@;A
+ at HiMom:1:1101:1316:2126
+CAATAGAC
++
+1>>7A###
+ at HiMom:1:1101:1327:2200
+GCCGTCGA
++
+BCCFDFFD
+ at HiMom:1:1101:1328:2225
+CAACTCTC
++
+??;=A:B=
+ at HiMom:1:1101:1338:2175
+GAAGGAAG
++
+CCCFFFFF
+ at HiMom:1:1101:1347:2149
+GACCAGGA
++
+CC at DFFFD
+ at HiMom:1:1101:1353:2226
+TATCTGCC
++
+ at B@FFEFF
+ at HiMom:1:1101:1363:2138
+CTAACTCG
++
+CCCFFFFF
+ at HiMom:1:1101:1399:2128
+CAATAGTC
++
+CCCFFFFF
+ at HiMom:1:1101:1403:2194
+CTGTAATC
++
+CCCFFFFF
+ at HiMom:1:1101:1406:2222
+AGCATGGA
++
+C@@DBFEF
+ at HiMom:1:1101:1419:2119
+TGTAATCA
++
+@@@DFDFD
+ at HiMom:1:1101:1420:2213
+CAGCGGTA
++
+ at C@FFFDF
+ at HiMom:1:1101:1435:2194
+TATCTGCC
++
+CCCFFFFF
+ at HiMom:1:1101:1441:2148
+CGCTATGT
++
+@@BFFDDD
+ at HiMom:1:1101:1452:2132
+AACGCATT
++
+ at CCFFFFF
+ at HiMom:1:1101:1460:2176
+GATATCCA
++
+CCCFFFFF
+ at HiMom:1:1101:1479:2221
+TCGCTAGA
++
+ at BCFFFFF
+ at HiMom:1:1101:1491:2120
+AGGTCGCA
++
+BCCDFFFF
+ at HiMom:1:1201:1018:2133
+ATTCCTCT
++
+8??=BBBA
+ at HiMom:1:1201:1018:2217
+ATTATCAA
++
+;<;:BBDD
+ at HiMom:1:1201:1028:2202
+GAAGGAAG
++
+CCCFFDFF
+ at HiMom:1:1201:1042:2174
+TCTGCAAG
++
+CCCFFFFF
+ at HiMom:1:1201:1043:2246
+CGCTATGT
++
+@<?DD:B=
+ at HiMom:1:1201:1045:2105
+CTGTAATC
++
+1112 at A##
+ at HiMom:1:1201:1054:2151
+CAATAGTC
++
+CCCFFFDF
+ at HiMom:1:1201:1064:2239
+TAAGCACA
++
+@@@FFADB
+ at HiMom:1:1201:1073:2225
+ATTCCTCT
++
+B@@BDEFF
+ at HiMom:1:1201:1083:2121
+CTATGCGT
++
+CCCFFFFD
+ at HiMom:1:1201:1084:2204
+TATCTGCC
++
+CCCFFFFF
+ at HiMom:1:1201:1095:2146
+GACCAGGA
++
+CCCFFFFF
+ at HiMom:1:1201:1103:2184
+TTGTCTAT
++
+ at CCFFFFF
+ at HiMom:1:1201:1107:2109
+TTGTCTAT
++
+B at CFFFFF
+ at HiMom:1:1201:1118:2198
+ATTATCAA
++
+@@@DDBDD
+ at HiMom:1:1201:1122:2227
+CGCCTTCC
++
+@@@DDFFF
+ at HiMom:1:1201:1123:2161
+GACCAGGA
++
+?;@DFDFF
+ at HiMom:1:1201:1127:2112
+CAACTCTC
++
+=??BA?BD
+ at HiMom:1:1201:1134:2144
+CGCTATGT
++
+CCCFFFFD
+ at HiMom:1:1201:1138:2227
+CCAACATT
++
+########
+ at HiMom:1:1201:1140:2125
+TATCCAGG
++
+CCCFFFFF
+ at HiMom:1:1201:1142:2242
+TATCTGCC
++
+??<D?D83
+ at HiMom:1:1201:1150:2161
+AACGCATT
++
+@@@FDDDD
+ at HiMom:1:1201:1159:2179
+AAAAAAAA
++
+########
+ at HiMom:1:1201:1160:2109
+CGCCTTCC
++
+C at BFFFFF
+ at HiMom:1:1201:1180:2119
+GACCGTTG
++
+CCCFFDFF
+ at HiMom:1:1201:1185:2143
+CTATGCGT
++
+CCCFFFFF
+ at HiMom:1:1201:1187:2100
+TATCTGCC
++
+CCCFFFFF
+ at HiMom:1:1201:1190:2194
+AGGTCGCA
++
+CCCFFFFF
+ at HiMom:1:1201:1204:2228
+CCAGCACC
++
+CCCFFFFF
+ at HiMom:1:1201:1208:2132
+TGTAATCA
++
+CC at FFFFF
+ at HiMom:1:1201:1219:2115
+CCATGCGT
++
+??<DDA?D
+ at HiMom:1:1201:1236:2187
+TATCCAGG
++
+@@BFFFFF
+ at HiMom:1:1201:1242:2207
+ATTCCTCT
++
+?BBDDDFF
+ at HiMom:1:1201:1252:2141
+TTGTCTAT
++
+CCCFFFFF
+ at HiMom:1:1201:1260:2165
+CCAACATT
++
+C at CFFFFF
+ at HiMom:1:1201:1280:2179
+GCCTAGCC
++
+BCCFFFFF
+ at HiMom:1:1201:1281:2133
+CCAACATT
++
+C at CFFFDF
+ at HiMom:1:1201:1285:2100
+TGCTGCTG
++
+@@@FFFFF
+ at HiMom:1:1201:1291:2158
+AGCATGGA
++
+ at CCFFFFF
+ at HiMom:1:1201:1300:2137
+GCCTAGCC
++
+8?84B23?
+ at HiMom:1:1201:1312:2112
+TCGCTAGA
++
+CCCFFFFF
+ at HiMom:1:1201:1331:2162
+CCAACATT
++
+CCCFFFFF
+ at HiMom:1:1201:1341:2116
+ACAGGTAT
++
+CCCFFBDD
+ at HiMom:1:1201:1344:2147
+TGTAATCA
++
+=?1AA:=D
+ at HiMom:1:1201:1345:2181
+CAATAGTC
++
+CCCFFFFF
+ at HiMom:1:1201:1364:2113
+CAGCGGTA
++
+C at CFFF@D
+ at HiMom:1:1201:1392:2109
+TATCTGCC
++
+CCCDF?DD
+ at HiMom:1:1201:1392:2184
+CAATAGTC
++
+ at CCFFDDE
+ at HiMom:1:1201:1393:2143
+CTAACTCG
++
+@@CFDDFD
+ at HiMom:1:1201:1414:2174
+AGAAAAGA
++
+########
+ at HiMom:1:1201:1416:2128
+TCGCTAGA
++
+CCCFFFFF
+ at HiMom:1:1201:1421:2154
+TGTAACTC
++
+@@@FFFFF
+ at HiMom:1:1201:1439:2156
+GACCAGGC
++
+########
+ at HiMom:1:1201:1452:2143
+CAACTCTC
++
+BC at DDFFF
+ at HiMom:1:1201:1458:2109
+ACTGTATC
++
+CCCFFFFF
+ at HiMom:1:1201:1472:2121
+CTATGCGC
++
+;?=D####
+ at HiMom:1:1201:1483:2126
+CTGTAATC
++
+ at C<DD:B?
+ at HiMom:1:1201:1486:2109
+GTCCACAG
++
+CCCFFFFD
+ at HiMom:1:1201:1486:2146
+CAACTCTC
++
+?@@1:DBD
+ at HiMom:1:2101:1011:2102
+CTGTAATC
++
+C at CFFFFF
+ at HiMom:1:2101:1013:2146
+CTATGCGT
++
+CCCFFFFF
+ at HiMom:1:2101:1021:2209
+ACTAAGAC
++
+ at CCDFFFF
+ at HiMom:1:2101:1023:2237
+GCCTAGCC
++
+########
+ at HiMom:1:2101:1031:2163
+GATATCCA
++
+B at BFFFFF
+ at HiMom:1:2101:1036:2087
+GACCGTTG
++
+B at CFFDFF
+ at HiMom:1:2101:1040:2208
+ACGAAATC
++
+########
+ at HiMom:1:2101:1048:2238
+ACAGTTGA
++
+?@7DDDDA
+ at HiMom:1:2101:1054:2162
+AGGTAAGG
++
+B at BDDFFF
+ at HiMom:1:2101:1059:2083
+TACCGTCT
++
+1:?D####
+ at HiMom:1:2101:1063:2206
+ACAGGTAT
++
+CCCFFDFF
+ at HiMom:1:2101:1064:2242
+TCGCTAGA
++
+;@<:AA at A
+ at HiMom:1:2101:1072:2170
+CAGCGGTA
++
+B@@DFDDF
+ at HiMom:1:2101:1077:2139
+AACAATGG
++
+CCCFFFFF
+ at HiMom:1:2101:1084:2188
+GAAGGAAG
++
+ at B@FFFFF
+ at HiMom:1:2101:1100:2085
+CCAGCACC
++
+CCCFFFFF
+ at HiMom:1:2101:1102:2221
+CTGCGGAT
++
+CCCFFFFF
+ at HiMom:1:2101:1105:2131
+ACTGTATC
++
+CCCFFFFF
+ at HiMom:1:2101:1112:2245
+AACAATGG
++
+@@?BBDDD
+ at HiMom:1:2101:1122:2136
+GCCGTCGA
++
+?@<DDDD?
+ at HiMom:1:2101:1123:2095
+CAGCGGTA
++
+@?@DDF@@
+ at HiMom:1:2101:1126:2082
+CTGCGGAT
++
+@@@FFFDA
+ at HiMom:1:2101:1133:2239
+TATCCATG
++
+@@@BDDDF
+ at HiMom:1:2101:1143:2137
+TCCGTCTA
++
+########
+ at HiMom:1:2101:1151:2182
+GAAAAAAA
++
+########
+ at HiMom:1:2101:1151:2236
+TAGCGGTA
++
+########
+ at HiMom:1:2101:1162:2139
+TGCTGCTG
++
+CCCFFFFF
+ at HiMom:1:2101:1163:2203
+AGGTAAGG
++
+CCCFFFFF
+ at HiMom:1:2101:1163:2222
+TGCAAGTA
++
+CCCFFFEF
+ at HiMom:1:2101:1172:2152
+CAATAGTC
++
+########
+ at HiMom:1:2101:1186:2093
+CCAACATT
++
+CCCFFFFF
+ at HiMom:1:2101:1188:2195
+AGGTCGCA
++
+BCCDFFFF
+ at HiMom:1:2101:1195:2150
+TGCTGCTG
++
+CCCFFFFF
+ at HiMom:1:2101:1207:2084
+GACCAGGA
++
+@@CDFFFF
+ at HiMom:1:2101:1208:2231
+GTAACATC
++
+1+:A1A22
+ at HiMom:1:2101:1215:2110
+AAAAGAAG
++
+########
+ at HiMom:1:2101:1216:2172
+CAGCGGAT
++
+C at CFFFFF
+ at HiMom:1:2101:1216:2193
+ACAGTTGA
++
+CCCFFFFF
+ at HiMom:1:2101:1226:2088
+GATATCCA
++
+@@@:DDDD
+ at HiMom:1:2101:1231:2208
+CTATGCGT
++
+@<@?D8 at D
+ at HiMom:1:2101:1233:2133
+CTATGCGT
++
+=??B####
+ at HiMom:1:2101:1240:2197
+AACGCATT
++
+88+AD@?8
+ at HiMom:1:2101:1245:2154
+CTGTAATC
++
+ at CCFFFFF
+ at HiMom:1:2101:1249:2231
+AGGTAAGG
++
+@@CBDFFF
+ at HiMom:1:2101:1258:2092
+TAAGCACA
++
+@@CDDFFF
+ at HiMom:1:2101:1262:2128
+ACTAAGAC
++
+1+8?ADD8
+ at HiMom:1:2101:1273:2119
+CTAACTCG
++
+=++==ADB
+ at HiMom:1:2101:1285:2105
+TATCTCGG
++
+########
+ at HiMom:1:2101:1312:2105
+GACCAGGA
++
+CCCFFFFF
+ at HiMom:1:2101:1325:2083
+ACAGGTAT
++
+@@@BD=DD
+ at HiMom:1:2101:1336:2109
+AACGCATT
++
+CCCFFFFF
+ at HiMom:1:2101:1349:2084
+ACTGTATC
++
+=;7+22<A
+ at HiMom:1:2101:1365:2094
+ACTGTACC
++
+########
+ at HiMom:1:2101:1370:2116
+AGCATGGA
++
+?:8A?3:B
+ at HiMom:1:2101:1386:2105
+CTGTAATC
++
+CCCFFFFF
+ at HiMom:1:2101:1414:2098
+CTAACTCG
++
+CCCFFFFF
+ at HiMom:1:2101:1427:2081
+AACGCATT
++
+CCCFFFFF
+ at HiMom:1:2101:1450:2134
+ACCAGTTG
++
+ at C@DDDB?
+ at HiMom:1:2101:1459:2083
+GCCGTCGA
++
+@@CFDDFD
+ at HiMom:1:2101:1491:2093
+CAATAGTC
++
+@@@FDEBD
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/AAAAAAAA.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/AAAAAAAA.sam
new file mode 100644
index 0000000..15e09bc
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/AAAAAAAA.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.AAAAAAAA LB:LN_AAAAAAAA SM:SA_AAAAAAAA CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/AAAAGAAG.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/AAAAGAAG.sam
new file mode 100644
index 0000000..fd8b3c0
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/AAAAGAAG.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.AAAAGAAG LB:LN_AAAAGAAG SM:SA_AAAAGAAG CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/AACAATGG.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/AACAATGG.sam
new file mode 100644
index 0000000..d92fa14
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/AACAATGG.sam
@@ -0,0 +1,10 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.AACAATGG LB:LN_AACAATGG SM:SA_AACAATGG CN:BI
+HiMom:1:1101:1138:2141 77 * 0 0 * * 0 0 .TTACCAAGGTTTTCTGTTTAGTGA #1=DDFFFHHFHHJJJIHJIJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1138:2141 141 * 0 0 * * 0 0 TCCGATCTGCTTCAGGTCGATCAGA CCCFFFFFHGHHHJJIGHIJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1206:2126 77 * 0 0 * * 0 0 .ATTCTGCCATATTGGTCCGACAGT #1=DDFFFHHHHHJJJJJJJJJIJJ RG:Z:HiMom.1
+HiMom:1:1101:1206:2126 141 * 0 0 * * 0 0 ATCTGTCCAGTGGTGCACTGAATGT CCCFFFFFHHHHHHIIJJJJIJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1077:2139 77 * 0 0 * * 0 0 CACAGGCTTCCACGGACTTAACGTC CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1077:2139 141 * 0 0 * * 0 0 .ATTAGTTGGCGGATGAAGCAGATA #4=DFFFFHHHHHJJJJJJJJJIJJ RG:Z:HiMom.1
+HiMom:1:2101:1112:2245 77 * 0 0 * * 0 0 TGCCATCTGCTCTGGGAAGCACCAG 1:=DDDDDFBC:DEFIFFFIEF at BE RG:Z:HiMom.1
+HiMom:1:2101:1112:2245 141 * 0 0 * * 0 0 TCGTAGTGTTGTAATTTCGTCTTCT ?8?DBDDDCCFCAACGGFFCBFFAE RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/AACGCATT.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/AACGCATT.sam
new file mode 100644
index 0000000..ed00daa
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/AACGCATT.sam
@@ -0,0 +1,16 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.AACGCATT LB:LN_AACGCATT SM:SA_AACGCATT CN:BI
+HiMom:1:1101:1197:2200 77 * 0 0 * * 0 0 GGGCGCCCCGTGAGGACCCAGTCCT @C at FFADDFFCFCEHIIJIJJIEFC RG:Z:HiMom.1
+HiMom:1:1101:1197:2200 141 * 0 0 * * 0 0 ATATTCCACTGGAACCACAGAACCC @@@FFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1308:2153 589 * 0 0 * * 0 0 TTTTGGAAGAGACCTCAATTACTGT ???DDDDD?:22AE:A2<3,AF?3A RG:Z:HiMom.1
+HiMom:1:1101:1308:2153 653 * 0 0 * * 0 0 TCTGTAAGGTAATCCCCGCATGTGT 1?1=4===AFFDFFGFDGFB at CFB: RG:Z:HiMom.1
+HiMom:1:1101:1452:2132 77 * 0 0 * * 0 0 .CGTCCTGGAAAACGGGGCGCGGCT #1=BDBDDFHHHHF at FHDHIGIIII RG:Z:HiMom.1
+HiMom:1:1101:1452:2132 141 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHJJJJJJJIJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1150:2161 77 * 0 0 * * 0 0 AAGTCACCTAATATCTTTTTTTTTT @@<??;?D?CFD,A4CDDHFBIIID RG:Z:HiMom.1
+HiMom:1:1201:1150:2161 141 * 0 0 * * 0 0 TTCTCACTACTGTGATTGTGCCACT @C at FFFFFGHHHHGIIIICEHCFGH RG:Z:HiMom.1
+HiMom:1:2101:1240:2197 589 * 0 0 * * 0 0 ATAAAACATAGCAATATTTTCCTAT ######################### RG:Z:HiMom.1
+HiMom:1:2101:1240:2197 653 * 0 0 * * 0 0 ACTGGAGATCCTTGTTACATGCCCA ??+++A:DD?:ADEE@::C4:C<E: RG:Z:HiMom.1
+HiMom:1:2101:1336:2109 77 * 0 0 * * 0 0 .ACTATCAGGATCGTGGCTATTTTG #1BDDFFFHHHHHJIJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1336:2109 141 * 0 0 * * 0 0 AGACCAGAACAGCTCCAGGTGCTCC CCCFFFFFHHHHHJJJJJJCGHIJJ RG:Z:HiMom.1
+HiMom:1:2101:1427:2081 77 * 0 0 * * 0 0 .CGAGTGCCTAGTGGGCCACTTTTG #4=DDBDFHHHHFHIJJJJIJJJJI RG:Z:HiMom.1
+HiMom:1:2101:1427:2081 141 * 0 0 * * 0 0 CCGACTTCCATGGCCACCGTCCTGC CCCFFFFFHHHHHJJJIIGFIIJJI RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/ACAAAATT.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/ACAAAATT.sam
new file mode 100644
index 0000000..042986f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/ACAAAATT.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ACAAAATT LB:LN_ACAAAATT SM:SA_ACAAAATT CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/ACAGGTAT.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/ACAGGTAT.sam
new file mode 100644
index 0000000..8d8481d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/ACAGGTAT.sam
@@ -0,0 +1,10 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ACAGGTAT LB:LN_ACAGGTAT SM:SA_ACAGGTAT CN:BI
+HiMom:1:1101:1236:2121 77 * 0 0 * * 0 0 .GGTGCTTCATATCCCTCTAGAGGA #1=BDDFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1236:2121 141 * 0 0 * * 0 0 TTGCGCTTACTTTGTAGCCTTCATC CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1341:2116 77 * 0 0 * * 0 0 .AGAAGCCCCAGGAGGAAGACAGTC #1=DDFFFHHHHHHHJIIJJJJJGI RG:Z:HiMom.1
+HiMom:1:1201:1341:2116 141 * 0 0 * * 0 0 ATAACAGCGAGACTGGCAACTTAAA ######################### RG:Z:HiMom.1
+HiMom:1:2101:1063:2206 77 * 0 0 * * 0 0 TCCTATTCGCCTACACAATTCTCCG CCCFFFFFHHHHHJJJJJJJHJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1063:2206 141 * 0 0 * * 0 0 .TGCTAGGATGAGGATGGATAGTAA #1=DDDFFHHHHHJHIIJHIIIHHJ RG:Z:HiMom.1
+HiMom:1:2101:1325:2083 77 * 0 0 * * 0 0 .CAGAAGAAAGGGCCTTGTCGGAGG #1=DDDDDHHFHDGI at EEHG:?FA8 RG:Z:HiMom.1
+HiMom:1:2101:1325:2083 141 * 0 0 * * 0 0 TGTGCTCTTCCGATCTGGAGAAAAA ######################### RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/ACAGTTGA.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/ACAGTTGA.sam
new file mode 100644
index 0000000..805405f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/ACAGTTGA.sam
@@ -0,0 +1,6 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ACAGTTGA LB:LN_ACAGTTGA SM:SA_ACAGTTGA CN:BI
+HiMom:1:2101:1048:2238 77 * 0 0 * * 0 0 .CTGCCGTGTCCTGACTTCTGGAAT #1:B?ADDACF<DCG;EG<FHH at CE RG:Z:HiMom.1
+HiMom:1:2101:1048:2238 141 * 0 0 * * 0 0 .GTCACATCGTTGAAGCACTGGATC #11ADDDB<CFFHCHGDBHGIIIII RG:Z:HiMom.1
+HiMom:1:2101:1216:2193 77 * 0 0 * * 0 0 TTTTCTTGGCCTCTGTTTTTTTTTT BCCFDFFFHHFFHJIGIJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1216:2193 141 * 0 0 * * 0 0 AGGCATGACACTGCATTTTAAATAC @@@DDDDDHFFHHGGDFHFHIIHGG RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/ACCAGTTG.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/ACCAGTTG.sam
new file mode 100644
index 0000000..ff3130b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/ACCAGTTG.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ACCAGTTG LB:LN_ACCAGTTG SM:SA_ACCAGTTG CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/ACGAAATC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/ACGAAATC.sam
new file mode 100644
index 0000000..a525086
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/ACGAAATC.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ACGAAATC LB:LN_ACGAAATC SM:SA_ACGAAATC CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/ACTAAGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/ACTAAGAC.sam
new file mode 100644
index 0000000..9d4aada
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/ACTAAGAC.sam
@@ -0,0 +1,10 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ACTAAGAC LB:LN_ACTAAGAC SM:SA_ACTAAGAC CN:BI
+HiMom:1:1101:1259:2152 77 * 0 0 * * 0 0 CACCTATAATCCCAGCTACTCCAGA CCCFFFFFHHHHHJJJJJJIJJJIJ RG:Z:HiMom.1
+HiMom:1:1101:1259:2152 141 * 0 0 * * 0 0 ATTTTTATATTTTTTTAGACATAGG CCCFFFFFGHHHHJJJJIGIIJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1261:2127 589 * 0 0 * * 0 0 .TGAAATCTGGATAGGCTGGAGTTA #0-@@@################### RG:Z:HiMom.1
+HiMom:1:1101:1261:2127 653 * 0 0 * * 0 0 TTTTTTTTTTTTTTTTTTTTTTTTT CCCFFFFFHGHHHJJIFDDDDDDDD RG:Z:HiMom.1
+HiMom:1:2101:1021:2209 77 * 0 0 * * 0 0 .GGCCCCACCCTCCTCCAGCACGTC #1=DDFFFHHHHHJJJJJJHIIHFH RG:Z:HiMom.1
+HiMom:1:2101:1021:2209 141 * 0 0 * * 0 0 ..GGAAGGCTGCTAGCTGGCCAGAG ##08@>??@@??@?????????>?@ RG:Z:HiMom.1
+HiMom:1:2101:1262:2128 589 * 0 0 * * 0 0 AGCAGAAGGGCAAAAGCTGGCTTGA 9;<@:@################### RG:Z:HiMom.1
+HiMom:1:2101:1262:2128 653 * 0 0 * * 0 0 TCTTGTGGTAACTTTTCTGACACCT -(---9@;@?:8>?4:>?@###### RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/ACTGTACC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/ACTGTACC.sam
new file mode 100644
index 0000000..97f5e52
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/ACTGTACC.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ACTGTACC LB:LN_ACTGTACC SM:SA_ACTGTACC CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/ACTGTATC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/ACTGTATC.sam
new file mode 100644
index 0000000..a65e0b6
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/ACTGTATC.sam
@@ -0,0 +1,10 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ACTGTATC LB:LN_ACTGTATC SM:SA_ACTGTATC CN:BI
+HiMom:1:1201:1458:2109 77 * 0 0 * * 0 0 .GAGACCATAGAGCGGATGCTTTCA #1=DDDFFHHGHGIJJIGIIJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1458:2109 141 * 0 0 * * 0 0 GATACGAACACACAAGAACTTTTTT CCCFFFFFHHHHHJJJJJJJJJJJI RG:Z:HiMom.1
+HiMom:1:2101:1105:2131 77 * 0 0 * * 0 0 TTGGAACACAGCGGGAATCACAGCA CCCFFFFFHHHHHJIJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1105:2131 141 * 0 0 * * 0 0 CAGCAGCAGCAACAGCAGAAACATG CCCFFFFFHHHHHJJJJJIJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1349:2084 77 * 0 0 * * 0 0 .CAAGTAGCAGTGTCACGCCTTAGC #1=DDBDDADFDDBEH at HC=CEGG@ RG:Z:HiMom.1
+HiMom:1:2101:1349:2084 141 * 0 0 * * 0 0 AGTCTGAATCATTGGTGTCTGAAGA <5;??=>=>>?############## RG:Z:HiMom.1
+HiMom:1:2101:1365:2094 77 * 0 0 * * 0 0 .AAGGTGAAGGCCGGCGCGCTCGCC #1=BDDDFFHHHHJGGGIGFIHIIJ RG:Z:HiMom.1
+HiMom:1:2101:1365:2094 141 * 0 0 * * 0 0 GCTCTTCCGATCTTGTGCTCTTCCG CCCFFFFDHFHHGJJIIJIJJIHII RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/AGAAAAGA.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/AGAAAAGA.sam
new file mode 100644
index 0000000..2c9984e
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/AGAAAAGA.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.AGAAAAGA LB:LN_AGAAAAGA SM:SA_AGAAAAGA CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/AGCATGGA.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/AGCATGGA.sam
new file mode 100644
index 0000000..3eee1bc
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/AGCATGGA.sam
@@ -0,0 +1,8 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.AGCATGGA LB:LN_AGCATGGA SM:SA_AGCATGGA CN:BI
+HiMom:1:1101:1406:2222 77 * 0 0 * * 0 0 CTCCCCCCGGGCTGAACCAGGGTAC CCCFFDDDDHDFHIIIIIIIII9DG RG:Z:HiMom.1
+HiMom:1:1101:1406:2222 141 * 0 0 * * 0 0 GGCTGGACTCCCCTGGTTCTGGGCA ;?@DDDBD?FHDFGIIIGIGHHIII RG:Z:HiMom.1
+HiMom:1:1201:1291:2158 77 * 0 0 * * 0 0 AGAAGGGGAAAGCCTTCATCTTGGC BCBFFFFFHHHHHJJJJJIIFIJIJ RG:Z:HiMom.1
+HiMom:1:1201:1291:2158 141 * 0 0 * * 0 0 CGTGTGCTCTTCCGATCTGATGGGC @CCFFFDD?FHHFGEHHIIDHIIII RG:Z:HiMom.1
+HiMom:1:2101:1370:2116 77 * 0 0 * * 0 0 .TGGTGGTCCATAGAGATTTGAAAC #1:4BD7DACF?FCA:4+<ACHIIH RG:Z:HiMom.1
+HiMom:1:2101:1370:2116 141 * 0 0 * * 0 0 CACCATCTGACATCATGTTTGAAAG @@@DFFFDFFHDHIGBHHII<HEDB RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/AGGTAAGG.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/AGGTAAGG.sam
new file mode 100644
index 0000000..f9c4fae
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/AGGTAAGG.sam
@@ -0,0 +1,10 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.AGGTAAGG LB:LN_AGGTAAGG SM:SA_AGGTAAGG CN:BI
+HiMom:1:1101:1263:2236 589 * 0 0 * * 0 0 CTTTGAAGACATTGTGAGATCTGTA <==A<42 at C+A4A?,2A@=4 at 7A?? RG:Z:HiMom.1
+HiMom:1:1101:1263:2236 653 * 0 0 * * 0 0 AGTTCTTCAGTAATTTTAGTACTGC ######################### RG:Z:HiMom.1
+HiMom:1:2101:1054:2162 77 * 0 0 * * 0 0 .CCAGGTGTCTTCCCGGGCCCTGCC #1=DDFBDFHHHHJJJJJIJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1054:2162 141 * 0 0 * * 0 0 .GGACAGGGAAGGGAAGGAAGGGTG #4=DDFDFHHHHHJIJIIDHHGICG RG:Z:HiMom.1
+HiMom:1:2101:1163:2203 77 * 0 0 * * 0 0 TCTCCATGTGAAACAAGCAAAAAGA CCCFFFFFHHHHGJJJIJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1163:2203 141 * 0 0 * * 0 0 TTGGTTCACTTATGTATTTATGAAT @CCFDFFFHHHHHJHIIJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1249:2231 77 * 0 0 * * 0 0 GTTATTGATAGGATACTGTACAAAC @BCFFFFDHHHHFIJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1249:2231 141 * 0 0 * * 0 0 TCTCTCGGCCTTCCACTCTAGCATA @@@FFFFFFHHGHIJJJGJIIJHIJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/AGGTCGCA.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/AGGTCGCA.sam
new file mode 100644
index 0000000..d722d26
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/AGGTCGCA.sam
@@ -0,0 +1,10 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.AGGTCGCA LB:LN_AGGTCGCA SM:SA_AGGTCGCA CN:BI
+HiMom:1:1101:1150:2228 77 * 0 0 * * 0 0 GCTACTCAGTAGACAGTCCCACCCT @@CADDDDFCFHHIIIIGGIIGGGI RG:Z:HiMom.1
+HiMom:1:1101:1150:2228 141 * 0 0 * * 0 0 ATGGGAGGCGATTCCTAGGGGGTTG 8?=DD8;@BH6DHD<FGGGEIGHIG RG:Z:HiMom.1
+HiMom:1:1101:1491:2120 77 * 0 0 * * 0 0 .GGCAGGTGCCCCCACTTGACTCTC #1?DFFFFGHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1491:2120 141 * 0 0 * * 0 0 GGCCAGGCTGAACTTCTGAGCTGCT CCCFFFFFHHHGHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1190:2194 77 * 0 0 * * 0 0 AACCTGGCGCTAAACCATTCGTAGA CCCFFFFFHHHHHJJJJJJJJIJJJ RG:Z:HiMom.1
+HiMom:1:1201:1190:2194 141 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1188:2195 77 * 0 0 * * 0 0 TTAGACCGTCGTGAGACAGGTTAGT @CCFFFFFHHHHHJJJJJIIEHIJH RG:Z:HiMom.1
+HiMom:1:2101:1188:2195 141 * 0 0 * * 0 0 GCACATACACCAAATGTCTGAACCT CCCFFFFFHHHHHJJJHIJJJJJJJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/ATTATCAA.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/ATTATCAA.sam
new file mode 100644
index 0000000..5dc56b9
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/ATTATCAA.sam
@@ -0,0 +1,12 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ATTATCAA LB:LN_ATTATCAA SM:SA_ATTATCAA CN:BI
+HiMom:1:1101:1100:2207 77 * 0 0 * * 0 0 ACGACAGACGTTCTTTCTTTGCTGC CCCFFFFFHHFHHJIJJJJJHIJJH RG:Z:HiMom.1
+HiMom:1:1101:1100:2207 141 * 0 0 * * 0 0 AGGCT............G....... ######################### RG:Z:HiMom.1
+HiMom:1:1101:1157:2135 77 * 0 0 * * 0 0 .GGACATTGTAATCATTTCTTACAA #1=DD?DDHHHHHGGHIIIIIIIII RG:Z:HiMom.1
+HiMom:1:1101:1157:2135 141 * 0 0 * * 0 0 TTTAAAGTCTTAATCAAAGATGATA CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1269:2170 77 * 0 0 * * 0 0 ACAGTGTGGGAGGCAGACGAAGAGA @@@DDDDDFA:C at EGA?FD<FFHII RG:Z:HiMom.1
+HiMom:1:1101:1269:2170 141 * 0 0 * * 0 0 TTCCAAGCCTGTGCTTTAAGGAAAA @@<ADBDBDF8DDCFH at GIE@@GGH RG:Z:HiMom.1
+HiMom:1:1201:1018:2217 589 * 0 0 * * 0 0 .TTTCTCTGGGCGCAAAGATGTTCA #07;8=8<<99(:=@@/@7>>6=?> RG:Z:HiMom.1
+HiMom:1:1201:1018:2217 653 * 0 0 * * 0 0 ......................... ######################### RG:Z:HiMom.1 XN:i:1
+HiMom:1:1201:1118:2198 77 * 0 0 * * 0 0 CAAGTGTACAGGATTAGACTGGGTT BCCFDEBDHHHHHIJJJGIIIJJGH RG:Z:HiMom.1
+HiMom:1:1201:1118:2198 141 * 0 0 * * 0 0 AATAAACTTTATTAAAGCAGTTAAA C at CFFFFFHDHHHGIIIJJJIJJJJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/ATTCCTCT.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/ATTCCTCT.sam
new file mode 100644
index 0000000..95b97b9
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/ATTCCTCT.sam
@@ -0,0 +1,10 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ATTCCTCT LB:LN_ATTCCTCT SM:SA_ATTCCTCT CN:BI
+HiMom:1:1101:1309:2210 77 * 0 0 * * 0 0 ACACCAACCACCCAACTATCTATAA CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1309:2210 141 * 0 0 * * 0 0 AGTGGGCTAGGGCATTTTTAATCTT @@?DFFDFHHHDFHJIJJIJGIIIJ RG:Z:HiMom.1
+HiMom:1:1201:1018:2133 77 * 0 0 * * 0 0 .AAAACTTGAGGATGCTATGCAAGC #1:B:ADDDDDDDEEAEBF9FFEBF RG:Z:HiMom.1
+HiMom:1:1201:1018:2133 141 * 0 0 * * 0 0 ......................... ######################### RG:Z:HiMom.1 XN:i:1
+HiMom:1:1201:1073:2225 77 * 0 0 * * 0 0 GGGGCTGAGACCTTTGCTGATGGTG @@@FFFFFHHHGHJJJJJIIIGICH RG:Z:HiMom.1
+HiMom:1:1201:1073:2225 141 * 0 0 * * 0 0 CGTGTGCTCTTCCGATCTGGAGGGT @BBDFFFFHHHHHJJJJJJJJJJJ: RG:Z:HiMom.1
+HiMom:1:1201:1242:2207 77 * 0 0 * * 0 0 ATGGCAAAGTGGTGTCTGAGACCAA BCCFFFFFGHHHHHIIIJFHIJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1242:2207 141 * 0 0 * * 0 0 ATCTTTTATTGGCCTCCTGCTCCCC CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/CAACTCTC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/CAACTCTC.sam
new file mode 100644
index 0000000..c2a8308
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/CAACTCTC.sam
@@ -0,0 +1,12 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CAACTCTC LB:LN_CAACTCTC SM:SA_CAACTCTC CN:BI
+HiMom:1:1101:1140:2120 77 * 0 0 * * 0 0 .CCCCAACATTCTAATTATGCCTCA #1:BDFFDHFFDFIJJJIIJIIIII RG:Z:HiMom.1
+HiMom:1:1101:1140:2120 141 * 0 0 * * 0 0 TTTTTTTTTTTTTAACTTTGCAAAT @@@DDDDDHHHHFB at 9FHI@BFH@@ RG:Z:HiMom.1
+HiMom:1:1101:1328:2225 77 * 0 0 * * 0 0 GAAATGCATCTGTCTTAGAAACTGG ??@=BDDDFDD<<,<2:C<F:FFEA RG:Z:HiMom.1
+HiMom:1:1101:1328:2225 141 * 0 0 * * 0 0 AGGAAATTAGGACTTACCTGACATA ######################### RG:Z:HiMom.1
+HiMom:1:1201:1127:2112 589 * 0 0 * * 0 0 .GTCAAGGATGTTCGTCGTGGCAAC #1=BDDDDDDDDDID<AE?@<CEEE RG:Z:HiMom.1
+HiMom:1:1201:1127:2112 653 * 0 0 * * 0 0 TAATCACCTGAGCAGTGAAGCCAGC @<@?BDDDHD?FDBHI?AHGGGDFH RG:Z:HiMom.1
+HiMom:1:1201:1452:2143 77 * 0 0 * * 0 0 TATCCCCTCTAAGACGGACCTGGGT CCCFFFFFHHHHHJJIIIJJJJJJG RG:Z:HiMom.1
+HiMom:1:1201:1452:2143 141 * 0 0 * * 0 0 TTTTAGTCTTAGCATTTACTTTCCC CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1486:2146 589 * 0 0 * * 0 0 GTTCTCTGTCCCCAGGTCCTGTCTC ===A7<7222<<=C=?+<7>@?ACB RG:Z:HiMom.1
+HiMom:1:1201:1486:2146 653 * 0 0 * * 0 0 TTTTTTTTTTTTTTTTTTTTTGGGC <<<@??@??@???????######## RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/CAATAGAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/CAATAGAC.sam
new file mode 100644
index 0000000..a69b8ed
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/CAATAGAC.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CAATAGAC LB:LN_CAATAGAC SM:SA_CAATAGAC CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/CAATAGTC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/CAATAGTC.sam
new file mode 100644
index 0000000..31a220d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/CAATAGTC.sam
@@ -0,0 +1,16 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CAATAGTC LB:LN_CAATAGTC SM:SA_CAATAGTC CN:BI
+HiMom:1:1101:1316:2126 77 * 0 0 * * 0 0 .AAAAAAAAAAAAAAAAAAAAAAAA #1BDFFFFHHHHHJJJJFDDDDDDD RG:Z:HiMom.1 XN:i:1
+HiMom:1:1101:1316:2126 141 * 0 0 * * 0 0 TCTTTTTTTTTTTTTTTTTTTTTTT CCCFFFFFHHHHHJJJJHFDDDDDD RG:Z:HiMom.1
+HiMom:1:1101:1399:2128 77 * 0 0 * * 0 0 .TGCCCTTCGTCCTGGGAAACGGGG #1BDFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1399:2128 141 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHIJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1054:2151 77 * 0 0 * * 0 0 .TAGTGCTGGGCACTAAGTAATACC #4=DDDFFHHHHHJJJJJHIJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1054:2151 141 * 0 0 * * 0 0 GTCAGGCACTGAGAATATATGGGTG CBCFFFFFHHHHHJJJJJJJJJJEG RG:Z:HiMom.1
+HiMom:1:1201:1345:2181 77 * 0 0 * * 0 0 GGATAATCCTATTTATTACCTCAGA BBBDDFFFHHHHHJJJJJJJJJIJJ RG:Z:HiMom.1
+HiMom:1:1201:1345:2181 141 * 0 0 * * 0 0 ATACGGATGTGTTTAGGAGTGGGAC CCCFFFFFHHHHHIIJJHJFHIJIJ RG:Z:HiMom.1
+HiMom:1:1201:1392:2184 77 * 0 0 * * 0 0 TTTCAGATTGGTCATTGTTAGTGTA ??@BDDDEHBHADHHIIEHDHFHFF RG:Z:HiMom.1
+HiMom:1:1201:1392:2184 141 * 0 0 * * 0 0 ATCTTTATTCATTTGTATGATCTTA @@BFFFFFHFFHFHIHIIJIJJJJI RG:Z:HiMom.1
+HiMom:1:2101:1172:2152 589 * 0 0 * * 0 0 AACACGGACAAAGGAGTCTAACACG <<<??8@@################# RG:Z:HiMom.1
+HiMom:1:2101:1172:2152 653 * 0 0 * * 0 0 ATCGTTTCTGGGGACTAGTGAGGCG ######################### RG:Z:HiMom.1
+HiMom:1:2101:1491:2093 77 * 0 0 * * 0 0 .CTATGCCGATCGGGTGTCCGCACT #1=DDDDDHHFHHIIEHHHBGHGII RG:Z:HiMom.1
+HiMom:1:2101:1491:2093 141 * 0 0 * * 0 0 AGAGACGGGGTCTCGCTATGTTGCC BCCDFFFFHHHHHJIIJJJJIJIJJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/CAGCGGAT.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/CAGCGGAT.sam
new file mode 100644
index 0000000..0065e69
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/CAGCGGAT.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CAGCGGAT LB:LN_CAGCGGAT SM:SA_CAGCGGAT CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/CAGCGGTA.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/CAGCGGTA.sam
new file mode 100644
index 0000000..01b4315
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/CAGCGGTA.sam
@@ -0,0 +1,12 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CAGCGGTA LB:LN_CAGCGGTA SM:SA_CAGCGGTA CN:BI
+HiMom:1:1101:1420:2213 77 * 0 0 * * 0 0 TACCTGGTTGATCCTGCCAGTAGCA @@CFFFFDDHHGHJGGHIJJIHGBH RG:Z:HiMom.1
+HiMom:1:1101:1420:2213 141 * 0 0 * * 0 0 TTCACTGTACCGGCCGTGCGTACTT @CCFFFFDHHHFGIJJJJJJGHIGG RG:Z:HiMom.1
+HiMom:1:1201:1364:2113 77 * 0 0 * * 0 0 .CACTCATTTTCTTATGTGGGATAT #1=DDFDFHHHHHIJJIFHIIHHHI RG:Z:HiMom.1
+HiMom:1:1201:1364:2113 141 * 0 0 * * 0 0 TAAAGAGAGCCAGTGGAGTTACGAC ######################### RG:Z:HiMom.1
+HiMom:1:2101:1072:2170 77 * 0 0 * * 0 0 ATCACCGCACTCATTTCCCGCTTCC CCCFFFFFHHHACEEGHIIBHIIII RG:Z:HiMom.1
+HiMom:1:2101:1072:2170 141 * 0 0 * * 0 0 .GGGGAGACAGAGAGGATCAGAAGT #4=BDDFDHHDFHEGFEGGIJIIIG RG:Z:HiMom.1
+HiMom:1:2101:1123:2095 77 * 0 0 * * 0 0 .TGGACAACATGTTCGAGAGCTACA #1=BBDDDFFFFDGFGIG?F;HHFI RG:Z:HiMom.1
+HiMom:1:2101:1123:2095 141 * 0 0 * * 0 0 TCCGCCTCCAGCTTCAGCTTCTCCT @@@FDDFFHHHHHJHGGJIJJJEHH RG:Z:HiMom.1
+HiMom:1:2101:1151:2236 589 * 0 0 * * 0 0 TTAAAGAGGTTCAGGGATGCAGAGT ######################### RG:Z:HiMom.1
+HiMom:1:2101:1151:2236 653 * 0 0 * * 0 0 TTTGAAGCCTCTTTATCCTTGGCAT ######################### RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/CCAACATT.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/CCAACATT.sam
new file mode 100644
index 0000000..5e5edad
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/CCAACATT.sam
@@ -0,0 +1,16 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CCAACATT LB:LN_CCAACATT SM:SA_CCAACATT CN:BI
+HiMom:1:1101:1083:2193 77 * 0 0 * * 0 0 TTCTACCTCACCTTAGGGAGAAGAC @@@DDBDDD>F><C<4CG?EHGHIG RG:Z:HiMom.1
+HiMom:1:1101:1083:2193 141 * 0 0 * * 0 0 AGGCT.................... ######################### RG:Z:HiMom.1
+HiMom:1:1101:1175:2197 77 * 0 0 * * 0 0 CCCCTGAGGACACCATCCCACTCCA CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1175:2197 141 * 0 0 * * 0 0 AAGAGCTGGGGAACATCCAGAAAGG BC at FFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1138:2227 589 * 0 0 * * 0 0 GCTGACACAATCTCTTCCGCCTGGT ######################### RG:Z:HiMom.1
+HiMom:1:1201:1138:2227 653 * 0 0 * * 0 0 GACAAATATAGGAAATAGAAGCTAT =1=A=AAA,2?4>7C<<4<A+3<AB RG:Z:HiMom.1
+HiMom:1:1201:1260:2165 77 * 0 0 * * 0 0 GGACACGGACAGGATTGACAGATTG BCBFFFFFHHHHHHIIJHIIIFHIJ RG:Z:HiMom.1
+HiMom:1:1201:1260:2165 141 * 0 0 * * 0 0 ATCTGATCTAAGTTGGGGGACGCCG @@@FFDFFHHHHHJJJIJIIIGIJJ RG:Z:HiMom.1
+HiMom:1:1201:1281:2133 77 * 0 0 * * 0 0 .GGAAATCCAGAAAACATAGAAGAT #1=DDFFFHHHHHIJJJJJJJJIJJ RG:Z:HiMom.1
+HiMom:1:1201:1281:2133 141 * 0 0 * * 0 0 GCAACAAAATTTCATATGACTTAGC CCCFFFFFHHHHHJJIIIHICHIIJ RG:Z:HiMom.1
+HiMom:1:1201:1331:2162 77 * 0 0 * * 0 0 ACGCTCGGCTAATTTTTGTATTTTT @CCFFFDFHHHHHIJJJJHIJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1331:2162 141 * 0 0 * * 0 0 TAATCCCAGTACTTTGGGAGGCCAA CCCFFFFFHHHHHJJJJIJJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1186:2093 77 * 0 0 * * 0 0 .CGACCATAAACGATGCCGACCGGC #4=DFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1186:2093 141 * 0 0 * * 0 0 AATGTTGGGAGGACAATGATGGAAA ######################### RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/CCAGCACC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/CCAGCACC.sam
new file mode 100644
index 0000000..f3100fa
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/CCAGCACC.sam
@@ -0,0 +1,8 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CCAGCACC LB:LN_CCAGCACC SM:SA_CCAGCACC CN:BI
+HiMom:1:1101:1212:2230 77 * 0 0 * * 0 0 TTTCTATTAGCTCTTAGTAAGATTA CCCFFFFFHHHHHJJJIJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1212:2230 141 * 0 0 * * 0 0 TTTTAGCTTTATTGGGGAGGGGGTG CCCFFFFFHHGHHJJJJGJJJJJDF RG:Z:HiMom.1
+HiMom:1:1201:1204:2228 77 * 0 0 * * 0 0 CCGATACGCTGAGTGTGGTTTGCGG CCCFFFFFHHHFHEGGHIHIJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1204:2228 141 * 0 0 * * 0 0 TCTTCTTGTCGATGAGGAACTTGGT @?@FFFFFDHHGHJIJJGHIIJJJH RG:Z:HiMom.1
+HiMom:1:2101:1100:2085 77 * 0 0 * * 0 0 .CACATGGATGAGGAGAATGAGGAT #1=DDFFFFHHHHJHIGIHHHIJEH RG:Z:HiMom.1
+HiMom:1:2101:1100:2085 141 * 0 0 * * 0 0 ATCTTGATCTCCTCCTTCTTGGCCT @@@DDDDDHHFHFEIIIIHHBAHBG RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/CCATGCGT.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/CCATGCGT.sam
new file mode 100644
index 0000000..2f1cf36
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/CCATGCGT.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CCATGCGT LB:LN_CCATGCGT SM:SA_CCATGCGT CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/CGCCTTCC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/CGCCTTCC.sam
new file mode 100644
index 0000000..3c3b08b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/CGCCTTCC.sam
@@ -0,0 +1,6 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CGCCTTCC LB:LN_CGCCTTCC SM:SA_CGCCTTCC CN:BI
+HiMom:1:1201:1122:2227 77 * 0 0 * * 0 0 AGAAGACGAGGCTGAGAGTGACATC @@@FFFFFHHHDHJGHGHCHHJJIJ RG:Z:HiMom.1
+HiMom:1:1201:1122:2227 141 * 0 0 * * 0 0 GTCATATAAGGCCCAGTCCAAGGAA @@@FFFFFHHHGGIJIGGIJFIJII RG:Z:HiMom.1
+HiMom:1:1201:1160:2109 77 * 0 0 * * 0 0 .AGAAGCCTTTGCACCCTGGGAGGA #1=DDDFFHHHHHJJJJJJJJIIJJ RG:Z:HiMom.1
+HiMom:1:1201:1160:2109 141 * 0 0 * * 0 0 ACATCCTTCCCATGCCACCAACTCG CCCFFFFFGHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/CGCTATGT.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/CGCTATGT.sam
new file mode 100644
index 0000000..8191da9
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/CGCTATGT.sam
@@ -0,0 +1,12 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CGCTATGT LB:LN_CGCTATGT SM:SA_CGCTATGT CN:BI
+HiMom:1:1101:1291:2150 77 * 0 0 * * 0 0 CGTGGGGAACCTGGCGCTAAACCAT @BBFFFFFHHHHHJJJJIJJJJJIJ RG:Z:HiMom.1
+HiMom:1:1101:1291:2150 141 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHFHHIJJJIIIGIJIJ RG:Z:HiMom.1
+HiMom:1:1101:1314:2233 77 * 0 0 * * 0 0 GTTTATTGGGGCATTCCTTATCCCA @??DDDDBDHF>FCHGGGBFAAED9 RG:Z:HiMom.1
+HiMom:1:1101:1314:2233 141 * 0 0 * * 0 0 AGGAAAGTTGGGCTGACCTGACAGA @@<DDD;=FBFADBCGDEH?F;FCG RG:Z:HiMom.1
+HiMom:1:1101:1441:2148 77 * 0 0 * * 0 0 ACTTTCACCGCTACACGACCGGGGG CCCFFFFFHGFFHIIFIHJIGGII> RG:Z:HiMom.1
+HiMom:1:1101:1441:2148 141 * 0 0 * * 0 0 TTTTGGCTCTAGAGGGGGTAGAGGG CCCFFFFFHHDFBHIIJJ1?FGHIJ RG:Z:HiMom.1
+HiMom:1:1201:1043:2246 77 * 0 0 * * 0 0 .TTCTCGGCTGTCATGTGCAACATT #1=DDBDFHHHDFFBHGHGHIIJEH RG:Z:HiMom.1
+HiMom:1:1201:1043:2246 141 * 0 0 * * 0 0 .GCATCATTTC..GCTTCTCTCTGT #0;@@??@=@>##22=;@??><@?? RG:Z:HiMom.1
+HiMom:1:1201:1134:2144 77 * 0 0 * * 0 0 TGCCAGGAAGTGTTTTTTCTGGGTC @CCFFEFFHHFFFGIJJJJJJJJGH RG:Z:HiMom.1
+HiMom:1:1201:1134:2144 141 * 0 0 * * 0 0 AGTGTGAGTAATGGTTGAGAGGTGG B@?DDDFFFHHGHJHHGFIHHIFGI RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/CTAACTCG.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/CTAACTCG.sam
new file mode 100644
index 0000000..1f8de56
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/CTAACTCG.sam
@@ -0,0 +1,10 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CTAACTCG LB:LN_CTAACTCG SM:SA_CTAACTCG CN:BI
+HiMom:1:1101:1363:2138 77 * 0 0 * * 0 0 .GTCTGGCCTGCACAGACATCCTAC #1=DDFFFHHHHHJJJIJJIJJJIJ RG:Z:HiMom.1
+HiMom:1:1101:1363:2138 141 * 0 0 * * 0 0 GTTCTTAAACCTGTTAGAACTTCTG C@@FFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1393:2143 77 * 0 0 * * 0 0 TGGTTGATCCTGCCAGTAGCATATG @@@ADADDFHFFDBHE?G at HIIIEE RG:Z:HiMom.1
+HiMom:1:1201:1393:2143 141 * 0 0 * * 0 0 GATAAATGCACGCATCCCCCCCGCG C at CFFFFFGGHHHHJJJJJJJJJJI RG:Z:HiMom.1
+HiMom:1:2101:1273:2119 589 * 0 0 * * 0 0 .AGATAAGAGTCCACACAGTTGAGT #11AAAAA<A?4=C=7?733<ACA3 RG:Z:HiMom.1
+HiMom:1:2101:1273:2119 653 * 0 0 * * 0 0 ATGATGGATCTTCTCTAACTTGTCA >=><AAAAA+2AA?CB4@@ABB3?A RG:Z:HiMom.1
+HiMom:1:2101:1414:2098 77 * 0 0 * * 0 0 .AGGACATCGATAAAGGCGAGGTGT #1=DDFFFHHHHHJJJJJJJJJHHG RG:Z:HiMom.1
+HiMom:1:2101:1414:2098 141 * 0 0 * * 0 0 TTGGGGCCGGTGCCGTCGGGCCCAA CCCFFFFFHHHHGJJIJJJJJJJIJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/CTATGCGC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/CTATGCGC.sam
new file mode 100644
index 0000000..ee4c13b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/CTATGCGC.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CTATGCGC LB:LN_CTATGCGC SM:SA_CTATGCGC CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/CTATGCGT.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/CTATGCGT.sam
new file mode 100644
index 0000000..cc86630
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/CTATGCGT.sam
@@ -0,0 +1,16 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CTATGCGT LB:LN_CTATGCGT SM:SA_CTATGCGT CN:BI
+HiMom:1:1201:1083:2121 77 * 0 0 * * 0 0 .AGAACTGGCGCTGCGGGATGAACC #1=BDFFFHHHHHJJJJJHIJIJJJ RG:Z:HiMom.1
+HiMom:1:1201:1083:2121 141 * 0 0 * * 0 0 ACACACAACACCACCGCCCTCCCCC ######################### RG:Z:HiMom.1
+HiMom:1:1201:1185:2143 77 * 0 0 * * 0 0 ATCTGCCTGGTTCGGCCCGCCTGCC CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1185:2143 141 * 0 0 * * 0 0 GCTGAAGGCCCGTGGGCCAGAGGTG @CCFFFFFHHHHHJJJJJJJJJJHI RG:Z:HiMom.1
+HiMom:1:1201:1219:2115 77 * 0 0 * * 0 0 .TATAGTGGAGGCCGGAGCAGGAAC #1:DABADHHHFHIIIGGHGIIIII RG:Z:HiMom.1
+HiMom:1:1201:1219:2115 141 * 0 0 * * 0 0 TGGGAGTAGTTCCCTGCTAAGGGAG ???DBDBDADDDDIEID:AFFD:?8 RG:Z:HiMom.1
+HiMom:1:1201:1472:2121 589 * 0 0 * * 0 0 .TAAAGTGTGAACAAGGAAGGTCAT #07>@<9=@################ RG:Z:HiMom.1
+HiMom:1:1201:1472:2121 653 * 0 0 * * 0 0 GTGTGCTCTTCCGATCTGGAGGATG =+=??A4A==A at 7A<?######### RG:Z:HiMom.1
+HiMom:1:2101:1013:2146 77 * 0 0 * * 0 0 .ACACTGCTGCAGATGACAAGCAGC #4BDFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1013:2146 141 * 0 0 * * 0 0 ....CGCTAGAACCAACTTATTCAT ####24=?@@?@?@@?@@@@@@?@@ RG:Z:HiMom.1
+HiMom:1:2101:1231:2208 77 * 0 0 * * 0 0 ACGCCGCAAGTCAGAGCCCCCCAGA @@@DDDFFFFB:DBBEBEFDHBDDB RG:Z:HiMom.1
+HiMom:1:2101:1231:2208 141 * 0 0 * * 0 0 AGCCAGTGTTGGTGTGTTGACTGTT @@;1ADABCF;BF<AACGCHEBHC< RG:Z:HiMom.1
+HiMom:1:2101:1233:2133 589 * 0 0 * * 0 0 GAGAGAAGCACTCTTGAGCGGGATA 0;(@((@)2@############### RG:Z:HiMom.1
+HiMom:1:2101:1233:2133 653 * 0 0 * * 0 0 TTTTTTTTTTTTTTTTTTTTTTTTT CCCFFFFFGHHHHJJJFDDDDDDDD RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/CTGCGGAT.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/CTGCGGAT.sam
new file mode 100644
index 0000000..d518e57
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/CTGCGGAT.sam
@@ -0,0 +1,8 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CTGCGGAT LB:LN_CTGCGGAT SM:SA_CTGCGGAT CN:BI
+HiMom:1:2101:1102:2221 77 * 0 0 * * 0 0 TTTCATCTTATTTCATTGGTTTATA CCCFFFFFHHHHHJIJJJJIJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1102:2221 141 * 0 0 * * 0 0 ATAACTGACTCTACTCAGTAGATTA CCCFFFFFHHHHHJJJJJIJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1126:2082 77 * 0 0 * * 0 0 .GTTTTAGGGGTGCGCAGGAGTCAA #11=A=DD?DF at D@CCGHIEFH at BG RG:Z:HiMom.1
+HiMom:1:2101:1126:2082 141 * 0 0 * * 0 0 TCTCTTTCCACCTTGGTCACCTTCC @C at DDDFFHHHHHJEGGIHHIJGIH RG:Z:HiMom.1
+HiMom:1:2101:1216:2172 77 * 0 0 * * 0 0 TTTCTTCGCAGGATTTTTCTGAGCC CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1216:2172 141 * 0 0 * * 0 0 GGACTTCTAGGGGATTTAGCGGGGT CCCFFFFFHHHHHJJJJJJJJJJJD RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/CTGTAATC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/CTGTAATC.sam
new file mode 100644
index 0000000..d24cc80
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/CTGTAATC.sam
@@ -0,0 +1,14 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CTGTAATC LB:LN_CTGTAATC SM:SA_CTGTAATC CN:BI
+HiMom:1:1101:1403:2194 77 * 0 0 * * 0 0 CTAAACAGAGAGAAGGTTTCTCTTT CCCFFFFFHHHHHJJJFHIJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1403:2194 141 * 0 0 * * 0 0 ACATGGTGAAACCCTGTCTCTACTA CCCFFFDDHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1045:2105 589 * 0 0 * * 0 0 .TAAAGAGAAATCAAGAATACTATT #-4@?(@)@@############### RG:Z:HiMom.1
+HiMom:1:1201:1045:2105 653 * 0 0 * * 0 0 .TTTTTTTTTT..TTTTTTTTTTTT #0;@@@@@@@?##0:????????=< RG:Z:HiMom.1
+HiMom:1:1201:1483:2126 589 * 0 0 * * 0 0 .TGATAAGGTGTTGCTATGTTACCC #1:D?DDDDA??2:<CC4:AEDF>? RG:Z:HiMom.1
+HiMom:1:1201:1483:2126 653 * 0 0 * * 0 0 GCATGCAGCTGGGTGCTGTGATGCA @@@DDDBB<DD8F<<CGG?AA?A<F RG:Z:HiMom.1
+HiMom:1:2101:1011:2102 77 * 0 0 * * 0 0 .AAACAAAACTGTAGAACTGTGTAT #1=DDFFFHHHHHJJIJJJIHHHJJ RG:Z:HiMom.1
+HiMom:1:2101:1011:2102 141 * 0 0 * * 0 0 .....TCACACATAATTTTAAAATT #####22@?@@??@@@@@??@@@@@ RG:Z:HiMom.1
+HiMom:1:2101:1245:2154 77 * 0 0 * * 0 0 TCGTTAAGTATATTCTTAGGTATTT CCCFFDFFFHFHHIIJJJJJFJJJI RG:Z:HiMom.1
+HiMom:1:2101:1245:2154 141 * 0 0 * * 0 0 ACCAATCAGTAGCACCACTATACAC CCCFFFFFHHHHHJJJJJJIJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1386:2105 77 * 0 0 * * 0 0 .TACTAAAGAAAAAGTTGAAGAACT #1=DDDFFHHHHHJJGHIJJJJIJJ RG:Z:HiMom.1
+HiMom:1:2101:1386:2105 141 * 0 0 * * 0 0 AGGAATTATTCTTCTGCCATAAGGT B@@DDFFFHGFHHIJJJJJGIGIJH RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/GAAAAAAA.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/GAAAAAAA.sam
new file mode 100644
index 0000000..a05c01a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/GAAAAAAA.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GAAAAAAA LB:LN_GAAAAAAA SM:SA_GAAAAAAA CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/GAACGAT..sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/GAACGAT..sam
new file mode 100644
index 0000000..8142ba9
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/GAACGAT..sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GAACGAT. LB:LN_GAACGAT. SM:SA_GAACGAT. CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/GAAGGAAG.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/GAAGGAAG.sam
new file mode 100644
index 0000000..5fa6e1f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/GAAGGAAG.sam
@@ -0,0 +1,8 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GAAGGAAG LB:LN_GAAGGAAG SM:SA_GAAGGAAG CN:BI
+HiMom:1:1101:1338:2175 77 * 0 0 * * 0 0 CCCACCTTCCGGCGGCCGAAGACAC CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1338:2175 141 * 0 0 * * 0 0 GCTTGTTGGCTTTAACATCCACAAT CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1028:2202 77 * 0 0 * * 0 0 .TCCTGGGAAACGGGGCGCGGCTGG #4BDDDFFHHHHHIJIIJJJJJJIJ RG:Z:HiMom.1
+HiMom:1:1201:1028:2202 141 * 0 0 * * 0 0 ..AAAC.C.T.......GG..TG.. ##42@?################### RG:Z:HiMom.1
+HiMom:1:2101:1084:2188 77 * 0 0 * * 0 0 TTGCTGCATGGGTTAATTGAGAATA CCCFFFFFHHHHFHHIIJJIJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1084:2188 141 * 0 0 * * 0 0 TACAAGGTCAAAATCAGCAACAAGT CCCFFFFDHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/GACCAGGA.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/GACCAGGA.sam
new file mode 100644
index 0000000..9affca8
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/GACCAGGA.sam
@@ -0,0 +1,16 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GACCAGGA LB:LN_GACCAGGA SM:SA_GACCAGGA CN:BI
+HiMom:1:1101:1089:2172 77 * 0 0 * * 0 0 TTCCAGCATGCGGTTTAAGTAGGAT @CCFDFDBDFBF:<CEBHAFHHICH RG:Z:HiMom.1
+HiMom:1:1101:1089:2172 141 * 0 0 * * 0 0 TCCGG.................... :<<??#################### RG:Z:HiMom.1
+HiMom:1:1101:1347:2149 77 * 0 0 * * 0 0 GAGCAGATCGGAAGAGCACAGATCG @@@FFDDDHHHHHIJJBGGHJIHEG RG:Z:HiMom.1
+HiMom:1:1101:1347:2149 141 * 0 0 * * 0 0 GCTCTTCCGATCTGTGCTCTTCCGA CCCFFFFFDFHHFIJDGIGGHGIGH RG:Z:HiMom.1
+HiMom:1:1201:1095:2146 77 * 0 0 * * 0 0 GCTGAGTCATGTAGTAAGCCTGTGC BB at FDDDFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1095:2146 141 * 0 0 * * 0 0 ACTGACAACACCAAATGCTGCTAAG CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1123:2161 589 * 0 0 * * 0 0 CACTAACTCCTGACCTCAAATAATC ?7?=DD?DD+CDBE>E at EEF@+<CF RG:Z:HiMom.1
+HiMom:1:1201:1123:2161 653 * 0 0 * * 0 0 CGTGTGCTCTTCCGATCTGCATACA ===AAAA8AAAA<AAA)@CBA9>A# RG:Z:HiMom.1
+HiMom:1:1201:1439:2156 77 * 0 0 * * 0 0 AGCCGCGAGGTGCTGGCGGACTTCC :;1BDDDAA88A<?<E1C:D##### RG:Z:HiMom.1
+HiMom:1:1201:1439:2156 141 * 0 0 * * 0 0 GGAGATTATTTGCCTTGAAGTAAGC -;(22<>>@>8@>8;@######### RG:Z:HiMom.1
+HiMom:1:2101:1207:2084 589 * 0 0 * * 0 0 .TAGATGACCAAAACTTGCAGGGCA #1:A<?@A+7A=?CBCCBCCBAAAA RG:Z:HiMom.1
+HiMom:1:2101:1207:2084 653 * 0 0 * * 0 0 TCACCACTCTTCTGGGCATCCCCTG @@@DDEDFHHHHHIJIHHGHGGJJJ RG:Z:HiMom.1
+HiMom:1:2101:1312:2105 77 * 0 0 * * 0 0 .TTCCCTCAGGATAGCTGGCGCTCT #1=DDFFFGHGHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1312:2105 141 * 0 0 * * 0 0 GTTGAGAATAGGTTGAGATCGTTTC @CCFFFDFHHFHDHIJJJJJJJIJJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/GACCAGGC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/GACCAGGC.sam
new file mode 100644
index 0000000..d18d0dc
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/GACCAGGC.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GACCAGGC LB:LN_GACCAGGC SM:SA_GACCAGGC CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/GACCGTTG.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/GACCGTTG.sam
new file mode 100644
index 0000000..126546f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/GACCGTTG.sam
@@ -0,0 +1,10 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GACCGTTG LB:LN_GACCGTTG SM:SA_GACCGTTG CN:BI
+HiMom:1:1101:1218:2200 77 * 0 0 * * 0 0 GCACCGGAAGAGCACACAGATCGGA CCCFFFFDFHGHHJJIJIJJJJJJI RG:Z:HiMom.1
+HiMom:1:1101:1218:2200 141 * 0 0 * * 0 0 GCTCTTCCGATCTATCTGCTCGTCC (-(=34???3;@############# RG:Z:HiMom.1
+HiMom:1:1101:1257:2223 77 * 0 0 * * 0 0 TGTATTCGAGAGATCAAAGAGAGAG @@=DDBDD?FFHHEIDBDFCEDBAF RG:Z:HiMom.1
+HiMom:1:1101:1257:2223 141 * 0 0 * * 0 0 TGCTCTTCCGATCTTTTAGCAAAGC :?@DDBDDHFFHDGIGIIJJJGGGI RG:Z:HiMom.1
+HiMom:1:1201:1180:2119 77 * 0 0 * * 0 0 .TGAAAGATTTAGAGAGCTTACAAA #1=DDDDDHHHGHJJIIJJJJIJJI RG:Z:HiMom.1
+HiMom:1:1201:1180:2119 141 * 0 0 * * 0 0 GCTCTAAATTTTGCTTTTCTACAGC CCCFFFFFHHHHHJJJJIJIJJIJJ RG:Z:HiMom.1
+HiMom:1:2101:1036:2087 77 * 0 0 * * 0 0 .TGTAGTTTCTTTAGGCAAATTTGT #4=BDDDFHHHHHJJJJJJIIJJJI RG:Z:HiMom.1
+HiMom:1:2101:1036:2087 141 * 0 0 * * 0 0 .GTCCACTTACGAAGCAAATACTTT #4=DDFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/GACCTAAC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/GACCTAAC.sam
new file mode 100644
index 0000000..92d814b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/GACCTAAC.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GACCTAAC LB:LN_GACCTAAC SM:SA_GACCTAAC CN:BI
+HiMom:1:1101:1302:2244 77 * 0 0 * * 0 0 GGAAAAGACGGAAAGGTTCTATCTC @C at DFFFDFHHHHJIJHHIJJJJJI RG:Z:HiMom.1
+HiMom:1:1101:1302:2244 141 * 0 0 * * 0 0 TGAATACATATAACAAATGCAAAAA CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/GATATCCA.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/GATATCCA.sam
new file mode 100644
index 0000000..6c13539
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/GATATCCA.sam
@@ -0,0 +1,8 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GATATCCA LB:LN_GATATCCA SM:SA_GATATCCA CN:BI
+HiMom:1:1101:1460:2176 77 * 0 0 * * 0 0 AGTCCAGGCTGAGCCCAGGGAAGAA CCCFFFFFHHHHGJIJJIJJHIJJI RG:Z:HiMom.1
+HiMom:1:1101:1460:2176 141 * 0 0 * * 0 0 AGGAAAAAGACACAACAAGTCCAAC ######################### RG:Z:HiMom.1
+HiMom:1:2101:1031:2163 77 * 0 0 * * 0 0 .TTTCCATGGCCGTCACCTTTGGGT #4=DDFFFHHHHHJJJJJJJJJJJI RG:Z:HiMom.1
+HiMom:1:2101:1031:2163 141 * 0 0 * * 0 0 ..ACATTTGTCACCACTAGCCACCA ##0<@?@@@@@@@@@@?@@@@@@@? RG:Z:HiMom.1
+HiMom:1:2101:1226:2088 77 * 0 0 * * 0 0 .GATCGGAAGAGCACACGTTTGACT #4=DAA=DDFHFHIIBFGHHIG>EG RG:Z:HiMom.1
+HiMom:1:2101:1226:2088 141 * 0 0 * * 0 0 GCTCTTCCGATCTAGGTAATAGCTA ==?BDFFFDCDDHFFFAFHDHIJGJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/GCCGTCGA.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/GCCGTCGA.sam
new file mode 100644
index 0000000..353c9f2
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/GCCGTCGA.sam
@@ -0,0 +1,12 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GCCGTCGA LB:LN_GCCGTCGA SM:SA_GCCGTCGA CN:BI
+HiMom:1:1101:1111:2148 77 * 0 0 * * 0 0 GTGGAGACCACCTCCGAGGCCTTGT BBCFFFFFHHHHHJJJIJJJJJJJI RG:Z:HiMom.1
+HiMom:1:1101:1111:2148 141 * 0 0 * * 0 0 GCGAA.A..........GGACGAC. ######################### RG:Z:HiMom.1
+HiMom:1:1101:1221:2143 77 * 0 0 * * 0 0 TTTGGTGGAAATTTTTTGTTATGAT CCCFFBDBHFD?FBFHIIGGIC at EF RG:Z:HiMom.1
+HiMom:1:1101:1221:2143 141 * 0 0 * * 0 0 CAATTGAATGTCTGCACAGCCGCTT @@@FFFFDHHHHHJJJIIIJGHIJJ RG:Z:HiMom.1
+HiMom:1:1101:1327:2200 589 * 0 0 * * 0 0 AGGGGGATCCGCCGGGGGACCACAA ######################### RG:Z:HiMom.1
+HiMom:1:1101:1327:2200 653 * 0 0 * * 0 0 GTCATCTGGGCTGTCGACAGGTGTC @B at FFFFFHHHHGIJJJJJJIFHHI RG:Z:HiMom.1
+HiMom:1:2101:1122:2136 77 * 0 0 * * 0 0 GTAGGCGCTCAGCAAATACTTGTCG @@@DDDD8?<CACEHHBBHDAAFH@ RG:Z:HiMom.1
+HiMom:1:2101:1122:2136 141 * 0 0 * * 0 0 CTTGCCAGCCTGCAGGCCCCGCGGC ???BBAABDD?DDIID)A:3<EADD RG:Z:HiMom.1
+HiMom:1:2101:1459:2083 77 * 0 0 * * 0 0 .CACACGCCACACGGAGCACACTTT #4=DDFFFHHHHHJJJJJJJJIIJJ RG:Z:HiMom.1
+HiMom:1:2101:1459:2083 141 * 0 0 * * 0 0 ATTTCACCAAAATAATCAGAAGGCC CCCFFFFDBHGHHIGGIJFJJGGFH RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/GCCTAGCC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/GCCTAGCC.sam
new file mode 100644
index 0000000..2f7fbb6
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/GCCTAGCC.sam
@@ -0,0 +1,12 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GCCTAGCC LB:LN_GCCTAGCC SM:SA_GCCTAGCC CN:BI
+HiMom:1:1101:1165:2239 77 * 0 0 * * 0 0 GGCGGAGGCAGCATTTCAGCTGTGA CCCFFDFFHHHHHIJJIGHHHJHHF RG:Z:HiMom.1
+HiMom:1:1101:1165:2239 141 * 0 0 * * 0 0 ATGGAAGTCGAGACAGAAGTGAGAA ######################### RG:Z:HiMom.1
+HiMom:1:1101:1290:2225 77 * 0 0 * * 0 0 CTTGGGCGCATGGTGAGGGAGGGAG @@@FFDDFHDFH??CBEBHHIGDCD RG:Z:HiMom.1
+HiMom:1:1101:1290:2225 141 * 0 0 * * 0 0 TCAGTTCACTGGCAAAGACAGTCAC C@@FBEDDFHFHGIIICEHGDHBHE RG:Z:HiMom.1
+HiMom:1:1201:1280:2179 77 * 0 0 * * 0 0 TTCAAGGAATCGTCCTGCCTCAGCC BCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1280:2179 141 * 0 0 * * 0 0 GAGGACTGCTTGAGTCCAGGAGTTC @@BFFDEFGHHHHIFGCHIJJJGGI RG:Z:HiMom.1
+HiMom:1:1201:1300:2137 77 * 0 0 * * 0 0 .TGTAATCCCAGCTCTCAGGGAGGC #1=ADDDDDDDBBA?@AE?E at FE8; RG:Z:HiMom.1
+HiMom:1:1201:1300:2137 141 * 0 0 * * 0 0 GCTCTTCCGATCTTTTTTTTAATTT @@?DDDDDFDHADEHGIGGED3?FD RG:Z:HiMom.1
+HiMom:1:2101:1023:2237 589 * 0 0 * * 0 0 .TAAACAGCTTCTGCACAGCCAAAG #00@@?>=39>9;<412@?###### RG:Z:HiMom.1
+HiMom:1:2101:1023:2237 653 * 0 0 * * 0 0 ..TTTGTTTGAGTTCCTTGTAGATT ##0:=@?>?@???@:>?@??>?;?< RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/GTAACATC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/GTAACATC.sam
new file mode 100644
index 0000000..9f8e2fa
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/GTAACATC.sam
@@ -0,0 +1,6 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GTAACATC LB:LN_GTAACATC SM:SA_GTAACATC CN:BI
+HiMom:1:1101:1188:2237 77 * 0 0 * * 0 0 TCCCCCTCCCTTTTGCGCACACACC @?@DDADDHDHBDH<EFHIIHG?HF RG:Z:HiMom.1
+HiMom:1:1101:1188:2237 141 * 0 0 * * 0 0 GCTTCCTTCAAGACAGAAGTGAGAA CCCFFDDEFHHFFE at FDHHAIAFHG RG:Z:HiMom.1
+HiMom:1:2101:1208:2231 589 * 0 0 * * 0 0 TCACTAAACATCCAAACATCACTTT ######################### RG:Z:HiMom.1
+HiMom:1:2101:1208:2231 653 * 0 0 * * 0 0 CTTTTTTTTTTTTTTTTTTTTTTTT CCCFFFFFHHHHHJJJHFDDDDDDD RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/GTCCACAG.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/GTCCACAG.sam
new file mode 100644
index 0000000..8e0d773
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/GTCCACAG.sam
@@ -0,0 +1,6 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GTCCACAG LB:LN_GTCCACAG SM:SA_GTCCACAG CN:BI
+HiMom:1:1101:1069:2159 77 * 0 0 * * 0 0 TCCCTTACCATCAAATCAATTG.CC CCCFFFFFHHHHHJJJJJJJJJ#3A RG:Z:HiMom.1
+HiMom:1:1101:1069:2159 141 * 0 0 * * 0 0 GACGT.................... <<<@?#################### RG:Z:HiMom.1
+HiMom:1:1201:1486:2109 77 * 0 0 * * 0 0 .CACCTCCTAGCCCCTCACTTCTGT #1=B;BDDHHHGFIIIIIIIIIGGG RG:Z:HiMom.1
+HiMom:1:1201:1486:2109 141 * 0 0 * * 0 0 ACGTGTGCTCTTCCCGATCTGTATA CCCFF?DDFBHHHJJIIDHJIJJJH RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/N.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/N.sam
new file mode 100644
index 0000000..c8b3cee
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/N.sam
@@ -0,0 +1,34 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.N LB:LN_N SM:SA_N CN:BI
+HiMom:1:1101:1031:2224 589 * 0 0 * * 0 0 .AATA............T....... #0;@@#################### BC:Z:NNNNNNNN RG:Z:HiMom.1
+HiMom:1:1101:1031:2224 653 * 0 0 * * 0 0 ......................... ######################### BC:Z:NNNNNNNN RG:Z:HiMom.1 XN:i:1
+HiMom:1:1101:1039:2147 589 * 0 0 * * 0 0 .CCAA.G..GG....ATGTAA.... #4;@@#4##2<####43@@@@#### BC:Z:NNNNNNNN RG:Z:HiMom.1
+HiMom:1:1101:1039:2147 653 * 0 0 * * 0 0 ......................... ######################### BC:Z:NNNNNNNN RG:Z:HiMom.1 XN:i:1
+HiMom:1:1101:1046:2175 589 * 0 0 * * 0 0 .TGCC.G.GTT.CG.GGTCTT.... #4;@@#################### BC:Z:NNNNNNNN RG:Z:HiMom.1
+HiMom:1:1101:1046:2175 653 * 0 0 * * 0 0 ..GGA.................... ######################### BC:Z:NNNNNNNN RG:Z:HiMom.1
+HiMom:1:1101:1047:2122 589 * 0 0 * * 0 0 .CTAA.G.ACT.TG.GTGTGC.... #0;@@#4#3@@#3@#2<@@@@#### BC:Z:NNNANNNN RG:Z:HiMom.1
+HiMom:1:1101:1047:2122 653 * 0 0 * * 0 0 ..TCA.................... ######################### BC:Z:NNNANNNN RG:Z:HiMom.1
+HiMom:1:1101:1048:2197 589 * 0 0 * * 0 0 .CTCC.G.TCA.CA.GTGGAG.... #0;?@#################### BC:Z:NNNCNNNN RG:Z:HiMom.1
+HiMom:1:1101:1048:2197 653 * 0 0 * * 0 0 ..GTG.................... ######################### BC:Z:NNNCNNNN RG:Z:HiMom.1
+HiMom:1:1101:1065:2193 77 * 0 0 * * 0 0 GAAGTACGCCCTGCCCCTGGTT.GC ?@@DAADAHHFHBEBEGGHG?#### BC:Z:GAACGATN RG:Z:HiMom.1
+HiMom:1:1101:1065:2193 141 * 0 0 * * 0 0 .CTTG.................... ######################### BC:Z:GAACGATN RG:Z:HiMom.1
+HiMom:1:1101:1162:2207 589 * 0 0 * * 0 0 ACCTTGAGGAGAACATAAGAGCAAA ######################### BC:Z:ACAAAATT RG:Z:HiMom.1
+HiMom:1:1101:1162:2207 653 * 0 0 * * 0 0 TAAAACTGGGGAAGTTAGAGGAATG ######################### BC:Z:ACAAAATT RG:Z:HiMom.1
+HiMom:1:1201:1159:2179 589 * 0 0 * * 0 0 GTTAGCACAGATATTGGATGAGTGA ######################### BC:Z:AAAAAAAA RG:Z:HiMom.1
+HiMom:1:1201:1159:2179 653 * 0 0 * * 0 0 TTTTTTTTTATTTTTCTAAATACTT ===AA#################### BC:Z:AAAAAAAA RG:Z:HiMom.1
+HiMom:1:1201:1414:2174 589 * 0 0 * * 0 0 GCCAAAAAAAAGAACCAGCCCAAGG ######################### BC:Z:AGAAAAGA RG:Z:HiMom.1
+HiMom:1:1201:1414:2174 653 * 0 0 * * 0 0 TTTTTTTTTTTTTTTTTTTTTTTTT @;@1BDADF????FFEB>B6=BBBB BC:Z:AGAAAAGA RG:Z:HiMom.1
+HiMom:1:2101:1040:2208 589 * 0 0 * * 0 0 .ATGCCCACCTCCCTCCTACGCACC ######################### BC:Z:ACGAAATC RG:Z:HiMom.1
+HiMom:1:2101:1040:2208 653 * 0 0 * * 0 0 .CTGATAGTCACTGAAATGAATTCA #-0=>(2 at .22@@############ BC:Z:ACGAAATC RG:Z:HiMom.1
+HiMom:1:2101:1059:2083 77 * 0 0 * * 0 0 .AAGAGGGGTCAAGAGTTAAACTTA #1=DDFFFHFHHGIGHGHJJJJJJI BC:Z:TACCGTCT RG:Z:HiMom.1
+HiMom:1:2101:1059:2083 141 * 0 0 * * 0 0 .GAATGTCTTAGAAGGATGCTTCTC #1=BDDDEHHGHHJJJJJIJJIIJJ BC:Z:TACCGTCT RG:Z:HiMom.1
+HiMom:1:2101:1143:2137 77 * 0 0 * * 0 0 ATGCAGCAGCTGCCACGGAGCACCA CC at FFDFDFHFHHGIDHEHIGJJJJ BC:Z:TCCGTCTA RG:Z:HiMom.1
+HiMom:1:2101:1143:2137 141 * 0 0 * * 0 0 GCTCTTCAGATCTAGGGGGAACAGC @@@DD?=DCAFFFHIIDG:EFHIII BC:Z:TCCGTCTA RG:Z:HiMom.1
+HiMom:1:2101:1151:2182 589 * 0 0 * * 0 0 TTGTTTTGGCTTATAATGACAAGAA ;;8-2).2())(<6=@8;?4??>>? BC:Z:GAAAAAAA RG:Z:HiMom.1
+HiMom:1:2101:1151:2182 653 * 0 0 * * 0 0 TTTTTTTTTTTTTTTTTTTTTTTTA 9<<?@?@;5=?############## BC:Z:GAAAAAAA RG:Z:HiMom.1
+HiMom:1:2101:1215:2110 77 * 0 0 * * 0 0 .AATATAATTTGGAGACCCTTTGTT #1=DDDDDEDDDDIDDBB3ABAB## BC:Z:AAAAGAAG RG:Z:HiMom.1
+HiMom:1:2101:1215:2110 141 * 0 0 * * 0 0 ATCTTTCCCCCATTAAGAACAGCAA ######################### BC:Z:AAAAGAAG RG:Z:HiMom.1
+HiMom:1:2101:1285:2105 589 * 0 0 * * 0 0 .GCGGGGAGCCGGGCGTGGAATGCG ######################### BC:Z:TATCTCGG RG:Z:HiMom.1
+HiMom:1:2101:1285:2105 653 * 0 0 * * 0 0 TGTCTATATCAACCAACACCTCTTC -(0(():94:9:???########## BC:Z:TATCTCGG RG:Z:HiMom.1
+HiMom:1:2101:1450:2134 77 * 0 0 * * 0 0 AGCACGCTGCCGCGGGACCTGCCCA ?@@AD at DDHFH?DGIIIIG at FGFBF BC:Z:ACCAGTTG RG:Z:HiMom.1
+HiMom:1:2101:1450:2134 141 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CC at FDFDFFDFHFGIIE1CGGHBGE BC:Z:ACCAGTTG RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/TAAGCACA.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/TAAGCACA.sam
new file mode 100644
index 0000000..51b342d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/TAAGCACA.sam
@@ -0,0 +1,6 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TAAGCACA LB:LN_TAAGCACA SM:SA_TAAGCACA CN:BI
+HiMom:1:1201:1064:2239 77 * 0 0 * * 0 0 CATGCAGCGCAAGTAGGTCTACAAG @@;DFAFFHHHHAHEGHFDGGFABG RG:Z:HiMom.1
+HiMom:1:1201:1064:2239 141 * 0 0 * * 0 0 GGGATGGGAGGGCGATGAGGACTAG 8?@:DDDACC:FHHGIH<EGDDDFH RG:Z:HiMom.1
+HiMom:1:2101:1258:2092 77 * 0 0 * * 0 0 .CACACACACACTCATTCACAGCTT #1=DDDFFHHHFHJJIJGGGIIGIJ RG:Z:HiMom.1
+HiMom:1:2101:1258:2092 141 * 0 0 * * 0 0 TTAGACAAAACACCAAAATAAAATA ######################### RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/TACCGTCT.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/TACCGTCT.sam
new file mode 100644
index 0000000..ebcf32d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/TACCGTCT.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TACCGTCT LB:LN_TACCGTCT SM:SA_TACCGTCT CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/TAGCGGTA.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/TAGCGGTA.sam
new file mode 100644
index 0000000..48afb69
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/TAGCGGTA.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TAGCGGTA LB:LN_TAGCGGTA SM:SA_TAGCGGTA CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/TATCAGCC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/TATCAGCC.sam
new file mode 100644
index 0000000..f3eca6c
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/TATCAGCC.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TATCAGCC LB:LN_TATCAGCC SM:SA_TATCAGCC CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/TATCCAGG.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/TATCCAGG.sam
new file mode 100644
index 0000000..958797b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/TATCCAGG.sam
@@ -0,0 +1,10 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TATCCAGG LB:LN_TATCCAGG SM:SA_TATCCAGG CN:BI
+HiMom:1:1101:1071:2233 77 * 0 0 * * 0 0 TTTGACAGTCTCTGAATGAGAA.GG CCCFFFFFHHHHHJIIIJJJIJ#4A RG:Z:HiMom.1
+HiMom:1:1101:1071:2233 141 * 0 0 * * 0 0 GTTTG.................... <<<@@#################### RG:Z:HiMom.1
+HiMom:1:1201:1140:2125 77 * 0 0 * * 0 0 .TTTCAGTTCAGAGAACTGCAGAAT #1=DBDFDHHHHGJIJJJJJIIIJI RG:Z:HiMom.1
+HiMom:1:1201:1140:2125 141 * 0 0 * * 0 0 TTCATAAATTGGTCTTAGATGTTGC CC at FFFFFHHHHFGIJIIIJIJIJJ RG:Z:HiMom.1
+HiMom:1:1201:1236:2187 77 * 0 0 * * 0 0 TTTAAATGGGTAAGAAGCCCGGCTC @BCDDFEFHHDHHJJJJJIJJIJJJ RG:Z:HiMom.1
+HiMom:1:1201:1236:2187 141 * 0 0 * * 0 0 CTCCTTAGCGGATTCCGACTTCCAT CCCFFFFDHHHHGIJJIGIGIJJGG RG:Z:HiMom.1
+HiMom:1:2101:1133:2239 77 * 0 0 * * 0 0 AGACAGAAGTACGGGAAGGCGAAGA @@@FFFFEHFHHHJJCGDHIIECD@ RG:Z:HiMom.1
+HiMom:1:2101:1133:2239 141 * 0 0 * * 0 0 AGCTTTTTGTTTCCTAGCTTGTCTT ?@?DDFFFHHHHF4ACFHIJHHHGH RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/TATCCATG.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/TATCCATG.sam
new file mode 100644
index 0000000..a005522
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/TATCCATG.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TATCCATG LB:LN_TATCCATG SM:SA_TATCCATG CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/TATCTCGG.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/TATCTCGG.sam
new file mode 100644
index 0000000..7ea4674
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/TATCTCGG.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TATCTCGG LB:LN_TATCTCGG SM:SA_TATCTCGG CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/TATCTGCC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/TATCTGCC.sam
new file mode 100644
index 0000000..36bd80e
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/TATCTGCC.sam
@@ -0,0 +1,16 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TATCTGCC LB:LN_TATCTGCC SM:SA_TATCTGCC CN:BI
+HiMom:1:1101:1267:2209 77 * 0 0 * * 0 0 GAGACGGAGGCCAACGGGGGCCTGG @@CFFFFD8FDHFHIGIBG?@BCDG RG:Z:HiMom.1
+HiMom:1:1101:1267:2209 141 * 0 0 * * 0 0 GGCAGAGTCTCCAACAGCCCCGTAC =;?DDDD?CCFHAIIIGGIIGE at EG RG:Z:HiMom.1
+HiMom:1:1101:1353:2226 77 * 0 0 * * 0 0 TTGCTTGTCTGTAAAGTATTTTATT @C at DDFFDHHFHFHHIBGG>IHHII RG:Z:HiMom.1
+HiMom:1:1101:1353:2226 141 * 0 0 * * 0 0 GTGCTCTTCCGATCTTCAGGTTACC BBBFFFFFHHHHHJJJJJJJIJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1435:2194 77 * 0 0 * * 0 0 GAGAAAGAACATGACTACAGAGATG CCCFFFFFHHHHHJJJJJJJJJHJJ RG:Z:HiMom.1
+HiMom:1:1101:1435:2194 141 * 0 0 * * 0 0 TTTTGTTTTCTTTTACTGAAGTGTA CCCFFDFFHHHHHJJJJIHIJHHHJ RG:Z:HiMom.1
+HiMom:1:1201:1084:2204 77 * 0 0 * * 0 0 GGCCCGTGGACGCCGCCGAAGAAGC CCCFFFFFHHHHHJJJJJIJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1084:2204 141 * 0 0 * * 0 0 TGGCTCCTCAGGCTCTCATCAGTTG CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1142:2242 77 * 0 0 * * 0 0 TGTTGATAGTCCTTCTTATCTTAGT ???DB?==CC2<AC:CC<CFEF<FF RG:Z:HiMom.1
+HiMom:1:1201:1142:2242 141 * 0 0 * * 0 0 GTAAAATGTAAAATAATAAAAAATG ?=?DDDD;AF<DF<FFFFIIIFF@< RG:Z:HiMom.1
+HiMom:1:1201:1187:2100 77 * 0 0 * * 0 0 .GCGGTAATTCCAGCTCCAATAGCG #1:BB2 at DHHFHHIIIIHHIIGHGG RG:Z:HiMom.1
+HiMom:1:1201:1187:2100 141 * 0 0 * * 0 0 AAAAAAGAGCCCGCATTGCCGAGAC =<=;AA################### RG:Z:HiMom.1
+HiMom:1:1201:1392:2109 77 * 0 0 * * 0 0 .CTGAAGAGGCCAAAGCGCCCTCCA #1=DDFFFHHHHHJJJJJJJJJJJI RG:Z:HiMom.1
+HiMom:1:1201:1392:2109 141 * 0 0 * * 0 0 GTCAGACAGGGGGATTTGGGCTGTG BBCFFFFFHHHHHHJJJHIJIJJJJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/TCCGTCTA.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/TCCGTCTA.sam
new file mode 100644
index 0000000..39a9ebc
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/TCCGTCTA.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TCCGTCTA LB:LN_TCCGTCTA SM:SA_TCCGTCTA CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/TCGCTAGA.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/TCGCTAGA.sam
new file mode 100644
index 0000000..6eaddd9
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/TCGCTAGA.sam
@@ -0,0 +1,12 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TCGCTAGA LB:LN_TCGCTAGA SM:SA_TCGCTAGA CN:BI
+HiMom:1:1101:1143:2192 77 * 0 0 * * 0 0 GGAGCGAGTCTGGGTCTCAGCCCCG CCCFFFFFHHHHHJGHIIIHJJJJI RG:Z:HiMom.1
+HiMom:1:1101:1143:2192 141 * 0 0 * * 0 0 CGACAAGTCTGGCTTATCACTCATC CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1479:2221 77 * 0 0 * * 0 0 TGTAAAGTATGCTGGCTCAGTGTAT BBBFDFFEHHHHHJJJJJJJIJHJJ RG:Z:HiMom.1
+HiMom:1:1101:1479:2221 141 * 0 0 * * 0 0 GGGGAAATCTATTTTTATGTAAAAA @CCFFFFFHHHHHJIGIJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1312:2112 77 * 0 0 * * 0 0 .TCCCAGCGAACCCGCGTGCAACCT #1=DFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1312:2112 141 * 0 0 * * 0 0 ATTTGCAGGAGCCGGCGCAGGTGCA CCCFFFFFHHHHHJJJIJJJJGHIJ RG:Z:HiMom.1
+HiMom:1:1201:1416:2128 77 * 0 0 * * 0 0 .ACAGGCGTGGAGGAGGCGGCGGCC #4=DDDFFHHHHHJIGJHFHHFFED RG:Z:HiMom.1
+HiMom:1:1201:1416:2128 141 * 0 0 * * 0 0 TTGGTGTGGAGGCGGTGGCGGGATC @@@DDDDDHHFHHII:?GGHIIB6? RG:Z:HiMom.1
+HiMom:1:2101:1064:2242 77 * 0 0 * * 0 0 ATGAACAAAGGAAGAATTATGCACG ?;?D;DDDF?;:+<<CFFCHE433A RG:Z:HiMom.1
+HiMom:1:2101:1064:2242 141 * 0 0 * * 0 0 .GGAAAAAGGTTGTCAAGCGTTAAA ######################### RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/TCTGCAAG.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/TCTGCAAG.sam
new file mode 100644
index 0000000..b1a4fda
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/TCTGCAAG.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TCTGCAAG LB:LN_TCTGCAAG SM:SA_TCTGCAAG CN:BI
+HiMom:1:1201:1042:2174 77 * 0 0 * * 0 0 .GTTGGTGTCTTCATTTTATGTATA #1=DDFDFHHHHHJIJJJHIJHIJJ RG:Z:HiMom.1
+HiMom:1:1201:1042:2174 141 * 0 0 * * 0 0 .TCAGGAAGGC..CAAAAAAAGAAA #0;@@@?@?<@##3<@@?@@????? RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/TGCAAGTA.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/TGCAAGTA.sam
new file mode 100644
index 0000000..1e37171
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/TGCAAGTA.sam
@@ -0,0 +1,6 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TGCAAGTA LB:LN_TGCAAGTA SM:SA_TGCAAGTA CN:BI
+HiMom:1:1101:1242:2170 77 * 0 0 * * 0 0 ATGGCAGGGCAGAGTTCTGATGAGT CCCFFFFFHHGGGIFHEIIGIIII? RG:Z:HiMom.1
+HiMom:1:1101:1242:2170 141 * 0 0 * * 0 0 GGAAGGAAAAGAAGCACAAGTACAT @@@DFDFFHHHGHHGIIGJJEHHIG RG:Z:HiMom.1
+HiMom:1:2101:1163:2222 77 * 0 0 * * 0 0 GAGCAGGCAAGGAGGACTTCTTGTT CCCFFFFFGHHHHJJHHIJJJJJIJ RG:Z:HiMom.1
+HiMom:1:2101:1163:2222 141 * 0 0 * * 0 0 GAGCGATAATGGTTCTTTTCCTCAC @@@DFFFFHHHHHJJJJJJJIJJJJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/TGCTGCTG.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/TGCTGCTG.sam
new file mode 100644
index 0000000..1eb5afe
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/TGCTGCTG.sam
@@ -0,0 +1,10 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TGCTGCTG LB:LN_TGCTGCTG SM:SA_TGCTGCTG CN:BI
+HiMom:1:1101:1084:2136 77 * 0 0 * * 0 0 .TCTCACTGTGAATTTGTGGTGGGC #1=DDFFFHHHHHJJJJGIJIJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1084:2136 141 * 0 0 * * 0 0 TTTCT.................... <<<@@#################### RG:Z:HiMom.1
+HiMom:1:1201:1285:2100 77 * 0 0 * * 0 0 .AATGACATGTTTAAAGATGGACTC #1:BDDFFHHFHHGIJIJIIIIGII RG:Z:HiMom.1
+HiMom:1:1201:1285:2100 141 * 0 0 * * 0 0 GATCTTTTTTGCTTTGTAGTTATAG @@@DFFFFHHHHHIIGIABCFFHBF RG:Z:HiMom.1
+HiMom:1:2101:1162:2139 77 * 0 0 * * 0 0 AGAGGTGAAATTCTTGGACCGGCGC @@@DDDDDHFHHHDB:EFHHCAG?D RG:Z:HiMom.1
+HiMom:1:2101:1162:2139 141 * 0 0 * * 0 0 ATCGTTTATGGTCGGAACTACGACG BCCFFFFFHHHHHIJJJJJJJIJJI RG:Z:HiMom.1
+HiMom:1:2101:1195:2150 77 * 0 0 * * 0 0 CCGAGAGAGTGAGAGCGCTCCTGGG CCCFFFFFHFHHHJJJJIJJJJIJJ RG:Z:HiMom.1
+HiMom:1:2101:1195:2150 141 * 0 0 * * 0 0 AATTGAACTTCACCACCCAGAGGAA CCCFFFFFHHHHHJJJJJJIJJJJJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/TGTAACTC.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/TGTAACTC.sam
new file mode 100644
index 0000000..6e11486
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/TGTAACTC.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TGTAACTC LB:LN_TGTAACTC SM:SA_TGTAACTC CN:BI
+HiMom:1:1201:1421:2154 77 * 0 0 * * 0 0 TGTGTGTGTGGGTGTGTGTATATAT ?@?DDFFFFFHH at GEFCCCHGIGJI RG:Z:HiMom.1
+HiMom:1:1201:1421:2154 141 * 0 0 * * 0 0 TGTGCTCTTCCGATCTTGTGCTCTT BC at DFFFFHHHHHJJJJFHIHHIJJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/TGTAATCA.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/TGTAATCA.sam
new file mode 100644
index 0000000..525a3f0
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/TGTAATCA.sam
@@ -0,0 +1,8 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TGTAATCA LB:LN_TGTAATCA SM:SA_TGTAATCA CN:BI
+HiMom:1:1101:1419:2119 77 * 0 0 * * 0 0 .ATGACTATGGTAACTGAAAGAAAA #1:A1BDADBFFDFIIIEEHECACF RG:Z:HiMom.1
+HiMom:1:1101:1419:2119 141 * 0 0 * * 0 0 ACTTTCCTTTTTTGTTTTACTTTAA ######################### RG:Z:HiMom.1
+HiMom:1:1201:1208:2132 77 * 0 0 * * 0 0 .CCTCAATGAGCGGCACTATGGGGG #1=DDFFFHHHHGJJIJJGHIJGIJ RG:Z:HiMom.1
+HiMom:1:1201:1208:2132 141 * 0 0 * * 0 0 CTGTAGAAAGGATGGTCGGGCTCCA @@CDFFFFGHFHHJIJJGJIBHJJG RG:Z:HiMom.1
+HiMom:1:1201:1344:2147 77 * 0 0 * * 0 0 TATCCTCCCTACTATGCCTAGAAGG =?@DADEFHBHDFG>EFGDHGFGHD RG:Z:HiMom.1
+HiMom:1:1201:1344:2147 141 * 0 0 * * 0 0 ACGATTAGTTTTAGCATTGGAGTAG @<??DDDDFHHHFGGHHIIIGGAGH RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/TTGTCTAT.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/TTGTCTAT.sam
new file mode 100644
index 0000000..69ec784
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/TTGTCTAT.sam
@@ -0,0 +1,10 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TTGTCTAT LB:LN_TTGTCTAT SM:SA_TTGTCTAT CN:BI
+HiMom:1:1101:1219:2164 77 * 0 0 * * 0 0 TCAAGCAGGAGCAGCTAAGTCCTAA CCCFFFFFHHHHHJJJJJJHIJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1219:2164 141 * 0 0 * * 0 0 ATCTTATCCACTCCTTCCACTTTGG CCCFFFFFHHHHHJJIJJJJJJJIJ RG:Z:HiMom.1
+HiMom:1:1201:1103:2184 77 * 0 0 * * 0 0 GTAAGAACTACCCTGGGTCCCCGTG @@BFFFFFHHHHHJJJJGIJJJJHI RG:Z:HiMom.1
+HiMom:1:1201:1103:2184 141 * 0 0 * * 0 0 AGAAGTTTCAGAATTGTGGCCCCAT B at BFFDEFHHHHHJJJGHIJJJJJI RG:Z:HiMom.1
+HiMom:1:1201:1107:2109 77 * 0 0 * * 0 0 .GGGAACCTGGCGCTAAACCATTCG #1=DFFFFHHHHHJJJJJJJJJIJJ RG:Z:HiMom.1
+HiMom:1:1201:1107:2109 141 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHGHHJJJJIIJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1252:2141 77 * 0 0 * * 0 0 .TTCCCCCCATGTAATTATTGTGAA #1=DDFFFHHHHHJJJJJJJJIJJJ RG:Z:HiMom.1
+HiMom:1:1201:1252:2141 141 * 0 0 * * 0 0 AGTTATTTTGCCTATGTCCAACAAG BCBFFFFFGHHHHJIJJJJJJJJJJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/barcode.params b/testdata/net/sf/picard/illumina/25T8B25T/sams/barcode.params
new file mode 100644
index 0000000..8046f3b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/barcode.params
@@ -0,0 +1,63 @@
+BARCODE SAMPLE_ALIAS LIBRARY_NAME
+AAAAAAAA SA_AAAAAAAA LN_AAAAAAAA
+AAAAGAAG SA_AAAAGAAG LN_AAAAGAAG
+AACAATGG SA_AACAATGG LN_AACAATGG
+AACGCATT SA_AACGCATT LN_AACGCATT
+ACAAAATT SA_ACAAAATT LN_ACAAAATT
+ACAGGTAT SA_ACAGGTAT LN_ACAGGTAT
+ACAGTTGA SA_ACAGTTGA LN_ACAGTTGA
+ACCAGTTG SA_ACCAGTTG LN_ACCAGTTG
+ACGAAATC SA_ACGAAATC LN_ACGAAATC
+ACTAAGAC SA_ACTAAGAC LN_ACTAAGAC
+ACTGTACC SA_ACTGTACC LN_ACTGTACC
+ACTGTATC SA_ACTGTATC LN_ACTGTATC
+AGAAAAGA SA_AGAAAAGA LN_AGAAAAGA
+AGCATGGA SA_AGCATGGA LN_AGCATGGA
+AGGTAAGG SA_AGGTAAGG LN_AGGTAAGG
+AGGTCGCA SA_AGGTCGCA LN_AGGTCGCA
+ATTATCAA SA_ATTATCAA LN_ATTATCAA
+ATTCCTCT SA_ATTCCTCT LN_ATTCCTCT
+CAACTCTC SA_CAACTCTC LN_CAACTCTC
+CAATAGAC SA_CAATAGAC LN_CAATAGAC
+CAATAGTC SA_CAATAGTC LN_CAATAGTC
+CAGCGGAT SA_CAGCGGAT LN_CAGCGGAT
+CAGCGGTA SA_CAGCGGTA LN_CAGCGGTA
+CCAACATT SA_CCAACATT LN_CCAACATT
+CCAGCACC SA_CCAGCACC LN_CCAGCACC
+CCATGCGT SA_CCATGCGT LN_CCATGCGT
+CGCCTTCC SA_CGCCTTCC LN_CGCCTTCC
+CGCTATGT SA_CGCTATGT LN_CGCTATGT
+CTAACTCG SA_CTAACTCG LN_CTAACTCG
+CTATGCGC SA_CTATGCGC LN_CTATGCGC
+CTATGCGT SA_CTATGCGT LN_CTATGCGT
+CTGCGGAT SA_CTGCGGAT LN_CTGCGGAT
+CTGTAATC SA_CTGTAATC LN_CTGTAATC
+GAAAAAAA SA_GAAAAAAA LN_GAAAAAAA
+GAACGAT. SA_GAACGAT. LN_GAACGAT.
+GAAGGAAG SA_GAAGGAAG LN_GAAGGAAG
+GACCAGGA SA_GACCAGGA LN_GACCAGGA
+GACCAGGC SA_GACCAGGC LN_GACCAGGC
+GACCGTTG SA_GACCGTTG LN_GACCGTTG
+GACCTAAC SA_GACCTAAC LN_GACCTAAC
+GATATCCA SA_GATATCCA LN_GATATCCA
+GCCGTCGA SA_GCCGTCGA LN_GCCGTCGA
+GCCTAGCC SA_GCCTAGCC LN_GCCTAGCC
+GTAACATC SA_GTAACATC LN_GTAACATC
+GTCCACAG SA_GTCCACAG LN_GTCCACAG
+TAAGCACA SA_TAAGCACA LN_TAAGCACA
+TACCGTCT SA_TACCGTCT LN_TACCGTCT
+TAGCGGTA SA_TAGCGGTA LN_TAGCGGTA
+TATCAGCC SA_TATCAGCC LN_TATCAGCC
+TATCCAGG SA_TATCCAGG LN_TATCCAGG
+TATCCATG SA_TATCCATG LN_TATCCATG
+TATCTCGG SA_TATCTCGG LN_TATCTCGG
+TATCTGCC SA_TATCTGCC LN_TATCTGCC
+TCCGTCTA SA_TCCGTCTA LN_TCCGTCTA
+TCGCTAGA SA_TCGCTAGA LN_TCGCTAGA
+TCTGCAAG SA_TCTGCAAG LN_TCTGCAAG
+TGCAAGTA SA_TGCAAGTA LN_TGCAAGTA
+TGCTGCTG SA_TGCTGCTG LN_TGCTGCTG
+TGTAACTC SA_TGTAACTC LN_TGTAACTC
+TGTAATCA SA_TGTAATCA LN_TGTAATCA
+TTGTCTAT SA_TTGTCTAT LN_TTGTCTAT
+N SA_N LN_N
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/multiplexed_positive_rgtags.params b/testdata/net/sf/picard/illumina/25T8B25T/sams/multiplexed_positive_rgtags.params
new file mode 100644
index 0000000..f56b403
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/multiplexed_positive_rgtags.params
@@ -0,0 +1,63 @@
+BARCODE_1 SAMPLE_ALIAS LIBRARY_NAME
+AAAAAAAA SA_AAAAAAAA LN_AAAAAAAA
+AAAAGAAG SA_AAAAGAAG LN_AAAAGAAG
+AACAATGG SA_AACAATGG LN_AACAATGG
+AACGCATT SA_AACGCATT LN_AACGCATT
+ACAAAATT SA_ACAAAATT LN_ACAAAATT
+ACAGGTAT SA_ACAGGTAT LN_ACAGGTAT
+ACAGTTGA SA_ACAGTTGA LN_ACAGTTGA
+ACCAGTTG SA_ACCAGTTG LN_ACCAGTTG
+ACGAAATC SA_ACGAAATC LN_ACGAAATC
+ACTAAGAC SA_ACTAAGAC LN_ACTAAGAC
+ACTGTACC SA_ACTGTACC LN_ACTGTACC
+ACTGTATC SA_ACTGTATC LN_ACTGTATC
+AGAAAAGA SA_AGAAAAGA LN_AGAAAAGA
+AGCATGGA SA_AGCATGGA LN_AGCATGGA
+AGGTAAGG SA_AGGTAAGG LN_AGGTAAGG
+AGGTCGCA SA_AGGTCGCA LN_AGGTCGCA
+ATTATCAA SA_ATTATCAA LN_ATTATCAA
+ATTCCTCT SA_ATTCCTCT LN_ATTCCTCT
+CAACTCTC SA_CAACTCTC LN_CAACTCTC
+CAATAGAC SA_CAATAGAC LN_CAATAGAC
+CAATAGTC SA_CAATAGTC LN_CAATAGTC
+CAGCGGAT SA_CAGCGGAT LN_CAGCGGAT
+CAGCGGTA SA_CAGCGGTA LN_CAGCGGTA
+CCAACATT SA_CCAACATT LN_CCAACATT
+CCAGCACC SA_CCAGCACC LN_CCAGCACC
+CCATGCGT SA_CCATGCGT LN_CCATGCGT
+CGCCTTCC SA_CGCCTTCC LN_CGCCTTCC
+CGCTATGT SA_CGCTATGT LN_CGCTATGT
+CTAACTCG SA_CTAACTCG LN_CTAACTCG
+CTATGCGC SA_CTATGCGC LN_CTATGCGC
+CTATGCGT SA_CTATGCGT LN_CTATGCGT
+CTGCGGAT SA_CTGCGGAT LN_CTGCGGAT
+CTGTAATC SA_CTGTAATC LN_CTGTAATC
+GAAAAAAA SA_GAAAAAAA LN_GAAAAAAA
+GAACGAT. SA_GAACGAT. LN_GAACGAT.
+GAAGGAAG SA_GAAGGAAG LN_GAAGGAAG
+GACCAGGA SA_GACCAGGA LN_GACCAGGA
+GACCAGGC SA_GACCAGGC LN_GACCAGGC
+GACCGTTG SA_GACCGTTG LN_GACCGTTG
+GACCTAAC SA_GACCTAAC LN_GACCTAAC
+GATATCCA SA_GATATCCA LN_GATATCCA
+GCCGTCGA SA_GCCGTCGA LN_GCCGTCGA
+GCCTAGCC SA_GCCTAGCC LN_GCCTAGCC
+GTAACATC SA_GTAACATC LN_GTAACATC
+GTCCACAG SA_GTCCACAG LN_GTCCACAG
+TAAGCACA SA_TAAGCACA LN_TAAGCACA
+TACCGTCT SA_TACCGTCT LN_TACCGTCT
+TAGCGGTA SA_TAGCGGTA LN_TAGCGGTA
+TATCAGCC SA_TATCAGCC LN_TATCAGCC
+TATCCAGG SA_TATCCAGG LN_TATCCAGG
+TATCCATG SA_TATCCATG LN_TATCCATG
+TATCTCGG SA_TATCTCGG LN_TATCTCGG
+TATCTGCC SA_TATCTGCC LN_TATCTGCC
+TCCGTCTA SA_TCCGTCTA LN_TCCGTCTA
+TCGCTAGA SA_TCGCTAGA LN_TCGCTAGA
+TCTGCAAG SA_TCTGCAAG LN_TCTGCAAG
+TGCAAGTA SA_TGCAAGTA LN_TGCAAGTA
+TGCTGCTG SA_TGCTGCTG LN_TGCTGCTG
+TGTAACTC SA_TGTAACTC LN_TGTAACTC
+TGTAATCA SA_TGTAATCA LN_TGTAATCA
+TTGTCTAT SA_TTGTCTAT LN_TTGTCTAT
+N SA_N LN_N
diff --git a/testdata/net/sf/picard/illumina/25T8B25T/sams/nonBarcoded.sam b/testdata/net/sf/picard/illumina/25T8B25T/sams/nonBarcoded.sam
new file mode 100644
index 0000000..ab6d41f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B25T/sams/nonBarcoded.sam
@@ -0,0 +1,182 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1 LB:Hello, World SM:HiDad CN:BI
+HiMom:1:1101:1031:2224 516 * 0 0 * * 0 0 ......................... ######################### RG:Z:HiMom.1 XN:i:1
+HiMom:1:1101:1039:2147 516 * 0 0 * * 0 0 ......................... ######################### RG:Z:HiMom.1 XN:i:1
+HiMom:1:1101:1046:2175 516 * 0 0 * * 0 0 ..GGA.................... ######################### RG:Z:HiMom.1
+HiMom:1:1101:1047:2122 516 * 0 0 * * 0 0 ..TCA.................... ######################### RG:Z:HiMom.1
+HiMom:1:1101:1048:2197 516 * 0 0 * * 0 0 ..GTG.................... ######################### RG:Z:HiMom.1
+HiMom:1:1101:1065:2193 4 * 0 0 * * 0 0 .CTTG.................... ######################### RG:Z:HiMom.1
+HiMom:1:1101:1069:2159 4 * 0 0 * * 0 0 GACGT.................... <<<@?#################### RG:Z:HiMom.1
+HiMom:1:1101:1071:2233 4 * 0 0 * * 0 0 GTTTG.................... <<<@@#################### RG:Z:HiMom.1
+HiMom:1:1101:1083:2193 4 * 0 0 * * 0 0 AGGCT.................... ######################### RG:Z:HiMom.1
+HiMom:1:1101:1084:2136 4 * 0 0 * * 0 0 TTTCT.................... <<<@@#################### RG:Z:HiMom.1
+HiMom:1:1101:1089:2172 4 * 0 0 * * 0 0 TCCGG.................... :<<??#################### RG:Z:HiMom.1
+HiMom:1:1101:1100:2207 4 * 0 0 * * 0 0 AGGCT............G....... ######################### RG:Z:HiMom.1
+HiMom:1:1101:1111:2148 4 * 0 0 * * 0 0 GCGAA.A..........GGACGAC. ######################### RG:Z:HiMom.1
+HiMom:1:1101:1138:2141 4 * 0 0 * * 0 0 TCCGATCTGCTTCAGGTCGATCAGA CCCFFFFFHGHHHJJIGHIJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1140:2120 4 * 0 0 * * 0 0 TTTTTTTTTTTTTAACTTTGCAAAT @@@DDDDDHHHHFB at 9FHI@BFH@@ RG:Z:HiMom.1
+HiMom:1:1101:1143:2192 4 * 0 0 * * 0 0 CGACAAGTCTGGCTTATCACTCATC CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1150:2228 4 * 0 0 * * 0 0 ATGGGAGGCGATTCCTAGGGGGTTG 8?=DD8;@BH6DHD<FGGGEIGHIG RG:Z:HiMom.1
+HiMom:1:1101:1157:2135 4 * 0 0 * * 0 0 TTTAAAGTCTTAATCAAAGATGATA CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1162:2207 516 * 0 0 * * 0 0 TAAAACTGGGGAAGTTAGAGGAATG ######################### RG:Z:HiMom.1
+HiMom:1:1101:1165:2239 4 * 0 0 * * 0 0 ATGGAAGTCGAGACAGAAGTGAGAA ######################### RG:Z:HiMom.1
+HiMom:1:1101:1175:2197 4 * 0 0 * * 0 0 AAGAGCTGGGGAACATCCAGAAAGG BC at FFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1188:2237 4 * 0 0 * * 0 0 GCTTCCTTCAAGACAGAAGTGAGAA CCCFFDDEFHHFFE at FDHHAIAFHG RG:Z:HiMom.1
+HiMom:1:1101:1197:2200 4 * 0 0 * * 0 0 ATATTCCACTGGAACCACAGAACCC @@@FFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1206:2126 4 * 0 0 * * 0 0 ATCTGTCCAGTGGTGCACTGAATGT CCCFFFFFHHHHHHIIJJJJIJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1212:2230 4 * 0 0 * * 0 0 TTTTAGCTTTATTGGGGAGGGGGTG CCCFFFFFHHGHHJJJJGJJJJJDF RG:Z:HiMom.1
+HiMom:1:1101:1218:2200 4 * 0 0 * * 0 0 GCTCTTCCGATCTATCTGCTCGTCC (-(=34???3;@############# RG:Z:HiMom.1
+HiMom:1:1101:1219:2164 4 * 0 0 * * 0 0 ATCTTATCCACTCCTTCCACTTTGG CCCFFFFFHHHHHJJIJJJJJJJIJ RG:Z:HiMom.1
+HiMom:1:1101:1221:2143 4 * 0 0 * * 0 0 CAATTGAATGTCTGCACAGCCGCTT @@@FFFFDHHHHHJJJIIIJGHIJJ RG:Z:HiMom.1
+HiMom:1:1101:1236:2121 4 * 0 0 * * 0 0 TTGCGCTTACTTTGTAGCCTTCATC CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1242:2170 4 * 0 0 * * 0 0 GGAAGGAAAAGAAGCACAAGTACAT @@@DFDFFHHHGHHGIIGJJEHHIG RG:Z:HiMom.1
+HiMom:1:1101:1257:2223 4 * 0 0 * * 0 0 TGCTCTTCCGATCTTTTAGCAAAGC :?@DDBDDHFFHDGIGIIJJJGGGI RG:Z:HiMom.1
+HiMom:1:1101:1259:2152 4 * 0 0 * * 0 0 ATTTTTATATTTTTTTAGACATAGG CCCFFFFFGHHHHJJJJIGIIJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1261:2127 516 * 0 0 * * 0 0 TTTTTTTTTTTTTTTTTTTTTTTTT CCCFFFFFHGHHHJJIFDDDDDDDD RG:Z:HiMom.1
+HiMom:1:1101:1263:2236 516 * 0 0 * * 0 0 AGTTCTTCAGTAATTTTAGTACTGC ######################### RG:Z:HiMom.1
+HiMom:1:1101:1267:2209 4 * 0 0 * * 0 0 GGCAGAGTCTCCAACAGCCCCGTAC =;?DDDD?CCFHAIIIGGIIGE at EG RG:Z:HiMom.1
+HiMom:1:1101:1269:2170 4 * 0 0 * * 0 0 TTCCAAGCCTGTGCTTTAAGGAAAA @@<ADBDBDF8DDCFH at GIE@@GGH RG:Z:HiMom.1
+HiMom:1:1101:1290:2225 4 * 0 0 * * 0 0 TCAGTTCACTGGCAAAGACAGTCAC C@@FBEDDFHFHGIIICEHGDHBHE RG:Z:HiMom.1
+HiMom:1:1101:1291:2150 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHFHHIJJJIIIGIJIJ RG:Z:HiMom.1
+HiMom:1:1101:1302:2244 4 * 0 0 * * 0 0 TGAATACATATAACAAATGCAAAAA CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1308:2153 516 * 0 0 * * 0 0 TCTGTAAGGTAATCCCCGCATGTGT 1?1=4===AFFDFFGFDGFB at CFB: RG:Z:HiMom.1
+HiMom:1:1101:1309:2210 4 * 0 0 * * 0 0 AGTGGGCTAGGGCATTTTTAATCTT @@?DFFDFHHHDFHJIJJIJGIIIJ RG:Z:HiMom.1
+HiMom:1:1101:1314:2233 4 * 0 0 * * 0 0 AGGAAAGTTGGGCTGACCTGACAGA @@<DDD;=FBFADBCGDEH?F;FCG RG:Z:HiMom.1
+HiMom:1:1101:1316:2126 4 * 0 0 * * 0 0 TCTTTTTTTTTTTTTTTTTTTTTTT CCCFFFFFHHHHHJJJJHFDDDDDD RG:Z:HiMom.1
+HiMom:1:1101:1327:2200 516 * 0 0 * * 0 0 GTCATCTGGGCTGTCGACAGGTGTC @B at FFFFFHHHHGIJJJJJJIFHHI RG:Z:HiMom.1
+HiMom:1:1101:1328:2225 4 * 0 0 * * 0 0 AGGAAATTAGGACTTACCTGACATA ######################### RG:Z:HiMom.1
+HiMom:1:1101:1338:2175 4 * 0 0 * * 0 0 GCTTGTTGGCTTTAACATCCACAAT CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1347:2149 4 * 0 0 * * 0 0 GCTCTTCCGATCTGTGCTCTTCCGA CCCFFFFFDFHHFIJDGIGGHGIGH RG:Z:HiMom.1
+HiMom:1:1101:1353:2226 4 * 0 0 * * 0 0 GTGCTCTTCCGATCTTCAGGTTACC BBBFFFFFHHHHHJJJJJJJIJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1363:2138 4 * 0 0 * * 0 0 GTTCTTAAACCTGTTAGAACTTCTG C@@FFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1399:2128 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHIJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1403:2194 4 * 0 0 * * 0 0 ACATGGTGAAACCCTGTCTCTACTA CCCFFFDDHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1406:2222 4 * 0 0 * * 0 0 GGCTGGACTCCCCTGGTTCTGGGCA ;?@DDDBD?FHDFGIIIGIGHHIII RG:Z:HiMom.1
+HiMom:1:1101:1419:2119 4 * 0 0 * * 0 0 ACTTTCCTTTTTTGTTTTACTTTAA ######################### RG:Z:HiMom.1
+HiMom:1:1101:1420:2213 4 * 0 0 * * 0 0 TTCACTGTACCGGCCGTGCGTACTT @CCFFFFDHHHFGIJJJJJJGHIGG RG:Z:HiMom.1
+HiMom:1:1101:1435:2194 4 * 0 0 * * 0 0 TTTTGTTTTCTTTTACTGAAGTGTA CCCFFDFFHHHHHJJJJIHIJHHHJ RG:Z:HiMom.1
+HiMom:1:1101:1441:2148 4 * 0 0 * * 0 0 TTTTGGCTCTAGAGGGGGTAGAGGG CCCFFFFFHHDFBHIIJJ1?FGHIJ RG:Z:HiMom.1
+HiMom:1:1101:1452:2132 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHJJJJJJJIJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1460:2176 4 * 0 0 * * 0 0 AGGAAAAAGACACAACAAGTCCAAC ######################### RG:Z:HiMom.1
+HiMom:1:1101:1479:2221 4 * 0 0 * * 0 0 GGGGAAATCTATTTTTATGTAAAAA @CCFFFFFHHHHHJIGIJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1101:1491:2120 4 * 0 0 * * 0 0 GGCCAGGCTGAACTTCTGAGCTGCT CCCFFFFFHHHGHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1018:2133 4 * 0 0 * * 0 0 ......................... ######################### RG:Z:HiMom.1 XN:i:1
+HiMom:1:1201:1018:2217 516 * 0 0 * * 0 0 ......................... ######################### RG:Z:HiMom.1 XN:i:1
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+HiMom:1:1201:1045:2105 516 * 0 0 * * 0 0 .TTTTTTTTTT..TTTTTTTTTTTT #0;@@@@@@@?##0:????????=< RG:Z:HiMom.1
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+HiMom:1:1201:1073:2225 4 * 0 0 * * 0 0 CGTGTGCTCTTCCGATCTGGAGGGT @BBDFFFFHHHHHJJJJJJJJJJJ: RG:Z:HiMom.1
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+HiMom:1:1201:1095:2146 4 * 0 0 * * 0 0 ACTGACAACACCAAATGCTGCTAAG CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1103:2184 4 * 0 0 * * 0 0 AGAAGTTTCAGAATTGTGGCCCCAT B at BFFDEFHHHHHJJJGHIJJJJJI RG:Z:HiMom.1
+HiMom:1:1201:1107:2109 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHGHHJJJJIIJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1118:2198 4 * 0 0 * * 0 0 AATAAACTTTATTAAAGCAGTTAAA C at CFFFFFHDHHHGIIIJJJIJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1122:2227 4 * 0 0 * * 0 0 GTCATATAAGGCCCAGTCCAAGGAA @@@FFFFFHHHGGIJIGGIJFIJII RG:Z:HiMom.1
+HiMom:1:1201:1123:2161 516 * 0 0 * * 0 0 CGTGTGCTCTTCCGATCTGCATACA ===AAAA8AAAA<AAA)@CBA9>A# RG:Z:HiMom.1
+HiMom:1:1201:1127:2112 516 * 0 0 * * 0 0 TAATCACCTGAGCAGTGAAGCCAGC @<@?BDDDHD?FDBHI?AHGGGDFH RG:Z:HiMom.1
+HiMom:1:1201:1134:2144 4 * 0 0 * * 0 0 AGTGTGAGTAATGGTTGAGAGGTGG B@?DDDFFFHHGHJHHGFIHHIFGI RG:Z:HiMom.1
+HiMom:1:1201:1138:2227 516 * 0 0 * * 0 0 GACAAATATAGGAAATAGAAGCTAT =1=A=AAA,2?4>7C<<4<A+3<AB RG:Z:HiMom.1
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+HiMom:1:1201:1142:2242 4 * 0 0 * * 0 0 GTAAAATGTAAAATAATAAAAAATG ?=?DDDD;AF<DF<FFFFIIIFF@< RG:Z:HiMom.1
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+HiMom:1:1201:1159:2179 516 * 0 0 * * 0 0 TTTTTTTTTATTTTTCTAAATACTT ===AA#################### RG:Z:HiMom.1
+HiMom:1:1201:1160:2109 4 * 0 0 * * 0 0 ACATCCTTCCCATGCCACCAACTCG CCCFFFFFGHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1180:2119 4 * 0 0 * * 0 0 GCTCTAAATTTTGCTTTTCTACAGC CCCFFFFFHHHHHJJJJIJIJJIJJ RG:Z:HiMom.1
+HiMom:1:1201:1185:2143 4 * 0 0 * * 0 0 GCTGAAGGCCCGTGGGCCAGAGGTG @CCFFFFFHHHHHJJJJJJJJJJHI RG:Z:HiMom.1
+HiMom:1:1201:1187:2100 4 * 0 0 * * 0 0 AAAAAAGAGCCCGCATTGCCGAGAC =<=;AA################### RG:Z:HiMom.1
+HiMom:1:1201:1190:2194 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1204:2228 4 * 0 0 * * 0 0 TCTTCTTGTCGATGAGGAACTTGGT @?@FFFFFDHHGHJIJJGHIIJJJH RG:Z:HiMom.1
+HiMom:1:1201:1208:2132 4 * 0 0 * * 0 0 CTGTAGAAAGGATGGTCGGGCTCCA @@CDFFFFGHFHHJIJJGJIBHJJG RG:Z:HiMom.1
+HiMom:1:1201:1219:2115 4 * 0 0 * * 0 0 TGGGAGTAGTTCCCTGCTAAGGGAG ???DBDBDADDDDIEID:AFFD:?8 RG:Z:HiMom.1
+HiMom:1:1201:1236:2187 4 * 0 0 * * 0 0 CTCCTTAGCGGATTCCGACTTCCAT CCCFFFFDHHHHGIJJIGIGIJJGG RG:Z:HiMom.1
+HiMom:1:1201:1242:2207 4 * 0 0 * * 0 0 ATCTTTTATTGGCCTCCTGCTCCCC CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1252:2141 4 * 0 0 * * 0 0 AGTTATTTTGCCTATGTCCAACAAG BCBFFFFFGHHHHJIJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1260:2165 4 * 0 0 * * 0 0 ATCTGATCTAAGTTGGGGGACGCCG @@@FFDFFHHHHHJJJIJIIIGIJJ RG:Z:HiMom.1
+HiMom:1:1201:1280:2179 4 * 0 0 * * 0 0 GAGGACTGCTTGAGTCCAGGAGTTC @@BFFDEFGHHHHIFGCHIJJJGGI RG:Z:HiMom.1
+HiMom:1:1201:1281:2133 4 * 0 0 * * 0 0 GCAACAAAATTTCATATGACTTAGC CCCFFFFFHHHHHJJIIIHICHIIJ RG:Z:HiMom.1
+HiMom:1:1201:1285:2100 4 * 0 0 * * 0 0 GATCTTTTTTGCTTTGTAGTTATAG @@@DFFFFHHHHHIIGIABCFFHBF RG:Z:HiMom.1
+HiMom:1:1201:1291:2158 4 * 0 0 * * 0 0 CGTGTGCTCTTCCGATCTGATGGGC @CCFFFDD?FHHFGEHHIIDHIIII RG:Z:HiMom.1
+HiMom:1:1201:1300:2137 4 * 0 0 * * 0 0 GCTCTTCCGATCTTTTTTTTAATTT @@?DDDDDFDHADEHGIGGED3?FD RG:Z:HiMom.1
+HiMom:1:1201:1312:2112 4 * 0 0 * * 0 0 ATTTGCAGGAGCCGGCGCAGGTGCA CCCFFFFFHHHHHJJJIJJJJGHIJ RG:Z:HiMom.1
+HiMom:1:1201:1331:2162 4 * 0 0 * * 0 0 TAATCCCAGTACTTTGGGAGGCCAA CCCFFFFFHHHHHJJJJIJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1341:2116 4 * 0 0 * * 0 0 ATAACAGCGAGACTGGCAACTTAAA ######################### RG:Z:HiMom.1
+HiMom:1:1201:1344:2147 4 * 0 0 * * 0 0 ACGATTAGTTTTAGCATTGGAGTAG @<??DDDDFHHHFGGHHIIIGGAGH RG:Z:HiMom.1
+HiMom:1:1201:1345:2181 4 * 0 0 * * 0 0 ATACGGATGTGTTTAGGAGTGGGAC CCCFFFFFHHHHHIIJJHJFHIJIJ RG:Z:HiMom.1
+HiMom:1:1201:1364:2113 4 * 0 0 * * 0 0 TAAAGAGAGCCAGTGGAGTTACGAC ######################### RG:Z:HiMom.1
+HiMom:1:1201:1392:2109 4 * 0 0 * * 0 0 GTCAGACAGGGGGATTTGGGCTGTG BBCFFFFFHHHHHHJJJHIJIJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1392:2184 4 * 0 0 * * 0 0 ATCTTTATTCATTTGTATGATCTTA @@BFFFFFHFFHFHIHIIJIJJJJI RG:Z:HiMom.1
+HiMom:1:1201:1393:2143 4 * 0 0 * * 0 0 GATAAATGCACGCATCCCCCCCGCG C at CFFFFFGGHHHHJJJJJJJJJJI RG:Z:HiMom.1
+HiMom:1:1201:1414:2174 516 * 0 0 * * 0 0 TTTTTTTTTTTTTTTTTTTTTTTTT @;@1BDADF????FFEB>B6=BBBB RG:Z:HiMom.1
+HiMom:1:1201:1416:2128 4 * 0 0 * * 0 0 TTGGTGTGGAGGCGGTGGCGGGATC @@@DDDDDHHFHHII:?GGHIIB6? RG:Z:HiMom.1
+HiMom:1:1201:1421:2154 4 * 0 0 * * 0 0 TGTGCTCTTCCGATCTTGTGCTCTT BC at DFFFFHHHHHJJJJFHIHHIJJ RG:Z:HiMom.1
+HiMom:1:1201:1439:2156 4 * 0 0 * * 0 0 GGAGATTATTTGCCTTGAAGTAAGC -;(22<>>@>8@>8;@######### RG:Z:HiMom.1
+HiMom:1:1201:1452:2143 4 * 0 0 * * 0 0 TTTTAGTCTTAGCATTTACTTTCCC CCCFFFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:1201:1458:2109 4 * 0 0 * * 0 0 GATACGAACACACAAGAACTTTTTT CCCFFFFFHHHHHJJJJJJJJJJJI RG:Z:HiMom.1
+HiMom:1:1201:1472:2121 516 * 0 0 * * 0 0 GTGTGCTCTTCCGATCTGGAGGATG =+=??A4A==A at 7A<?######### RG:Z:HiMom.1
+HiMom:1:1201:1483:2126 516 * 0 0 * * 0 0 GCATGCAGCTGGGTGCTGTGATGCA @@@DDDBB<DD8F<<CGG?AA?A<F RG:Z:HiMom.1
+HiMom:1:1201:1486:2109 4 * 0 0 * * 0 0 ACGTGTGCTCTTCCCGATCTGTATA CCCFF?DDFBHHHJJIIDHJIJJJH RG:Z:HiMom.1
+HiMom:1:1201:1486:2146 516 * 0 0 * * 0 0 TTTTTTTTTTTTTTTTTTTTTGGGC <<<@??@??@???????######## RG:Z:HiMom.1
+HiMom:1:2101:1011:2102 4 * 0 0 * * 0 0 .....TCACACATAATTTTAAAATT #####22@?@@??@@@@@??@@@@@ RG:Z:HiMom.1
+HiMom:1:2101:1013:2146 4 * 0 0 * * 0 0 ....CGCTAGAACCAACTTATTCAT ####24=?@@?@?@@?@@@@@@?@@ RG:Z:HiMom.1
+HiMom:1:2101:1021:2209 4 * 0 0 * * 0 0 ..GGAAGGCTGCTAGCTGGCCAGAG ##08@>??@@??@?????????>?@ RG:Z:HiMom.1
+HiMom:1:2101:1023:2237 516 * 0 0 * * 0 0 ..TTTGTTTGAGTTCCTTGTAGATT ##0:=@?>?@???@:>?@??>?;?< RG:Z:HiMom.1
+HiMom:1:2101:1031:2163 4 * 0 0 * * 0 0 ..ACATTTGTCACCACTAGCCACCA ##0<@?@@@@@@@@@@?@@@@@@@? RG:Z:HiMom.1
+HiMom:1:2101:1036:2087 4 * 0 0 * * 0 0 .GTCCACTTACGAAGCAAATACTTT #4=DDFFFHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1040:2208 516 * 0 0 * * 0 0 .CTGATAGTCACTGAAATGAATTCA #-0=>(2 at .22@@############ RG:Z:HiMom.1
+HiMom:1:2101:1048:2238 4 * 0 0 * * 0 0 .GTCACATCGTTGAAGCACTGGATC #11ADDDB<CFFHCHGDBHGIIIII RG:Z:HiMom.1
+HiMom:1:2101:1054:2162 4 * 0 0 * * 0 0 .GGACAGGGAAGGGAAGGAAGGGTG #4=DDFDFHHHHHJIJIIDHHGICG RG:Z:HiMom.1
+HiMom:1:2101:1059:2083 4 * 0 0 * * 0 0 .GAATGTCTTAGAAGGATGCTTCTC #1=BDDDEHHGHHJJJJJIJJIIJJ RG:Z:HiMom.1
+HiMom:1:2101:1063:2206 4 * 0 0 * * 0 0 .TGCTAGGATGAGGATGGATAGTAA #1=DDDFFHHHHHJHIIJHIIIHHJ RG:Z:HiMom.1
+HiMom:1:2101:1064:2242 4 * 0 0 * * 0 0 .GGAAAAAGGTTGTCAAGCGTTAAA ######################### RG:Z:HiMom.1
+HiMom:1:2101:1072:2170 4 * 0 0 * * 0 0 .GGGGAGACAGAGAGGATCAGAAGT #4=BDDFDHHDFHEGFEGGIJIIIG RG:Z:HiMom.1
+HiMom:1:2101:1077:2139 4 * 0 0 * * 0 0 .ATTAGTTGGCGGATGAAGCAGATA #4=DFFFFHHHHHJJJJJJJJJIJJ RG:Z:HiMom.1
+HiMom:1:2101:1084:2188 4 * 0 0 * * 0 0 TACAAGGTCAAAATCAGCAACAAGT CCCFFFFDHHHHHJJJJJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1100:2085 4 * 0 0 * * 0 0 ATCTTGATCTCCTCCTTCTTGGCCT @@@DDDDDHHFHFEIIIIHHBAHBG RG:Z:HiMom.1
+HiMom:1:2101:1102:2221 4 * 0 0 * * 0 0 ATAACTGACTCTACTCAGTAGATTA CCCFFFFFHHHHHJJJJJIJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1105:2131 4 * 0 0 * * 0 0 CAGCAGCAGCAACAGCAGAAACATG CCCFFFFFHHHHHJJJJJIJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1112:2245 4 * 0 0 * * 0 0 TCGTAGTGTTGTAATTTCGTCTTCT ?8?DBDDDCCFCAACGGFFCBFFAE RG:Z:HiMom.1
+HiMom:1:2101:1122:2136 4 * 0 0 * * 0 0 CTTGCCAGCCTGCAGGCCCCGCGGC ???BBAABDD?DDIID)A:3<EADD RG:Z:HiMom.1
+HiMom:1:2101:1123:2095 4 * 0 0 * * 0 0 TCCGCCTCCAGCTTCAGCTTCTCCT @@@FDDFFHHHHHJHGGJIJJJEHH RG:Z:HiMom.1
+HiMom:1:2101:1126:2082 4 * 0 0 * * 0 0 TCTCTTTCCACCTTGGTCACCTTCC @C at DDDFFHHHHHJEGGIHHIJGIH RG:Z:HiMom.1
+HiMom:1:2101:1133:2239 4 * 0 0 * * 0 0 AGCTTTTTGTTTCCTAGCTTGTCTT ?@?DDFFFHHHHF4ACFHIJHHHGH RG:Z:HiMom.1
+HiMom:1:2101:1143:2137 4 * 0 0 * * 0 0 GCTCTTCAGATCTAGGGGGAACAGC @@@DD?=DCAFFFHIIDG:EFHIII RG:Z:HiMom.1
+HiMom:1:2101:1151:2182 516 * 0 0 * * 0 0 TTTTTTTTTTTTTTTTTTTTTTTTA 9<<?@?@;5=?############## RG:Z:HiMom.1
+HiMom:1:2101:1151:2236 516 * 0 0 * * 0 0 TTTGAAGCCTCTTTATCCTTGGCAT ######################### RG:Z:HiMom.1
+HiMom:1:2101:1162:2139 4 * 0 0 * * 0 0 ATCGTTTATGGTCGGAACTACGACG BCCFFFFFHHHHHIJJJJJJJIJJI RG:Z:HiMom.1
+HiMom:1:2101:1163:2203 4 * 0 0 * * 0 0 TTGGTTCACTTATGTATTTATGAAT @CCFDFFFHHHHHJHIIJJJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1163:2222 4 * 0 0 * * 0 0 GAGCGATAATGGTTCTTTTCCTCAC @@@DFFFFHHHHHJJJJJJJIJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1172:2152 516 * 0 0 * * 0 0 ATCGTTTCTGGGGACTAGTGAGGCG ######################### RG:Z:HiMom.1
+HiMom:1:2101:1186:2093 4 * 0 0 * * 0 0 AATGTTGGGAGGACAATGATGGAAA ######################### RG:Z:HiMom.1
+HiMom:1:2101:1188:2195 4 * 0 0 * * 0 0 GCACATACACCAAATGTCTGAACCT CCCFFFFFHHHHHJJJHIJJJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1195:2150 4 * 0 0 * * 0 0 AATTGAACTTCACCACCCAGAGGAA CCCFFFFFHHHHHJJJJJJIJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1207:2084 516 * 0 0 * * 0 0 TCACCACTCTTCTGGGCATCCCCTG @@@DDEDFHHHHHIJIHHGHGGJJJ RG:Z:HiMom.1
+HiMom:1:2101:1208:2231 516 * 0 0 * * 0 0 CTTTTTTTTTTTTTTTTTTTTTTTT CCCFFFFFHHHHHJJJHFDDDDDDD RG:Z:HiMom.1
+HiMom:1:2101:1215:2110 4 * 0 0 * * 0 0 ATCTTTCCCCCATTAAGAACAGCAA ######################### RG:Z:HiMom.1
+HiMom:1:2101:1216:2172 4 * 0 0 * * 0 0 GGACTTCTAGGGGATTTAGCGGGGT CCCFFFFFHHHHHJJJJJJJJJJJD RG:Z:HiMom.1
+HiMom:1:2101:1216:2193 4 * 0 0 * * 0 0 AGGCATGACACTGCATTTTAAATAC @@@DDDDDHFFHHGGDFHFHIIHGG RG:Z:HiMom.1
+HiMom:1:2101:1226:2088 4 * 0 0 * * 0 0 GCTCTTCCGATCTAGGTAATAGCTA ==?BDFFFDCDDHFFFAFHDHIJGJ RG:Z:HiMom.1
+HiMom:1:2101:1231:2208 4 * 0 0 * * 0 0 AGCCAGTGTTGGTGTGTTGACTGTT @@;1ADABCF;BF<AACGCHEBHC< RG:Z:HiMom.1
+HiMom:1:2101:1233:2133 516 * 0 0 * * 0 0 TTTTTTTTTTTTTTTTTTTTTTTTT CCCFFFFFGHHHHJJJFDDDDDDDD RG:Z:HiMom.1
+HiMom:1:2101:1240:2197 516 * 0 0 * * 0 0 ACTGGAGATCCTTGTTACATGCCCA ??+++A:DD?:ADEE@::C4:C<E: RG:Z:HiMom.1
+HiMom:1:2101:1245:2154 4 * 0 0 * * 0 0 ACCAATCAGTAGCACCACTATACAC CCCFFFFFHHHHHJJJJJJIJJJJJ RG:Z:HiMom.1
+HiMom:1:2101:1249:2231 4 * 0 0 * * 0 0 TCTCTCGGCCTTCCACTCTAGCATA @@@FFFFFFHHGHIJJJGJIIJHIJ RG:Z:HiMom.1
+HiMom:1:2101:1258:2092 4 * 0 0 * * 0 0 TTAGACAAAACACCAAAATAAAATA ######################### RG:Z:HiMom.1
+HiMom:1:2101:1262:2128 516 * 0 0 * * 0 0 TCTTGTGGTAACTTTTCTGACACCT -(---9@;@?:8>?4:>?@###### RG:Z:HiMom.1
+HiMom:1:2101:1273:2119 516 * 0 0 * * 0 0 ATGATGGATCTTCTCTAACTTGTCA >=><AAAAA+2AA?CB4@@ABB3?A RG:Z:HiMom.1
+HiMom:1:2101:1285:2105 516 * 0 0 * * 0 0 TGTCTATATCAACCAACACCTCTTC -(0(():94:9:???########## RG:Z:HiMom.1
+HiMom:1:2101:1312:2105 4 * 0 0 * * 0 0 GTTGAGAATAGGTTGAGATCGTTTC @CCFFFDFHHFHDHIJJJJJJJIJJ RG:Z:HiMom.1
+HiMom:1:2101:1325:2083 4 * 0 0 * * 0 0 TGTGCTCTTCCGATCTGGAGAAAAA ######################### RG:Z:HiMom.1
+HiMom:1:2101:1336:2109 4 * 0 0 * * 0 0 AGACCAGAACAGCTCCAGGTGCTCC CCCFFFFFHHHHHJJJJJJCGHIJJ RG:Z:HiMom.1
+HiMom:1:2101:1349:2084 4 * 0 0 * * 0 0 AGTCTGAATCATTGGTGTCTGAAGA <5;??=>=>>?############## RG:Z:HiMom.1
+HiMom:1:2101:1365:2094 4 * 0 0 * * 0 0 GCTCTTCCGATCTTGTGCTCTTCCG CCCFFFFDHFHHGJJIIJIJJIHII RG:Z:HiMom.1
+HiMom:1:2101:1370:2116 4 * 0 0 * * 0 0 CACCATCTGACATCATGTTTGAAAG @@@DFFFDFFHDHIGBHHII<HEDB RG:Z:HiMom.1
+HiMom:1:2101:1386:2105 4 * 0 0 * * 0 0 AGGAATTATTCTTCTGCCATAAGGT B@@DDFFFHGFHHIJJJJJGIGIJH RG:Z:HiMom.1
+HiMom:1:2101:1414:2098 4 * 0 0 * * 0 0 TTGGGGCCGGTGCCGTCGGGCCCAA CCCFFFFFHHHHGJJIJJJJJJJIJ RG:Z:HiMom.1
+HiMom:1:2101:1427:2081 4 * 0 0 * * 0 0 CCGACTTCCATGGCCACCGTCCTGC CCCFFFFFHHHHHJJJIIGFIIJJI RG:Z:HiMom.1
+HiMom:1:2101:1450:2134 4 * 0 0 * * 0 0 ACAAACCCTTGTGTCGAGGGCTGAC CC at FDFDFFDFHFGIIE1CGGHBGE RG:Z:HiMom.1
+HiMom:1:2101:1459:2083 4 * 0 0 * * 0 0 ATTTCACCAAAATAATCAGAAGGCC CCCFFFFDBHGHHIGGIJFJJGGFH RG:Z:HiMom.1
+HiMom:1:2101:1491:2093 4 * 0 0 * * 0 0 AGAGACGGGGTCTCGCTATGTTGCC BCCDFFFFHHHHHJIIJJJJIJIJJ RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl
new file mode 100755
index 0000000..7ea8e90
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl
new file mode 100755
index 0000000..0ad6ae1
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl
new file mode 100755
index 0000000..a2cd5a1
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl
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diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl
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diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl
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index 0000000..9fd50b6
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diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl
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index 0000000..1776a81
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diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl
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index 0000000..410f50a
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diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl
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index 0000000..e72f153
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl
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index 0000000..6b2a0db
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C59.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C59.1/s_1_1101.bcl
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index 0000000..c57e8a1
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C59.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl
new file mode 100755
index 0000000..a4ff492
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diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C60.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C60.1/s_1_1101.bcl
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index 0000000..757ba0f
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C60.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C61.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C61.1/s_1_1101.bcl
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index 0000000..5dcafb5
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C61.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C62.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C62.1/s_1_1101.bcl
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index 0000000..246a35e
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C62.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C63.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C63.1/s_1_1101.bcl
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index 0000000..9ab9025
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C63.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C64.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C64.1/s_1_1101.bcl
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index 0000000..19d3ce3
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C64.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C65.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C65.1/s_1_1101.bcl
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index 0000000..7311d45
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C65.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C66.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C66.1/s_1_1101.bcl
new file mode 100755
index 0000000..07754e5
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C66.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl
new file mode 100755
index 0000000..653c2a9
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl
new file mode 100755
index 0000000..f1f542f
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl
new file mode 100755
index 0000000..216f321
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/s_1_1101.filter b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/s_1_1101.filter
new file mode 100755
index 0000000..d1f2a37
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/s_1_1101.filter differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/s_1_1101_barcode.txt b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/s_1_1101_barcode.txt
new file mode 100755
index 0000000..b398f93
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/s_1_1101_barcode.txt
@@ -0,0 +1,60 @@
+CAATAGTCCGACTCTC Y CAATAGTCCGACTCTC 0 7
+CTGTAATCCTATTAGC Y CTGTAATCCTATTAGC 0 7
+CTCCCTCTTCCTTCTT N attcctcttcaggctt 5 7
+TGTATCTCTTACTCTT N tgtaactccgacagtt 5 7
+AGGTCGCATTCCTTTC N aggtcgcaatccttaa 3 8
+TGTTCCGAAACCTCTT Y TGTTCCGAAACCTCTT 0 7
+TGTCGGTTTTTTGCTT N tgtcggataattgctt 3 7
+GCCGTCGAAGGTACCC Y GCCGTCGAAGGTACCA 1 7
+ATAGCGTCTTGGTCTG Y ATAGCGTCTTGGTCTG 0 8
+CCTATTCTTCGTTTTC N attatgtttccacttc 7 7
+CATGTTCGCGCCTTTT N catgatcgcgcatatt 3 7
+ACAGTTGAATCTTCTC Y ACAGTTGAATCTTCTC 0 7
+TTCCTCCTCACCATCC N ttgagcctcactagcc 5 7
+AACTTGACGCTCTCTT Y AACTTGACGCTCTCTT 0 7
+GTCTGATGGAACTTCG Y GTCTGATGGAACTTCG 0 8
+TCCTTGGTGCTGCACT Y TCCTTGGTGCTGCACT 0 8
+CATGCTTTTAGCATTG Y CATGCTTATAGCATTG 1 8
+ACCTACTGCTTCCCTT N accaactgcatcactt 3 8
+GCCTAGCCCTTGAATC Y GCCTAGCCCTTGAATC 0 7
+CCTCTTCTCTCGCTTT N aatgttctctggctat 5 8
+GCTATCCACCTCCCCC N gatatccagctcacca 4 7
+ATTGTCTGGATTCACA N attgtctgcacgattc 7 8
+TTAATCAGCTGGTATT Y TTAATCAGCTGGTATT 0 8
+ACTAAGACGTCCTCAT Y ACTAAGACGTCCTCAT 0 7
+CAGCGGTATGTACTGC Y CAGCGGTAAGTACTGC 1 8
+GCCGTCGATGGTACCC Y GCCGTCGAAGGTACCA 2 7
+TGCTCGACTTCACAGT Y TGCTCGACTTCACAGA 1 7
+AGTTGCTTTGACTTGG Y AGTTGCTTTGACTTGG 0 8
+CCAGAGCTCAACTGAT Y CCAGAGCTCAACTGAT 0 7
+AGGTTATCTTAGCCAG Y AGGTTATCTTAGCCAG 0 8
+GACCAGGACCATCACA Y GACCAGGACCATCACA 0 8
+CAGCAAGGGCGATATT Y CAGCAAGGGCGATATT 0 7
+ACAGTTGAATCTTCTC Y ACAGTTGAATCTTCTC 0 7
+ACCAACTGCATCACTT Y ACCAACTGCATCACTT 0 7
+CCTCTTTCTTCTGCTC N actgtatctgcttcac 6 7
+ATTATCAACACCATAC N attgtctgcacgattc 5 6
+TCGCCTTGCCAACGCT Y TCGCCTTGCCAACGCT 0 7
+GTCTGATGTCACTTCC N gtctgatggaacttcg 3 8
+CCAGAGCTCAACTGAT Y CCAGAGCTCAACTGAT 0 7
+TACTTAGCGTCTGCAC Y TACTTAGCGTCTGCAC 0 8
+ACAGGTATCACTTCAT Y ACAGGTATCACTTCAT 0 7
+CATGCTTATAGCATTT Y CATGCTTATAGCATTG 1 9
+AGGTGCGAGACATTAA Y AGGTGCGAGACATTAA 0 6
+CCCGATTTTCTCTCCC N aacgcattcctgtcat 8 8
+TTCTCATCTTCCTTCC N gtctgatggaacttcg 7 8
+CCTTCGCAGAATCGAC Y CCTTCGCAGAATCGAC 0 7
+AAGACACTAGTCTCCT Y AAGACACTAGTCACCT 1 7
+CCTTCTTTTATCATTT N catgcttatagcattg 5 7
+TGCAAGTACGAACTTC Y TGCAAGTACGAACTTC 0 7
+TCCCCGTTCCAACTTC N tgcaagtacgaacttc 5 6
+TTATATCTTCATGTCT Y TTATATCTTCATGTCT 0 7
+TACTTAGCGTCTGCAC Y TACTTAGCGTCTGCAC 0 8
+CGCTATGTTTCTCCTT Y CGCTATGTTTCACCTT 1 9
+TGCAAGTACGAACTTC Y TGCAAGTACGAACTTC 0 7
+TTCCCCAGTGCTTTTA N gtccacagtgctatta 3 8
+CCTATGCCAATTGGCC Y CCTATGCCAATTGGCC 0 7
+CTACCAGGTTCTTGGC Y CTACCAGGTTCTTGGC 0 8
+TGTAATCACCTCTAAC Y TGTAATCACCTCTAAC 0 8
+GTATAACATATTCAAC Y GTATAACAAATTCAAC 1 7
+TTGAATAGATATCCGA Y TTGAATAGATATCCGA 0 9
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/L001/s_1_1101.locs b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/L001/s_1_1101.locs
new file mode 100755
index 0000000..912e48a
Binary files /dev/null and b/testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/L001/s_1_1101.locs differ
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.1.fastq
new file mode 100644
index 0000000..5493d14
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14221:1451 1:N:0:AACTTGACGCTCTCTT
+TTTTTTTTTCTTTTACTTTTTTTTT
++
+>1>1>111>0@@31311B21AAA##
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.2.fastq
new file mode 100644
index 0000000..4aaf72e
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14221:1451 2:N:0:AACTTGACGCTCTCTT
+TTTTTTTTTCTTTTTTTTCCTTTTT
++
+1111111>>0 at 331B00/011221A
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.barcode_1.fastq
new file mode 100644
index 0000000..958d0d0
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14221:1451 :N:0:AACTTGACGCTCTCTT
+AACTTGAC
++
+11>AA11B
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.barcode_2.fastq
new file mode 100644
index 0000000..3dc1787
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14221:1451 :N:0:AACTTGACGCTCTCTT
+GCTCTCTT
++
+3>>>>DDD
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.1.fastq
new file mode 100644
index 0000000..4f2c0e6
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15405:1531 1:N:0:AAGACACTAGTCACCT
+TTTCCTTCTTTTTTTTTTTTTTTAT
++
+11>11331 at 13111000A#######
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.2.fastq
new file mode 100644
index 0000000..fab9892
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15405:1531 2:N:0:AAGACACTAGTCACCT
+TTCTTTTTTCTTTTTCTTTGTTCTT
++
+11111@@11>1331B11333B03A3
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.barcode_1.fastq
new file mode 100644
index 0000000..a4d53ff
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15405:1531 :N:0:AAGACACTAGTCACCT
+AAGACACT
++
+111111>B
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.barcode_2.fastq
new file mode 100644
index 0000000..79a9355
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15405:1531 :N:0:AAGACACTAGTCACCT
+AGTCTCCT
++
+11>11B11
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCTCCT.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCTCCT.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCTCCT.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCTCCT.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCTCCT.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCTCCT.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCTCCT.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCTCCT.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.1.fastq
new file mode 100644
index 0000000..aee1f21
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14342:1520 1:N:0:ACAGGTATCACTTCAT
+CTTTCTTTTCTCCTTTTTTTCTTTC
++
+11>>1@@@1313111311AA0BAAA
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.2.fastq
new file mode 100644
index 0000000..830665f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14342:1520 2:N:0:ACAGGTATCACTTCAT
+TCGTGTTTTTTCTTTTTGCTTTCCC
++
+111>1>>>11111331A013A3111
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.barcode_1.fastq
new file mode 100644
index 0000000..7910411
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14342:1520 :N:0:ACAGGTATCACTTCAT
+ACAGGTAT
++
+1>111B1B
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.barcode_2.fastq
new file mode 100644
index 0000000..1b9e646
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14342:1520 :N:0:ACAGGTATCACTTCAT
+CACTTCAT
++
+>1>>>B3@
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.1.fastq
new file mode 100644
index 0000000..67a5f80
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14133:1507 1:N:0:ACAGTTGAATCTTCTC
+TCCTCTTTGCTTTTTGCTATCACTC
++
+111>1B1 at 313131111A33A33D1
+ at machine1:HiMom:abcdeACXX:1:1101:14753:1450 1:N:0:ACAGTTGAATCTTCTC
+CTTTTTCCTCTTTTTTTCTTTTGTT
++
+1>>>>@1131B1311100BA31100
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.2.fastq
new file mode 100644
index 0000000..77ff2e4
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14133:1507 2:N:0:ACAGTTGAATCTTCTC
+TCCTTTATTATCTTTGTTCCTTTTT
++
+111>>313 at 333AAA3A1333331A
+ at machine1:HiMom:abcdeACXX:1:1101:14753:1450 2:N:0:ACAGTTGAATCTTCTC
+TCCCTTTTTTTTCTTTTCTCTTTTT
++
+1111>@11@>1001331313331AA
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.barcode_1.fastq
new file mode 100644
index 0000000..ae43ed5
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.barcode_1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14133:1507 :N:0:ACAGTTGAATCTTCTC
+ACAGTTGA
++
+1>11>D13
+ at machine1:HiMom:abcdeACXX:1:1101:14753:1450 :N:0:ACAGTTGAATCTTCTC
+ACAGTTGA
++
+1>11>B13
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.barcode_2.fastq
new file mode 100644
index 0000000..012c966
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.barcode_2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14133:1507 :N:0:ACAGTTGAATCTTCTC
+ATCTTCTC
++
+3>AAADDD
+ at machine1:HiMom:abcdeACXX:1:1101:14753:1450 :N:0:ACAGTTGAATCTTCTC
+ATCTTCTC
++
+3>>AAD@@
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.1.fastq
new file mode 100644
index 0000000..99ab52d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15221:1507 1:N:0:ACCAACTGCATCACTT
+CTTTTTTCTTTCTTTGTTTTTGTAT
++
+1>1>1111@@33A3B3311000033
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.2.fastq
new file mode 100644
index 0000000..56e7e51
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15221:1507 2:N:0:ACCAACTGCATCACTT
+CTCTTTTTTTTCTCTCTTCTTTCCT
++
+111>13111>0013A11313B321A
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.barcode_1.fastq
new file mode 100644
index 0000000..8ceb5f1
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15221:1507 :N:0:ACCAACTGCATCACTT
+ACCAACTG
++
+3>>33>C4
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.barcode_2.fastq
new file mode 100644
index 0000000..4687cc7
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15221:1507 :N:0:ACCAACTGCATCACTT
+CATCACTT
++
+>1>A1BB@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCTACTGCTTCCCTT.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCTACTGCTTCCCTT.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCTACTGCTTCCCTT.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCTACTGCTTCCCTT.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCTACTGCTTCCCTT.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCTACTGCTTCCCTT.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCTACTGCTTCCCTT.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCTACTGCTTCCCTT.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.1.fastq
new file mode 100644
index 0000000..0a726e3
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17324:1480 1:N:0:ACTAAGACGTCCTCAT
+TCTCTGTGTTTTTTTTTTTTTTACT
++
+>111>333 at 11111A000///A/1A
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.2.fastq
new file mode 100644
index 0000000..8e10143
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17324:1480 2:N:0:ACTAAGACGTCCTCAT
+CTTTTTTTTCTTCTCTTTCCTTCCT
++
+1>>1111>00 at 333133331AA101
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.barcode_1.fastq
new file mode 100644
index 0000000..941ec7d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17324:1480 :N:0:ACTAAGACGTCCTCAT
+ACTAAGAC
++
+1>>1111B
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.barcode_2.fastq
new file mode 100644
index 0000000..86ff79a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17324:1480 :N:0:ACTAAGACGTCCTCAT
+GTCCTCAT
++
+1>>>>D1B
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTCGCATTCCTTTC.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTCGCATTCCTTTC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTCGCATTCCTTTC.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTCGCATTCCTTTC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTCGCATTCCTTTC.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTCGCATTCCTTTC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTCGCATTCCTTTC.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTCGCATTCCTTTC.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.1.fastq
new file mode 100644
index 0000000..f0e0379
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15634:1526 1:N:0:AGGTGCGAGACATTAA
+TTTTTTTTTTCTTTGGTTATTTTAT
++
+1>>>>>AA00>11B100A1BBAB2A
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.2.fastq
new file mode 100644
index 0000000..54133d1
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15634:1526 2:N:0:AGGTGCGAGACATTAA
+CCTCTCTTCTTTTTTTCTCCTTTTT
++
+111>1>131 at 131110A1B1ABBA1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.barcode_1.fastq
new file mode 100644
index 0000000..2271790
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15634:1526 :N:0:AGGTGCGAGACATTAA
+AGGTGCGA
++
+111>1B11
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.barcode_2.fastq
new file mode 100644
index 0000000..4212464
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15634:1526 :N:0:AGGTGCGAGACATTAA
+GACATTAA
++
+11>1>B13
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.1.fastq
new file mode 100644
index 0000000..ca71c9b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17862:1503 1:N:0:AGGTTATCTTAGCCAG
+TTTTTTTCCTACTTTGCTTTAGTTT
++
+>1>1>1>1133113A11A1A1133A
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.2.fastq
new file mode 100644
index 0000000..8a2e6b6
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17862:1503 2:N:0:AGGTTATCTTAGCCAG
+TCTTCCCCTTCTTTATTTATTTGCT
++
+1>1111111>1 at AA3A3B33AA333
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.barcode_1.fastq
new file mode 100644
index 0000000..5ac27fb
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17862:1503 :N:0:AGGTTATCTTAGCCAG
+AGGTTATC
++
+111>>1DD
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.barcode_2.fastq
new file mode 100644
index 0000000..c62a121
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17862:1503 :N:0:AGGTTATCTTAGCCAG
+TTAGCCAG
++
+>>11>B11
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.1.fastq
new file mode 100644
index 0000000..370c768
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14369:1492 1:N:0:AGTTGCTTTGACTTGG
+TTTCTTCTTTCTTTTTGTAAAGTTT
++
+1>>11333 at B3BB31111333333B
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.2.fastq
new file mode 100644
index 0000000..0ee84dd
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14369:1492 2:N:0:AGTTGCTTTGACTTGG
+TCCTTCTTTTTCTCTTTTTTTTCTT
++
+1>11>@1131111AAAAA1100011
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.barcode_1.fastq
new file mode 100644
index 0000000..84ab91b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14369:1492 :N:0:AGTTGCTTTGACTTGG
+AGTTGCTT
++
+11>>1 at DF
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.barcode_2.fastq
new file mode 100644
index 0000000..3f2aa6e
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14369:1492 :N:0:AGTTGCTTTGACTTGG
+TGACTTGG
++
+>33>>B at 4
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.1.fastq
new file mode 100644
index 0000000..30ea53a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17049:1423 1:N:0:ATAGCGTCTTGGTCTG
+CTCTTTTCTTTCTTTCTCTTCCTCT
++
+1>111 at 13@3333A33A3331111A
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.2.fastq
new file mode 100644
index 0000000..6bd92e7
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17049:1423 2:N:0:ATAGCGTCTTGGTCTG
+TTTTCTCCTCCTCTTCCTCTTTTTT
++
+1111113111111111111113110
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.barcode_1.fastq
new file mode 100644
index 0000000..ae3a57f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17049:1423 :N:0:ATAGCGTCTTGGTCTG
+ATAGCGTC
++
+1>1111>>
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.barcode_2.fastq
new file mode 100644
index 0000000..60138f2
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17049:1423 :N:0:ATAGCGTCTTGGTCTG
+TTGGTCTG
++
+>>11>BB1
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATTATCAACACCATAC.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATTATCAACACCATAC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATTATCAACACCATAC.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATTATCAACACCATAC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATTATCAACACCATAC.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATTATCAACACCATAC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATTATCAACACCATAC.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATTATCAACACCATAC.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATTGTCTGGATTCACA.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATTGTCTGGATTCACA.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATTGTCTGGATTCACA.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATTGTCTGGATTCACA.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATTGTCTGGATTCACA.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATTGTCTGGATTCACA.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATTGTCTGGATTCACA.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATTGTCTGGATTCACA.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.1.fastq
new file mode 100644
index 0000000..46a43c6
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15479:1337 1:N:0:CAATAGTCCGACTCTC
+CTCTCTTTTTTTTCTTTTTTATTCT
++
+1111113311110013311001222
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.2.fastq
new file mode 100644
index 0000000..afaf667
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15479:1337 2:N:0:CAATAGTCCGACTCTC
+TTTTCCTTCCTTTCTCTTCCCTCCT
++
+111111 at 311133133331111111
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.barcode_1.fastq
new file mode 100644
index 0000000..6784a4f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15479:1337 :N:0:CAATAGTCCGACTCTC
+CAATAGTC
++
+>11>11B@
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.barcode_2.fastq
new file mode 100644
index 0000000..c091895
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15479:1337 :N:0:CAATAGTCCGACTCTC
+CGACTCTC
++
+>111>>@@
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.1.fastq
new file mode 100644
index 0000000..b4b7b25
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17475:1506 1:N:0:CAGCAAGGGCGATATT
+TCTTTTTTTTTCTCTCGTGTGTTGG
++
+>111>B11>0>013310A0A0BB##
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.2.fastq
new file mode 100644
index 0000000..32b5754
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17475:1506 2:N:0:CAGCAAGGGCGATATT
+CCTTTTTCTTTTCTCTCCTCTTTCC
++
+11111111 at 33131331111A1331
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.barcode_1.fastq
new file mode 100644
index 0000000..5d54f92
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17475:1506 :N:0:CAGCAAGGGCGATATT
+CAGCAAGG
++
+>11>1111
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.barcode_2.fastq
new file mode 100644
index 0000000..85e8e4b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17475:1506 :N:0:CAGCAAGGGCGATATT
+GCGATATT
++
+1>11>1>B
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.1.fastq
new file mode 100644
index 0000000..bd849a7
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13678:1483 1:N:0:CAGCGGTAAGTACTGC
+TCTTTTCTTTTTTTTTTTCTTTTTT
++
+>1>>>131331111000A01AB###
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.2.fastq
new file mode 100644
index 0000000..6d2e7f1
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13678:1483 2:N:0:CAGCGGTAAGTACTGC
+TTTTTTTTCTTTCCTCTCTTTTTTT
++
+11111111013331A##########
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.barcode_1.fastq
new file mode 100644
index 0000000..37ac86f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13678:1483 :N:0:CAGCGGTAAGTACTGC
+CAGCGGTA
++
+>11111>1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.barcode_2.fastq
new file mode 100644
index 0000000..d3894f2
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13678:1483 :N:0:CAGCGGTAAGTACTGC
+TGTACTGC
++
+11>11 at 31
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTATGTACTGC.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTATGTACTGC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTATGTACTGC.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTATGTACTGC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTATGTACTGC.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTATGTACTGC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTATGTACTGC.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTATGTACTGC.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.1.fastq
new file mode 100644
index 0000000..364e991
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13947:1464 1:N:0:CATGCTTATAGCATTG
+CTCCTTTTCTTCTTCTTCTCTTTTT
++
+1>11113 at 313331331331A3311
+ at machine1:HiMom:abcdeACXX:1:1101:17987:1524 1:N:0:CATGCTTATAGCATTG
+CCTCTTTTTCTGTTTTTTTTGCTGG
++
+111>11 at 111133331110001B11
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.2.fastq
new file mode 100644
index 0000000..b8e9574
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13947:1464 2:N:0:CATGCTTATAGCATTG
+TTTTTTTTTCCCTCCCCTTTCCCTT
++
+1111111100111000000111111
+ at machine1:HiMom:abcdeACXX:1:1101:17987:1524 2:N:0:CATGCTTATAGCATTG
+TCTTCTTTTCTTTCTTCTTTATTTG
++
+111>13131313A3A33A1A33A33
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.barcode_1.fastq
new file mode 100644
index 0000000..5ded8ed
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.barcode_1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13947:1464 :N:0:CATGCTTATAGCATTG
+CATGCTTT
++
+11>1>B at 3
+ at machine1:HiMom:abcdeACXX:1:1101:17987:1524 :N:0:CATGCTTATAGCATTG
+CATGCTTA
++
+A3>3>DF5
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.barcode_2.fastq
new file mode 100644
index 0000000..dc13b1d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.barcode_2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13947:1464 :N:0:CATGCTTATAGCATTG
+TAGCATTG
++
+>11>1 at 31
+ at machine1:HiMom:abcdeACXX:1:1101:17987:1524 :N:0:CATGCTTATAGCATTG
+TAGCATTT
++
+>11>13B3
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTT.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTT.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTT.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTT.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTT.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTT.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTT.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTT.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTTTAGCATTG.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTTTAGCATTG.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTTTAGCATTG.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTTTAGCATTG.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTTTAGCATTG.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTTTAGCATTG.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTTTAGCATTG.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTTTAGCATTG.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGTTCGCGCCTTTT.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGTTCGCGCCTTTT.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGTTCGCGCCTTTT.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGTTCGCGCCTTTT.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGTTCGCGCCTTTT.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGTTCGCGCCTTTT.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGTTCGCGCCTTTT.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGTTCGCGCCTTTT.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.1.fastq
new file mode 100644
index 0000000..dcd4ce2
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16357:1518 1:N:0:CCAGAGCTCAACTGAT
+GTCTTCTGCTTCGCTCACGCTGGGT
++
+1>>>>3 at 113B311AA1111A0000
+ at machine1:HiMom:abcdeACXX:1:1101:17387:1497 1:N:0:CCAGAGCTCAACTGAT
+CCCCTTTTTTGTTGTGCTTTAGCCT
++
+111>>111111111A01B3311111
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.2.fastq
new file mode 100644
index 0000000..2e61400
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16357:1518 2:N:0:CCAGAGCTCAACTGAT
+TCCTTCTCTCTTTTTTTTTAATTCT
++
+>1111111B at BB311AA0001ABAB
+ at machine1:HiMom:abcdeACXX:1:1101:17387:1497 2:N:0:CCAGAGCTCAACTGAT
+CTTTTTGTCTTTCTTCCCCCTGCTT
++
+111>11113@@@3333111AA0011
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.barcode_1.fastq
new file mode 100644
index 0000000..7336722
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.barcode_1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16357:1518 :N:0:CCAGAGCTCAACTGAT
+CCAGAGCT
++
+>A3334>D
+ at machine1:HiMom:abcdeACXX:1:1101:17387:1497 :N:0:CCAGAGCTCAACTGAT
+CCAGAGCT
++
+>>1111BD
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.barcode_2.fastq
new file mode 100644
index 0000000..b4a32a4
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.barcode_2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16357:1518 :N:0:CCAGAGCTCAACTGAT
+CAACTGAT
++
+>33AAB4B
+ at machine1:HiMom:abcdeACXX:1:1101:17387:1497 :N:0:CCAGAGCTCAACTGAT
+CAACTGAT
++
+>11>>11@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCCGATTTTCTCTCCC.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCCGATTTTCTCTCCC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCCGATTTTCTCTCCC.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCCGATTTTCTCTCCC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCCGATTTTCTCTCCC.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCCGATTTTCTCTCCC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCCGATTTTCTCTCCC.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCCGATTTTCTCTCCC.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.1.fastq
new file mode 100644
index 0000000..61981c1
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17516:1540 1:N:0:CCTATGCCAATTGGCC
+CTTTCGTTTTTCTTTCCTATACATC
++
+1>>1111B>1>1B3331B3A11333
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.2.fastq
new file mode 100644
index 0000000..2f76d89
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17516:1540 2:N:0:CCTATGCCAATTGGCC
+TTCTTTTTTTTCCCTTTCCCTTTTC
++
+1>111 at B@11>0111B11AA1A112
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.barcode_1.fastq
new file mode 100644
index 0000000..267a06e
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17516:1540 :N:0:CCTATGCCAATTGGCC
+CCTATGCC
++
+AAA3>4 at B
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.barcode_2.fastq
new file mode 100644
index 0000000..683c65a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17516:1540 :N:0:CCTATGCCAATTGGCC
+AATTGGCC
++
+11>>11>1
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATTCTTCGTTTTC.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATTCTTCGTTTTC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATTCTTCGTTTTC.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATTCTTCGTTTTC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATTCTTCGTTTTC.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATTCTTCGTTTTC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATTCTTCGTTTTC.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATTCTTCGTTTTC.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.1.fastq
new file mode 100644
index 0000000..db6d5c0
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15248:1531 1:N:0:CCTTCGCAGAATCGAC
+CCCTACCTGTCTGCTATCCATCCCC
++
+111>11111B1311313A13B111A
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.2.fastq
new file mode 100644
index 0000000..a021705
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15248:1531 2:N:0:CCTTCGCAGAATCGAC
+TTCTCCTTCTATTTCTCTTGTCTTC
++
+11111@@B@@3333333331A1333
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.barcode_1.fastq
new file mode 100644
index 0000000..533b5f3
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15248:1531 :N:0:CCTTCGCAGAATCGAC
+CCTTCGCA
++
+AAAAA?A3
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.barcode_2.fastq
new file mode 100644
index 0000000..5d65d47
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15248:1531 :N:0:CCTTCGCAGAATCGAC
+GAATCGAC
++
+111>>11>
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCTTTTATCATTT.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCTTTTATCATTT.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCTTTTATCATTT.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCTTTTATCATTT.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCTTTTATCATTT.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCTTTTATCATTT.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCTTTTATCATTT.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCTTTTATCATTT.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.1.fastq
new file mode 100644
index 0000000..e1d88fa
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17615:1538 1:N:0:CGCTATGTTTCACCTT
+CTTTTTTTTTTTTCCTTTTTTTCTT
++
+>>>>11110000A011AA1A//0A1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.2.fastq
new file mode 100644
index 0000000..feb4ac9
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17615:1538 2:N:0:CGCTATGTTTCACCTT
+TTCTTTCCTTTTCTTTTTTCTGTTT
++
+11>1133133 at 131331111A3333
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.barcode_1.fastq
new file mode 100644
index 0000000..8153796
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17615:1538 :N:0:CGCTATGTTTCACCTT
+CGCTATGT
++
+>11>1>1B
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.barcode_2.fastq
new file mode 100644
index 0000000..82ee466
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17615:1538 :N:0:CGCTATGTTTCACCTT
+TTCTCCTT
++
+1>>11B at 1
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCTCCTT.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCTCCTT.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCTCCTT.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCTCCTT.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCTCCTT.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCTCCTT.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCTCCTT.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCTCCTT.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.1.fastq
new file mode 100644
index 0000000..d951b85
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14790:1540 1:N:0:CTACCAGGTTCTTGGC
+TTCTCTCTTTTCTCTTTCTTGTTGT
++
+A>1>13113313A3AAAAAB11B1B
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.2.fastq
new file mode 100644
index 0000000..ecd158b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14790:1540 2:N:0:CTACCAGGTTCTTGGC
+CTCTGTATTTTCCTTTTTCTTCTTT
++
+11111 at 33@@33133A1BB1A3A1B
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.barcode_1.fastq
new file mode 100644
index 0000000..16c71bb
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14790:1540 :N:0:CTACCAGGTTCTTGGC
+CTACCAGG
++
+A>3AAB43
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.barcode_2.fastq
new file mode 100644
index 0000000..c1eaa7c
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14790:1540 :N:0:CTACCAGGTTCTTGGC
+TTCTTGGC
++
+AAAAA5 at 4
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.1.fastq
new file mode 100644
index 0000000..2c85fd8
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15029:1349 1:N:0:CTGTAATCCTATTAGC
+CTTCTCCTTTTCTTTTTTTTTTTTT
++
+1>11111113 at 313A##########
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.2.fastq
new file mode 100644
index 0000000..b08b11e
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15029:1349 2:N:0:CTGTAATCCTATTAGC
+TTTCTTTTTCTTTTTTCTTTCTTTT
++
+1111>3 at 111133111113333331
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.barcode_1.fastq
new file mode 100644
index 0000000..8f8ea09
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15029:1349 :N:0:CTGTAATCCTATTAGC
+CTGTAATC
++
+>>1>13B@
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.barcode_2.fastq
new file mode 100644
index 0000000..bd1085d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15029:1349 :N:0:CTGTAATCCTATTAGC
+CTATTAGC
++
+111>>331
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.1.fastq
new file mode 100644
index 0000000..87fbffe
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16241:1505 1:N:0:GACCAGGACCATCACA
+CTTCTTTTTTTTCTTCCCTTTGCTC
++
+11>1113 at 11100A331011A1111
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.2.fastq
new file mode 100644
index 0000000..0d4b943
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16241:1505 2:N:0:GACCAGGACCATCACA
+CTGTGGTTTTTTTCTTGTCTTTTCC
++
+111>11111111001A111333AA1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.barcode_1.fastq
new file mode 100644
index 0000000..d3688bf
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16241:1505 :N:0:GACCAGGACCATCACA
+GACCAGGA
++
+11>>1111
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.barcode_2.fastq
new file mode 100644
index 0000000..e7e1b08
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16241:1505 :N:0:GACCAGGACCATCACA
+CCATCACA
++
+1>1>>1B1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.1.fastq
new file mode 100644
index 0000000..9f9d53c
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13789:1486 1:N:0:GCCGTCGAAGGTACCA
+CTTTTTTCTTCCTCTTTCTTTTTCT
++
+1111111113311AAB33333A10A
+ at machine1:HiMom:abcdeACXX:1:1101:14791:1400 1:N:0:GCCGTCGAAGGTACCA
+TTTTTTTCTTTTTCTTTTTTTCTTT
++
+>>1>>111 at 3@@11A3B1BA001A1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.2.fastq
new file mode 100644
index 0000000..9965eed
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13789:1486 2:N:0:GCCGTCGAAGGTACCA
+TTTTTCTCTCCTTCTCTTCTCCTTC
++
+1111111331111111331311111
+ at machine1:HiMom:abcdeACXX:1:1101:14791:1400 2:N:0:GCCGTCGAAGGTACCA
+TCCTTTTTCTTTCCTTTTCTTTTTT
++
+111>131 at 1133313331313311A
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.barcode_1.fastq
new file mode 100644
index 0000000..0121ed3
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.barcode_1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13789:1486 :N:0:GCCGTCGAAGGTACCA
+GCCGTCGA
++
+11>1>>11
+ at machine1:HiMom:abcdeACXX:1:1101:14791:1400 :N:0:GCCGTCGAAGGTACCA
+GCCGTCGA
++
+1>>1>>11
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.barcode_2.fastq
new file mode 100644
index 0000000..c99048d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.barcode_2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13789:1486 :N:0:GCCGTCGAAGGTACCA
+TGGTACCC
++
+111>1B at 1
+ at machine1:HiMom:abcdeACXX:1:1101:14791:1400 :N:0:GCCGTCGAAGGTACCA
+AGGTACCC
++
+111>1 at B1
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCC.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCC.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCC.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCC.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCC.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGATGGTACCC.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGATGGTACCC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGATGGTACCC.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGATGGTACCC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGATGGTACCC.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGATGGTACCC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGATGGTACCC.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGATGGTACCC.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.1.fastq
new file mode 100644
index 0000000..ac36e67
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14517:1469 1:N:0:GCCTAGCCCTTGAATC
+TTTCTTTTTTTTCCCTTTCCTCTTT
++
+>111133111>001111111B1111
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.2.fastq
new file mode 100644
index 0000000..6f4224a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14517:1469 2:N:0:GCCTAGCCCTTGAATC
+CCTCCTTTTTCTTCTTTTCCTTTTT
++
+11111113111133AA3A313331A
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.barcode_1.fastq
new file mode 100644
index 0000000..2dbb4aa
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14517:1469 :N:0:GCCTAGCCCTTGAATC
+GCCTAGCC
++
+11>>11 at B
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.barcode_2.fastq
new file mode 100644
index 0000000..905f5f1
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14517:1469 :N:0:GCCTAGCCCTTGAATC
+CTTGAATC
++
+11>111 at 3
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCTATCCACCTCCCCC.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCTATCCACCTCCCCC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCTATCCACCTCCCCC.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCTATCCACCTCCCCC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCTATCCACCTCCCCC.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCTATCCACCTCCCCC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCTATCCACCTCCCCC.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCTATCCACCTCCCCC.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.1.fastq
new file mode 100644
index 0000000..2bcbb35
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14857:1542 1:N:0:GTATAACAAATTCAAC
+TTTTCTCTTTTTGTTTTTTTCTTCT
++
+1>>>1 at 33B3111ABB11AA01333
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.2.fastq
new file mode 100644
index 0000000..b99a457
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14857:1542 2:N:0:GTATAACAAATTCAAC
+TCTTCCTTTTTTTTTTTTCTTTCTT
++
+111111133@@110000/AB1122A
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.barcode_1.fastq
new file mode 100644
index 0000000..a78dd3a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14857:1542 :N:0:GTATAACAAATTCAAC
+GTATAACA
++
+1>1>1311
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.barcode_2.fastq
new file mode 100644
index 0000000..e6580a2
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:14857:1542 :N:0:GTATAACAAATTCAAC
+TATTCAAC
++
+11>>>33@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACATATTCAAC.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACATATTCAAC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACATATTCAAC.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACATATTCAAC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACATATTCAAC.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACATATTCAAC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACATATTCAAC.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACATATTCAAC.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.1.fastq
new file mode 100644
index 0000000..2a4f95b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16578:1461 1:N:0:GTCTGATGGAACTTCG
+TTTTTTCTCTTTTTTTTGTTTCTGC
++
+>1>111113@@31A0A0000B2B21
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.2.fastq
new file mode 100644
index 0000000..dfea9e0
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16578:1461 2:N:0:GTCTGATGGAACTTCG
+CTTTTTCTTTCTTTTTCTCTCTTCT
++
+111111>133333311113A11313
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.barcode_1.fastq
new file mode 100644
index 0000000..5ba3fed
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16578:1461 :N:0:GTCTGATGGAACTTCG
+GTCTGATG
++
+11>>11B1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.barcode_2.fastq
new file mode 100644
index 0000000..1bc3bc6
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16578:1461 :N:0:GTCTGATGGAACTTCG
+GAACTTCG
++
+111>>3B1
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGTCACTTCC.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGTCACTTCC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGTCACTTCC.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGTCACTTCC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGTCACTTCC.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGTCACTTCC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGTCACTTCC.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGTCACTTCC.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/NN.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/NN.1.fastq
new file mode 100644
index 0000000..f2b882a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/NN.1.fastq
@@ -0,0 +1,76 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13743:1511 1:N:0:
+TCCTTCTTTTCCCTCCCCTTTCCTT
++
+>11>111@@@3111A111ABA1133
+ at machine1:HiMom:abcdeACXX:1:1101:13844:1536 1:N:0:
+TTTCTTTTTTCTTTTCCCTTTATTT
++
+1111>3311111331311B111333
+ at machine1:HiMom:abcdeACXX:1:1101:14281:1532 1:N:0:
+CTTTTTTCCTTTTTTTCTTTTTTCT
++
+1>>11111133 at 1A00013311A01
+ at machine1:HiMom:abcdeACXX:1:1101:14340:1451 1:N:0:
+TTTTTTCCTTCTCCCCTTTTTCCTT
++
+>11111113311111111111013A
+ at machine1:HiMom:abcdeACXX:1:1101:14809:1476 1:N:0:
+TTTTTCCCTTTCTCTTTTCTTTTCT
++
+>1>>111111113333313AAA131
+ at machine1:HiMom:abcdeACXX:1:1101:14852:1366 1:N:0:
+TTCTCTCCCTCTTTTTTTCTTCTTT
++
+111>1311111113A1AA0133313
+ at machine1:HiMom:abcdeACXX:1:1101:14927:1516 1:N:0:
+CTCCTTTTCTCTTTTCCCCCTGTGC
++
+11111 at 3131333313111111111
+ at machine1:HiMom:abcdeACXX:1:1101:14943:1353 1:N:0:
+TTTTTTTTTCTTTTTTTTTTTTTTT
++
+1>1>111100 at 33A###########
+ at machine1:HiMom:abcdeACXX:1:1101:15334:1365 1:N:0:
+TTTTTTTCTTCTCTTTCTTTTCTTT
++
+111>111113331333333B13133
+ at machine1:HiMom:abcdeACXX:1:1101:15424:1475 1:N:0:
+CTTTTTTCTTTTTCTTTTTTTTTCT
++
+1>>11 at 1113311113311000001
+ at machine1:HiMom:abcdeACXX:1:1101:15736:1478 1:N:0:
+CCTCTCTTTTTTCCTTTCCCTGCCT
++
+1111111 at 3B1111A33111A1001
+ at machine1:HiMom:abcdeACXX:1:1101:15785:1528 1:N:0:
+CTTTTTTTTTTCTCTCTTTTTTTTT
++
+11>111>100001221B########
+ at machine1:HiMom:abcdeACXX:1:1101:15865:1540 1:N:0:
+GCTTTCCTTGTTTTCTGTCCCCTTC
++
+11111113311BB13A33A111B10
+ at machine1:HiMom:abcdeACXX:1:1101:15987:1510 1:N:0:
+CTTTTTTTTTTTCCCTTTTTACCTT
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:15998:1432 1:N:0:
+TTCTTCCTCTTCTTCTTCTTCCTTT
++
+111>131111113133133A31133
+ at machine1:HiMom:abcdeACXX:1:1101:16070:1386 1:N:0:
+TTTTTTTTTTTTTTTTCCTTCCTTT
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:16085:1467 1:N:0:
+TTTTTTCCTTTTCTTTTCCTCTTCT
++
+1>>11>113B31313A13131111A
+ at machine1:HiMom:abcdeACXX:1:1101:16098:1529 1:N:0:
+TTTTTTTTTTCTCTCCCTTTCTCTT
++
+1>1>>11100012210001112222
+ at machine1:HiMom:abcdeACXX:1:1101:16530:1425 1:N:0:
+TTTTTTTTTTTTTTCTTTTTTTTTT
++
+1111>>110000A############
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/NN.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/NN.2.fastq
new file mode 100644
index 0000000..1f892c7
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/NN.2.fastq
@@ -0,0 +1,76 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13743:1511 2:N:0:
+CCCCCTTCCCTCTTTTTTCCTTCCC
++
+1111111111 at 11131100133100
+ at machine1:HiMom:abcdeACXX:1:1101:13844:1536 2:N:0:
+TCTTCTTTTTTTTTTTTCTTTTCCT
++
+111113131111A############
+ at machine1:HiMom:abcdeACXX:1:1101:14281:1532 2:N:0:
+TTTCTCTTTTTTTTTCTCCCTTCCT
++
+>111133331111000121001001
+ at machine1:HiMom:abcdeACXX:1:1101:14340:1451 2:N:0:
+TCCCTTCCTCCCCTCCTTCTTTTTC
++
+1111111111111111111113110
+ at machine1:HiMom:abcdeACXX:1:1101:14809:1476 2:N:0:
+TCTCTTTTTCTTTTTTCTCCTTTCT
++
+>111133111133111113111313
+ at machine1:HiMom:abcdeACXX:1:1101:14852:1366 2:N:0:
+TCCTTTTTCTTTTCTTTTCTTTTCC
++
+1111131111331313313133131
+ at machine1:HiMom:abcdeACXX:1:1101:14927:1516 2:N:0:
+TTCCTCCCCCTCCTCCCCCTCCCTC
++
+11111111>1111111100000A00
+ at machine1:HiMom:abcdeACXX:1:1101:14943:1353 2:N:0:
+CTCCCTTTTTTTTTTCTTCCTCTCT
++
+1111111111110000112111101
+ at machine1:HiMom:abcdeACXX:1:1101:15334:1365 2:N:0:
+TCTCTCTTTCTTCTCTTTTTTTTTT
++
+1111111333333313331110000
+ at machine1:HiMom:abcdeACXX:1:1101:15424:1475 2:N:0:
+TTCCTTCTTTCCTTCTCTCTTTCTT
++
+1111131113313311131133333
+ at machine1:HiMom:abcdeACXX:1:1101:15736:1478 2:N:0:
+CTCTTCCCTTTCCCCCTCTTCTTCT
++
+111>111111111111A11113A33
+ at machine1:HiMom:abcdeACXX:1:1101:15785:1528 2:N:0:
+TCTTCTCTTTCTCTTTTTCTTTTCT
++
+1111131 at 3@3333331A1133131
+ at machine1:HiMom:abcdeACXX:1:1101:15865:1540 2:N:0:
+CTTTTTTATTTTCCTTTTGCATCCT
++
+11111111333 at 31333B1133301
+ at machine1:HiMom:abcdeACXX:1:1101:15987:1510 2:N:0:
+TTCCCCTTCCCTTCTCTTTTCTTCT
++
+111111>1111 at 1111333131333
+ at machine1:HiMom:abcdeACXX:1:1101:15998:1432 2:N:0:
+CTTTTTTTCTTTTCTCCTCCTTTTT
++
+11111 at 111@3313A31A000131A
+ at machine1:HiMom:abcdeACXX:1:1101:16070:1386 2:N:0:
+TTTTTTTTCTCTCTTTTTTTTTTTT
++
+11111111013311331A#######
+ at machine1:HiMom:abcdeACXX:1:1101:16085:1467 2:N:0:
+TTTTTTTTTTTTCCTCTTTTTTTCC
++
+#########################
+ at machine1:HiMom:abcdeACXX:1:1101:16098:1529 2:N:0:
+CCCTCTCCACTTTTCTTTCCTCCCT
++
+11111>1111111331333131110
+ at machine1:HiMom:abcdeACXX:1:1101:16530:1425 2:N:0:
+TTCTTTCCCTTTTCTTTTCCTTCTC
++
+1111133111111313313133111
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/NN.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/NN.barcode_1.fastq
new file mode 100644
index 0000000..e53e969
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/NN.barcode_1.fastq
@@ -0,0 +1,76 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13743:1511 :N:0:
+ATTATCAA
++
+1>>1>B33
+ at machine1:HiMom:abcdeACXX:1:1101:13844:1536 :N:0:
+TCCCCGTT
++
+>1111111
+ at machine1:HiMom:abcdeACXX:1:1101:14281:1532 :N:0:
+CCTTCTTT
++
+111111B3
+ at machine1:HiMom:abcdeACXX:1:1101:14340:1451 :N:0:
+TTCCTCCT
++
+11111111
+ at machine1:HiMom:abcdeACXX:1:1101:14809:1476 :N:0:
+GCTATCCA
++
+1111>>13
+ at machine1:HiMom:abcdeACXX:1:1101:14852:1366 :N:0:
+AGGTCGCA
++
+111>>1>1
+ at machine1:HiMom:abcdeACXX:1:1101:14927:1516 :N:0:
+GTCTGATG
++
+1>>111 at 1
+ at machine1:HiMom:abcdeACXX:1:1101:14943:1353 :N:0:
+CTCCCTCT
++
+11111>11
+ at machine1:HiMom:abcdeACXX:1:1101:15334:1365 :N:0:
+TGTATCTC
++
+11111333
+ at machine1:HiMom:abcdeACXX:1:1101:15424:1475 :N:0:
+CCTCTTCT
++
+11111 at 1B
+ at machine1:HiMom:abcdeACXX:1:1101:15736:1478 :N:0:
+ATTGTCTG
++
+1>>1>BD1
+ at machine1:HiMom:abcdeACXX:1:1101:15785:1528 :N:0:
+CCCGATTT
++
+11111111
+ at machine1:HiMom:abcdeACXX:1:1101:15865:1540 :N:0:
+TTCCCCAG
++
+111>11>1
+ at machine1:HiMom:abcdeACXX:1:1101:15987:1510 :N:0:
+CCTCTTTC
++
+1111>13B
+ at machine1:HiMom:abcdeACXX:1:1101:15998:1432 :N:0:
+CATGTTCG
++
+>1>11 at 31
+ at machine1:HiMom:abcdeACXX:1:1101:16070:1386 :N:0:
+TGTCGGTT
++
+>1>1111>
+ at machine1:HiMom:abcdeACXX:1:1101:16085:1467 :N:0:
+ACCTACTG
++
+1>>111 at 1
+ at machine1:HiMom:abcdeACXX:1:1101:16098:1529 :N:0:
+TTCTCATC
++
+11>>1331
+ at machine1:HiMom:abcdeACXX:1:1101:16530:1425 :N:0:
+CCTATTCT
++
+>1111333
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/NN.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/NN.barcode_2.fastq
new file mode 100644
index 0000000..73d7126
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/NN.barcode_2.fastq
@@ -0,0 +1,76 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13743:1511 :N:0:
+CACCATAC
++
+11>>111>
+ at machine1:HiMom:abcdeACXX:1:1101:13844:1536 :N:0:
+CCAACTTC
++
+>111>B13
+ at machine1:HiMom:abcdeACXX:1:1101:14281:1532 :N:0:
+TATCATTT
++
+111>13B3
+ at machine1:HiMom:abcdeACXX:1:1101:14340:1451 :N:0:
+CACCATCC
++
+11>111B1
+ at machine1:HiMom:abcdeACXX:1:1101:14809:1476 :N:0:
+CCTCCCCC
++
+11>11>11
+ at machine1:HiMom:abcdeACXX:1:1101:14852:1366 :N:0:
+TTCCTTTC
++
+1>>>>B31
+ at machine1:HiMom:abcdeACXX:1:1101:14927:1516 :N:0:
+TCACTTCC
++
+111>>1B1
+ at machine1:HiMom:abcdeACXX:1:1101:14943:1353 :N:0:
+TCCTTCTT
++
+1111>111
+ at machine1:HiMom:abcdeACXX:1:1101:15334:1365 :N:0:
+TTACTCTT
++
+11111131
+ at machine1:HiMom:abcdeACXX:1:1101:15424:1475 :N:0:
+CTCGCTTT
++
+11111111
+ at machine1:HiMom:abcdeACXX:1:1101:15736:1478 :N:0:
+GATTCACA
++
+11>>>313
+ at machine1:HiMom:abcdeACXX:1:1101:15785:1528 :N:0:
+TCTCTCCC
++
+11>11111
+ at machine1:HiMom:abcdeACXX:1:1101:15865:1540 :N:0:
+TGCTTTTA
++
+1>111 at 13
+ at machine1:HiMom:abcdeACXX:1:1101:15987:1510 :N:0:
+TTCTGCTC
++
+11111131
+ at machine1:HiMom:abcdeACXX:1:1101:15998:1432 :N:0:
+CGCCTTTT
++
+111111 at B
+ at machine1:HiMom:abcdeACXX:1:1101:16070:1386 :N:0:
+TTTTGCTT
++
+11>>11 at 1
+ at machine1:HiMom:abcdeACXX:1:1101:16085:1467 :N:0:
+CTTCCCTT
++
+111>1B@@
+ at machine1:HiMom:abcdeACXX:1:1101:16098:1529 :N:0:
+TTCCTTCC
++
+11111311
+ at machine1:HiMom:abcdeACXX:1:1101:16530:1425 :N:0:
+TCGTTTTC
++
+1111>1>@
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.1.fastq
new file mode 100644
index 0000000..77adb41
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13898:1519 1:N:0:TACTTAGCGTCTGCAC
+CCTTCTCTACTTTTTTTTCTATTTT
++
+111>111B31 at 33311A0A1333BA
+ at machine1:HiMom:abcdeACXX:1:1101:14983:1536 1:N:0:TACTTAGCGTCTGCAC
+CCTTCTTCTTGTTCCCTCGCCAGGC
++
+11>>1113 at B11133AA111A0000
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.2.fastq
new file mode 100644
index 0000000..5cac4d9
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13898:1519 2:N:0:TACTTAGCGTCTGCAC
+TTTTTTCTTTTCTCTTCCTCTTTTC
++
+11>11111 at 3131A3A111A11313
+ at machine1:HiMom:abcdeACXX:1:1101:14983:1536 2:N:0:TACTTAGCGTCTGCAC
+TCCTTATCCTTTTTACTGCCCTGTA
++
+1111>331@@331A11A311111B3
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.barcode_1.fastq
new file mode 100644
index 0000000..bde2930
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.barcode_1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13898:1519 :N:0:TACTTAGCGTCTGCAC
+TACTTAGC
++
+A3>AA55B
+ at machine1:HiMom:abcdeACXX:1:1101:14983:1536 :N:0:TACTTAGCGTCTGCAC
+TACTTAGC
++
+A3AAAB5@
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.barcode_2.fastq
new file mode 100644
index 0000000..ae3d55a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.barcode_2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13898:1519 :N:0:TACTTAGCGTCTGCAC
+GTCTGCAC
++
+1>>>113B
+ at machine1:HiMom:abcdeACXX:1:1101:14983:1536 :N:0:TACTTAGCGTCTGCAC
+GTCTGCAC
++
+1>>>1 at 3C
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCCCGTTCCAACTTC.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCCCGTTCCAACTTC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCCCGTTCCAACTTC.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCCCGTTCCAACTTC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCCCGTTCCAACTTC.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCCCGTTCCAACTTC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCCCGTTCCAACTTC.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCCCGTTCCAACTTC.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.1.fastq
new file mode 100644
index 0000000..60a3c0c
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17106:1463 1:N:0:TCCTTGGTGCTGCACT
+TTTCTTTTTTTTCTTTTCTCTTCCT
++
+11>113 at 1111>0A3A131333111
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.2.fastq
new file mode 100644
index 0000000..1c953fe
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17106:1463 2:N:0:TCCTTGGTGCTGCACT
+TTCATTTTCTTCTTTTTCTTCCTCT
++
+1111133331333131111331111
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.barcode_1.fastq
new file mode 100644
index 0000000..0519c0e
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17106:1463 :N:0:TCCTTGGTGCTGCACT
+TCCTTGGT
++
+1>>>A111
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.barcode_2.fastq
new file mode 100644
index 0000000..a127011
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17106:1463 :N:0:TCCTTGGTGCTGCACT
+GCTGCACT
++
+11>111 at 1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.1.fastq
new file mode 100644
index 0000000..1258713
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15287:1512 1:N:0:TCGCCTTGCCAACGCT
+CCTCCTCCTTTTATTTCTTTTCCCT
++
+111111>1B131333333331A111
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.2.fastq
new file mode 100644
index 0000000..42bddd1
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15287:1512 2:N:0:TCGCCTTGCCAACGCT
+CTTTTTTCTTTTTTTCGTCTTTCTT
++
+1111111113 at 111000000A2221
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.barcode_1.fastq
new file mode 100644
index 0000000..4a06f22
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15287:1512 :N:0:TCGCCTTGCCAACGCT
+TCGCCTTG
++
+>A11>>A1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.barcode_2.fastq
new file mode 100644
index 0000000..cbe5481
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15287:1512 :N:0:TCGCCTTGCCAACGCT
+CCAACGCT
++
+1>11>1>1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.1.fastq
new file mode 100644
index 0000000..f4d00bc
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13416:1538 1:N:0:TGCAAGTACGAACTTC
+TTTTGTCTATCACTTTGTTTATTCA
++
+>11>11333333311A13113BBA3
+ at machine1:HiMom:abcdeACXX:1:1101:16315:1534 1:N:0:TGCAAGTACGAACTTC
+TTTCTGTTTTATTCTTTTCTTATGT
++
+>1>113333B333333AB31A331D
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.2.fastq
new file mode 100644
index 0000000..15e3d34
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13416:1538 2:N:0:TGCAAGTACGAACTTC
+TTTTCTTCCCTTTCTTTCTCTGTTT
++
+111111331111B133A33333D33
+ at machine1:HiMom:abcdeACXX:1:1101:16315:1534 2:N:0:TGCAAGTACGAACTTC
+TTTTTCTCCTCCTTTTTTTGTTCCT
++
+111111131 at 11A1A111000B333
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.barcode_1.fastq
new file mode 100644
index 0000000..eb3cc6c
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.barcode_1.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13416:1538 :N:0:TGCAAGTACGAACTTC
+TGCAAGTA
++
+>1>111B3
+ at machine1:HiMom:abcdeACXX:1:1101:16315:1534 :N:0:TGCAAGTACGAACTTC
+TGCAAGTA
++
+>1>111B3
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.barcode_2.fastq
new file mode 100644
index 0000000..3226f6e
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.barcode_2.fastq
@@ -0,0 +1,8 @@
+ at machine1:HiMom:abcdeACXX:1:1101:13416:1538 :N:0:TGCAAGTACGAACTTC
+CGAACTTC
++
+>111>1 at B
+ at machine1:HiMom:abcdeACXX:1:1101:16315:1534 :N:0:TGCAAGTACGAACTTC
+CGAACTTC
++
+1111>>@@
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.1.fastq
new file mode 100644
index 0000000..934a92d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15028:1491 1:N:0:TGCTCGACTTCACAGA
+TTTTTTTTTTTTTTTTTTTTTTTTT
++
+>1>>111>>000/A###########
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.2.fastq
new file mode 100644
index 0000000..179bc18
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15028:1491 2:N:0:TGCTCGACTTCACAGA
+TTCTTTTTTTTCTTTTTTTTTCTCT
++
+1111131111001331100//0A22
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.barcode_1.fastq
new file mode 100644
index 0000000..980ce72
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15028:1491 :N:0:TGCTCGACTTCACAGA
+TGCTCGAC
++
+>11>>11>
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.barcode_2.fastq
new file mode 100644
index 0000000..4a925c7
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15028:1491 :N:0:TGCTCGACTTCACAGA
+TTCACAGT
++
+1>111311
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGT.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGT.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGT.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGT.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGT.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGT.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGT.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGT.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.1.fastq
new file mode 100644
index 0000000..307c316
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15439:1540 1:N:0:TGTAATCACCTCTAAC
+CTTCTTTCATATTCTTAAATTTGCA
++
+1>>11B333B333ABA331ABA333
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.2.fastq
new file mode 100644
index 0000000..788beb6
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15439:1540 2:N:0:TGTAATCACCTCTAAC
+TTTTGTTTGAGTGTTATAGAAACAG
++
+111>11BB111113B3333313110
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.barcode_1.fastq
new file mode 100644
index 0000000..d1d82fd
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15439:1540 :N:0:TGTAATCACCTCTAAC
+TGTAATCA
++
+A?A3?FF5
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.barcode_2.fastq
new file mode 100644
index 0000000..96c6c7a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:15439:1540 :N:0:TGTAATCACCTCTAAC
+CCTCTAAC
++
+AAAAA45D
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTATCTCTTACTCTT.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTATCTCTTACTCTT.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTATCTCTTACTCTT.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTATCTCTTACTCTT.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTATCTCTTACTCTT.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTATCTCTTACTCTT.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTATCTCTTACTCTT.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTATCTCTTACTCTT.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.1.fastq
new file mode 100644
index 0000000..721c088
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16256:1385 1:N:0:TGTTCCGAAACCTCTT
+TTTCTCTTTTTTTTTCCTTTTTTTT
++
+>>11>3 at 3@@11AAA01A22AA0/A
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.2.fastq
new file mode 100644
index 0000000..df55ba2
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16256:1385 2:N:0:TGTTCCGAAACCTCTT
+TCTTTTTCTTTTTTCTTTTCTCTTT
++
+11111111 at 33111113A13A3A33
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.barcode_1.fastq
new file mode 100644
index 0000000..6e3bf8b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16256:1385 :N:0:TGTTCCGAAACCTCTT
+TGTTCCGA
++
+>1>>>B11
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.barcode_2.fastq
new file mode 100644
index 0000000..455640c
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16256:1385 :N:0:TGTTCCGAAACCTCTT
+AACCTCTT
++
+11>>>>B1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.1.fastq
new file mode 100644
index 0000000..1ff4d1e
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17703:1479 1:N:0:TTAATCAGCTGGTATT
+TTTTTTTTTTCCTCCTTTTTTTCCT
++
+111111110001110012A1//01A
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.2.fastq
new file mode 100644
index 0000000..5f97d3b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17703:1479 2:N:0:TTAATCAGCTGGTATT
+TCTTTTTTCCTTCTCTTTTTTCTTT
++
+11111 at 1111331113331100133
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.barcode_1.fastq
new file mode 100644
index 0000000..0ab8920
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17703:1479 :N:0:TTAATCAGCTGGTATT
+TTAATCAG
++
+1>11>D31
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.barcode_2.fastq
new file mode 100644
index 0000000..97df4c8
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:17703:1479 :N:0:TTAATCAGCTGGTATT
+CTGGTATT
++
+1111>1B@
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.1.fastq
new file mode 100644
index 0000000..2d8f858
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16819:1536 1:N:0:TTATATCTTCATGTCT
+TTTTTTTGTTTTGTCCTTTCTTCCT
++
+>1>111>1111>0A3AA33AAB31B
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.2.fastq
new file mode 100644
index 0000000..f31ded3
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16819:1536 2:N:0:TTATATCTTCATGTCT
+TTTTTTTTTCATCCCTCTCTTCCCT
++
+1>1>>>>>>0333A010A0A2A101
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.barcode_1.fastq
new file mode 100644
index 0000000..1dc9e36
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16819:1536 :N:0:TTATATCTTCATGTCT
+TTATATCT
++
+>A1>1BDD
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.barcode_2.fastq
new file mode 100644
index 0000000..29a141d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16819:1536 :N:0:TTATATCTTCATGTCT
+TCATGTCT
++
+>>1>1BB3
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCCTCCTCACCATCC.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCCTCCTCACCATCC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCCTCCTCACCATCC.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCCTCCTCACCATCC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCCTCCTCACCATCC.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCCTCCTCACCATCC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCCTCCTCACCATCC.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCCTCCTCACCATCC.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCTCATCTTCCTTCC.1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCTCATCTTCCTTCC.1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCTCATCTTCCTTCC.2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCTCATCTTCCTTCC.2.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCTCATCTTCCTTCC.barcode_1.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCTCATCTTCCTTCC.barcode_1.fastq
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCTCATCTTCCTTCC.barcode_2.fastq
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTCTCATCTTCCTTCC.barcode_2.fastq
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.1.fastq
new file mode 100644
index 0000000..704a027
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16891:1545 1:N:0:TTGAATAGATATCCGA
+CTTTTGCCTGTGTTTTTTCTCTCAT
++
+1>1>>11111B1BABA11AAA3A13
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.2.fastq
new file mode 100644
index 0000000..73d7067
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16891:1545 2:N:0:TTGAATAGATATCCGA
+CTTTTTTCTGACTTTCTTCTAGACT
++
+11>1>1>>13311A3AB3AB33313
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.barcode_1.fastq
new file mode 100644
index 0000000..01ad3c2
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.barcode_1.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16891:1545 :N:0:TTGAATAGATATCCGA
+TTGAATAG
++
+>A333B54
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.barcode_2.fastq b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.barcode_2.fastq
new file mode 100644
index 0000000..b94b113
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.barcode_2.fastq
@@ -0,0 +1,4 @@
+ at machine1:HiMom:abcdeACXX:1:1101:16891:1545 :N:0:TTGAATAGATATCCGA
+ATATCCGA
++
+1>>AAD11
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/barcode_double.params b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/barcode_double.params
new file mode 100644
index 0000000..a291ce1
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/fastq/barcode_double.params
@@ -0,0 +1,65 @@
+BARCODE_1 BARCODE_2 SAMPLE_ALIAS LIBRARY_NAME
+AACTTGAC GCTCTCTT SA_AACTTGACGCTCTCTT LN_AACTTGACGCTCTCTT
+AAGACACT AGTCTCCT SA_AAGACACTAGTCTCCT LN_AAGACACTAGTCTCCT
+ACAGGTAT CACTTCAT SA_ACAGGTATCACTTCAT LN_ACAGGTATCACTTCAT
+ACAGTTGA ATCTTCTC SA_ACAGTTGAATCTTCTC LN_ACAGTTGAATCTTCTC
+ACCAACTG CATCACTT SA_ACCAACTGCATCACTT LN_ACCAACTGCATCACTT
+ACCTACTG CTTCCCTT SA_ACCTACTGCTTCCCTT LN_ACCTACTGCTTCCCTT
+ACTAAGAC GTCCTCAT SA_ACTAAGACGTCCTCAT LN_ACTAAGACGTCCTCAT
+AGGTCGCA TTCCTTTC SA_AGGTCGCATTCCTTTC LN_AGGTCGCATTCCTTTC
+AGGTGCGA GACATTAA SA_AGGTGCGAGACATTAA LN_AGGTGCGAGACATTAA
+AGGTTATC TTAGCCAG SA_AGGTTATCTTAGCCAG LN_AGGTTATCTTAGCCAG
+AGTTGCTT TGACTTGG SA_AGTTGCTTTGACTTGG LN_AGTTGCTTTGACTTGG
+ATAGCGTC TTGGTCTG SA_ATAGCGTCTTGGTCTG LN_ATAGCGTCTTGGTCTG
+ATTATCAA CACCATAC SA_ATTATCAACACCATAC LN_ATTATCAACACCATAC
+ATTGTCTG GATTCACA SA_ATTGTCTGGATTCACA LN_ATTGTCTGGATTCACA
+CAGCAAGG GCGATATT SA_CAGCAAGGGCGATATT LN_CAGCAAGGGCGATATT
+CAGCGGTA TGTACTGC SA_CAGCGGTATGTACTGC LN_CAGCGGTATGTACTGC
+CATGCTTA TAGCATTT SA_CATGCTTATAGCATTT LN_CATGCTTATAGCATTT
+CATGCTTT TAGCATTG SA_CATGCTTTTAGCATTG LN_CATGCTTTTAGCATTG
+CATGTTCG CGCCTTTT SA_CATGTTCGCGCCTTTT LN_CATGTTCGCGCCTTTT
+CCAGAGCT CAACTGAT SA_CCAGAGCTCAACTGAT LN_CCAGAGCTCAACTGAT
+CCCGATTT TCTCTCCC SA_CCCGATTTTCTCTCCC LN_CCCGATTTTCTCTCCC
+CCTATGCC AATTGGCC SA_CCTATGCCAATTGGCC LN_CCTATGCCAATTGGCC
+CCTATTCT TCGTTTTC SA_CCTATTCTTCGTTTTC LN_CCTATTCTTCGTTTTC
+CCTCTTCT CTCGCTTT SA_CCTCTTCTCTCGCTTT LN_CCTCTTCTCTCGCTTT
+CCTCTTTC TTCTGCTC SA_CCTCTTTCTTCTGCTC LN_CCTCTTTCTTCTGCTC
+CCTTCGCA GAATCGAC SA_CCTTCGCAGAATCGAC LN_CCTTCGCAGAATCGAC
+CCTTCTTT TATCATTT SA_CCTTCTTTTATCATTT LN_CCTTCTTTTATCATTT
+CGCTATGT TTCTCCTT SA_CGCTATGTTTCTCCTT LN_CGCTATGTTTCTCCTT
+CTACCAGG TTCTTGGC SA_CTACCAGGTTCTTGGC LN_CTACCAGGTTCTTGGC
+CTCCCTCT TCCTTCTT SA_CTCCCTCTTCCTTCTT LN_CTCCCTCTTCCTTCTT
+CTGTAATC CTATTAGC SA_CTGTAATCCTATTAGC LN_CTGTAATCCTATTAGC
+GACCAGGA CCATCACA SA_GACCAGGACCATCACA LN_GACCAGGACCATCACA
+GCCGTCGA AGGTACCC SA_GCCGTCGAAGGTACCC LN_GCCGTCGAAGGTACCC
+GCCGTCGA TGGTACCC SA_GCCGTCGATGGTACCC LN_GCCGTCGATGGTACCC
+GCCTAGCC CTTGAATC SA_GCCTAGCCCTTGAATC LN_GCCTAGCCCTTGAATC
+GCTATCCA CCTCCCCC SA_GCTATCCACCTCCCCC LN_GCTATCCACCTCCCCC
+GTATAACA TATTCAAC SA_GTATAACATATTCAAC LN_GTATAACATATTCAAC
+GTCTGATG GAACTTCG SA_GTCTGATGGAACTTCG LN_GTCTGATGGAACTTCG
+GTCTGATG TCACTTCC SA_GTCTGATGTCACTTCC LN_GTCTGATGTCACTTCC
+TACTTAGC GTCTGCAC SA_TACTTAGCGTCTGCAC LN_TACTTAGCGTCTGCAC
+TCCCCGTT CCAACTTC SA_TCCCCGTTCCAACTTC LN_TCCCCGTTCCAACTTC
+TCCTTGGT GCTGCACT SA_TCCTTGGTGCTGCACT LN_TCCTTGGTGCTGCACT
+TCGCCTTG CCAACGCT SA_TCGCCTTGCCAACGCT LN_TCGCCTTGCCAACGCT
+TGCAAGTA CGAACTTC SA_TGCAAGTACGAACTTC LN_TGCAAGTACGAACTTC
+TGCTCGAC TTCACAGT SA_TGCTCGACTTCACAGT LN_TGCTCGACTTCACAGT
+TGTAATCA CCTCTAAC SA_TGTAATCACCTCTAAC LN_TGTAATCACCTCTAAC
+TGTATCTC TTACTCTT SA_TGTATCTCTTACTCTT LN_TGTATCTCTTACTCTT
+TGTCGGTT TTTTGCTT SA_TGTCGGTTTTTTGCTT LN_TGTCGGTTTTTTGCTT
+TGTTCCGA AACCTCTT SA_TGTTCCGAAACCTCTT LN_TGTTCCGAAACCTCTT
+TTAATCAG CTGGTATT SA_TTAATCAGCTGGTATT LN_TTAATCAGCTGGTATT
+TTATATCT TCATGTCT SA_TTATATCTTCATGTCT LN_TTATATCTTCATGTCT
+TTCCCCAG TGCTTTTA SA_TTCCCCAGTGCTTTTA LN_TTCCCCAGTGCTTTTA
+TTCCTCCT CACCATCC SA_TTCCTCCTCACCATCC LN_TTCCTCCTCACCATCC
+TTCTCATC TTCCTTCC SA_TTCTCATCTTCCTTCC LN_TTCTCATCTTCCTTCC
+TTGAATAG ATATCCGA SA_TTGAATAGATATCCGA LN_TTGAATAGATATCCGA
+CAATAGTC CGACTCTC SA_CAATAGTCCGACTCTC LN_CAATAGTCCGACTCTC
+GCCGTCGA AGGTACCA SA_GCCGTCGAAGGTACCA LN_GCCGTCGAAGGTACCA
+CATGCTTA TAGCATTG SA_CATGCTTATAGCATTG LN_CATGCTTATAGCATTG
+CAGCGGTA AGTACTGC SA_CAGCGGTAAGTACTGC LN_CAGCGGTAAGTACTGC
+TGCTCGAC TTCACAGA SA_TGCTCGACTTCACAGA LN_TGCTCGACTTCACAGA
+AAGACACT AGTCACCT SA_AAGACACTAGTCACCT LN_AAGACACTAGTCACCT
+CGCTATGT TTCACCTT SA_CGCTATGTTTCACCTT LN_CGCTATGTTTCACCTT
+GTATAACA AATTCAAC SA_GTATAACAAATTCAAC LN_GTATAACAAATTCAAC
+N N SA_N LN_N
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/library.params b/testdata/net/sf/picard/illumina/25T8B8B25T/library.params
new file mode 100644
index 0000000..a291ce1
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/library.params
@@ -0,0 +1,65 @@
+BARCODE_1 BARCODE_2 SAMPLE_ALIAS LIBRARY_NAME
+AACTTGAC GCTCTCTT SA_AACTTGACGCTCTCTT LN_AACTTGACGCTCTCTT
+AAGACACT AGTCTCCT SA_AAGACACTAGTCTCCT LN_AAGACACTAGTCTCCT
+ACAGGTAT CACTTCAT SA_ACAGGTATCACTTCAT LN_ACAGGTATCACTTCAT
+ACAGTTGA ATCTTCTC SA_ACAGTTGAATCTTCTC LN_ACAGTTGAATCTTCTC
+ACCAACTG CATCACTT SA_ACCAACTGCATCACTT LN_ACCAACTGCATCACTT
+ACCTACTG CTTCCCTT SA_ACCTACTGCTTCCCTT LN_ACCTACTGCTTCCCTT
+ACTAAGAC GTCCTCAT SA_ACTAAGACGTCCTCAT LN_ACTAAGACGTCCTCAT
+AGGTCGCA TTCCTTTC SA_AGGTCGCATTCCTTTC LN_AGGTCGCATTCCTTTC
+AGGTGCGA GACATTAA SA_AGGTGCGAGACATTAA LN_AGGTGCGAGACATTAA
+AGGTTATC TTAGCCAG SA_AGGTTATCTTAGCCAG LN_AGGTTATCTTAGCCAG
+AGTTGCTT TGACTTGG SA_AGTTGCTTTGACTTGG LN_AGTTGCTTTGACTTGG
+ATAGCGTC TTGGTCTG SA_ATAGCGTCTTGGTCTG LN_ATAGCGTCTTGGTCTG
+ATTATCAA CACCATAC SA_ATTATCAACACCATAC LN_ATTATCAACACCATAC
+ATTGTCTG GATTCACA SA_ATTGTCTGGATTCACA LN_ATTGTCTGGATTCACA
+CAGCAAGG GCGATATT SA_CAGCAAGGGCGATATT LN_CAGCAAGGGCGATATT
+CAGCGGTA TGTACTGC SA_CAGCGGTATGTACTGC LN_CAGCGGTATGTACTGC
+CATGCTTA TAGCATTT SA_CATGCTTATAGCATTT LN_CATGCTTATAGCATTT
+CATGCTTT TAGCATTG SA_CATGCTTTTAGCATTG LN_CATGCTTTTAGCATTG
+CATGTTCG CGCCTTTT SA_CATGTTCGCGCCTTTT LN_CATGTTCGCGCCTTTT
+CCAGAGCT CAACTGAT SA_CCAGAGCTCAACTGAT LN_CCAGAGCTCAACTGAT
+CCCGATTT TCTCTCCC SA_CCCGATTTTCTCTCCC LN_CCCGATTTTCTCTCCC
+CCTATGCC AATTGGCC SA_CCTATGCCAATTGGCC LN_CCTATGCCAATTGGCC
+CCTATTCT TCGTTTTC SA_CCTATTCTTCGTTTTC LN_CCTATTCTTCGTTTTC
+CCTCTTCT CTCGCTTT SA_CCTCTTCTCTCGCTTT LN_CCTCTTCTCTCGCTTT
+CCTCTTTC TTCTGCTC SA_CCTCTTTCTTCTGCTC LN_CCTCTTTCTTCTGCTC
+CCTTCGCA GAATCGAC SA_CCTTCGCAGAATCGAC LN_CCTTCGCAGAATCGAC
+CCTTCTTT TATCATTT SA_CCTTCTTTTATCATTT LN_CCTTCTTTTATCATTT
+CGCTATGT TTCTCCTT SA_CGCTATGTTTCTCCTT LN_CGCTATGTTTCTCCTT
+CTACCAGG TTCTTGGC SA_CTACCAGGTTCTTGGC LN_CTACCAGGTTCTTGGC
+CTCCCTCT TCCTTCTT SA_CTCCCTCTTCCTTCTT LN_CTCCCTCTTCCTTCTT
+CTGTAATC CTATTAGC SA_CTGTAATCCTATTAGC LN_CTGTAATCCTATTAGC
+GACCAGGA CCATCACA SA_GACCAGGACCATCACA LN_GACCAGGACCATCACA
+GCCGTCGA AGGTACCC SA_GCCGTCGAAGGTACCC LN_GCCGTCGAAGGTACCC
+GCCGTCGA TGGTACCC SA_GCCGTCGATGGTACCC LN_GCCGTCGATGGTACCC
+GCCTAGCC CTTGAATC SA_GCCTAGCCCTTGAATC LN_GCCTAGCCCTTGAATC
+GCTATCCA CCTCCCCC SA_GCTATCCACCTCCCCC LN_GCTATCCACCTCCCCC
+GTATAACA TATTCAAC SA_GTATAACATATTCAAC LN_GTATAACATATTCAAC
+GTCTGATG GAACTTCG SA_GTCTGATGGAACTTCG LN_GTCTGATGGAACTTCG
+GTCTGATG TCACTTCC SA_GTCTGATGTCACTTCC LN_GTCTGATGTCACTTCC
+TACTTAGC GTCTGCAC SA_TACTTAGCGTCTGCAC LN_TACTTAGCGTCTGCAC
+TCCCCGTT CCAACTTC SA_TCCCCGTTCCAACTTC LN_TCCCCGTTCCAACTTC
+TCCTTGGT GCTGCACT SA_TCCTTGGTGCTGCACT LN_TCCTTGGTGCTGCACT
+TCGCCTTG CCAACGCT SA_TCGCCTTGCCAACGCT LN_TCGCCTTGCCAACGCT
+TGCAAGTA CGAACTTC SA_TGCAAGTACGAACTTC LN_TGCAAGTACGAACTTC
+TGCTCGAC TTCACAGT SA_TGCTCGACTTCACAGT LN_TGCTCGACTTCACAGT
+TGTAATCA CCTCTAAC SA_TGTAATCACCTCTAAC LN_TGTAATCACCTCTAAC
+TGTATCTC TTACTCTT SA_TGTATCTCTTACTCTT LN_TGTATCTCTTACTCTT
+TGTCGGTT TTTTGCTT SA_TGTCGGTTTTTTGCTT LN_TGTCGGTTTTTTGCTT
+TGTTCCGA AACCTCTT SA_TGTTCCGAAACCTCTT LN_TGTTCCGAAACCTCTT
+TTAATCAG CTGGTATT SA_TTAATCAGCTGGTATT LN_TTAATCAGCTGGTATT
+TTATATCT TCATGTCT SA_TTATATCTTCATGTCT LN_TTATATCTTCATGTCT
+TTCCCCAG TGCTTTTA SA_TTCCCCAGTGCTTTTA LN_TTCCCCAGTGCTTTTA
+TTCCTCCT CACCATCC SA_TTCCTCCTCACCATCC LN_TTCCTCCTCACCATCC
+TTCTCATC TTCCTTCC SA_TTCTCATCTTCCTTCC LN_TTCTCATCTTCCTTCC
+TTGAATAG ATATCCGA SA_TTGAATAGATATCCGA LN_TTGAATAGATATCCGA
+CAATAGTC CGACTCTC SA_CAATAGTCCGACTCTC LN_CAATAGTCCGACTCTC
+GCCGTCGA AGGTACCA SA_GCCGTCGAAGGTACCA LN_GCCGTCGAAGGTACCA
+CATGCTTA TAGCATTG SA_CATGCTTATAGCATTG LN_CATGCTTATAGCATTG
+CAGCGGTA AGTACTGC SA_CAGCGGTAAGTACTGC LN_CAGCGGTAAGTACTGC
+TGCTCGAC TTCACAGA SA_TGCTCGACTTCACAGA LN_TGCTCGACTTCACAGA
+AAGACACT AGTCACCT SA_AAGACACTAGTCACCT LN_AAGACACTAGTCACCT
+CGCTATGT TTCACCTT SA_CGCTATGTTTCACCTT LN_CGCTATGTTTCACCTT
+GTATAACA AATTCAAC SA_GTATAACAAATTCAAC LN_GTATAACAAATTCAAC
+N N SA_N LN_N
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AACTTGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AACTTGAC.sam
new file mode 100644
index 0000000..57e8020
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AACTTGAC.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.AACTTGAC-GCTCTCTT LB:LN_AACTTGACGCTCTCTT SM:SA_AACTTGACGCTCTCTT CN:BI
+HiMom:1:1101:14221:1451 589 * 0 0 * * 0 0 TTTTTTTTTCTTTTACTTTTTTTTT >1>1>111>0@@31311B21AAA## RG:Z:HiMom.1
+HiMom:1:1101:14221:1451 653 * 0 0 * * 0 0 TTTTTTTTTCTTTTTTTTCCTTTTT 1111111>>0 at 331B00/011221A RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AAGACACT.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AAGACACT.sam
new file mode 100644
index 0000000..75fa9b3
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AAGACACT.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.AAGACACT-AGTCTCCT LB:LN_AAGACACTAGTCTCCT SM:SA_AAGACACTAGTCTCCT CN:BI
+HiMom:1:1101:15405:1531 589 * 0 0 * * 0 0 TTTCCTTCTTTTTTTTTTTTTTTAT 11>11331 at 13111000A####### RG:Z:HiMom.1
+HiMom:1:1101:15405:1531 653 * 0 0 * * 0 0 TTCTTTTTTCTTTTTCTTTGTTCTT 11111@@11>1331B11333B03A3 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACAGGTAT.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACAGGTAT.sam
new file mode 100644
index 0000000..80f7080
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACAGGTAT.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ACAGGTAT-CACTTCAT LB:LN_ACAGGTATCACTTCAT SM:SA_ACAGGTATCACTTCAT CN:BI
+HiMom:1:1101:14342:1520 589 * 0 0 * * 0 0 CTTTCTTTTCTCCTTTTTTTCTTTC 11>>1@@@1313111311AA0BAAA RG:Z:HiMom.1
+HiMom:1:1101:14342:1520 653 * 0 0 * * 0 0 TCGTGTTTTTTCTTTTTGCTTTCCC 111>1>>>11111331A013A3111 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACAGTTGA.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACAGTTGA.sam
new file mode 100644
index 0000000..11cfedc
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACAGTTGA.sam
@@ -0,0 +1,6 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ACAGTTGA-ATCTTCTC LB:LN_ACAGTTGAATCTTCTC SM:SA_ACAGTTGAATCTTCTC CN:BI
+HiMom:1:1101:14133:1507 589 * 0 0 * * 0 0 TCCTCTTTGCTTTTTGCTATCACTC 111>1B1 at 313131111A33A33D1 RG:Z:HiMom.1
+HiMom:1:1101:14133:1507 653 * 0 0 * * 0 0 TCCTTTATTATCTTTGTTCCTTTTT 111>>313 at 333AAA3A1333331A RG:Z:HiMom.1
+HiMom:1:1101:14753:1450 589 * 0 0 * * 0 0 CTTTTTCCTCTTTTTTTCTTTTGTT 1>>>>@1131B1311100BA31100 RG:Z:HiMom.1
+HiMom:1:1101:14753:1450 653 * 0 0 * * 0 0 TCCCTTTTTTTTCTTTTCTCTTTTT 1111>@11@>1001331313331AA RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACCAACTG.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACCAACTG.sam
new file mode 100644
index 0000000..f3e7c05
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACCAACTG.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ACCAACTG-CATCACTT LB:LN_ACCAACTGCATCACTT SM:SA_ACCAACTGCATCACTT CN:BI
+HiMom:1:1101:15221:1507 589 * 0 0 * * 0 0 CTTTTTTCTTTCTTTGTTTTTGTAT 1>1>1111@@33A3B3311000033 RG:Z:HiMom.1
+HiMom:1:1101:15221:1507 653 * 0 0 * * 0 0 CTCTTTTTTTTCTCTCTTCTTTCCT 111>13111>0013A11313B321A RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACCTACTG.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACCTACTG.sam
new file mode 100644
index 0000000..8ad7c10
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACCTACTG.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ACCTACTG-CTTCCCTT LB:LN_ACCTACTGCTTCCCTT SM:SA_ACCTACTGCTTCCCTT CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACTAAGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACTAAGAC.sam
new file mode 100644
index 0000000..8aa38c5
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACTAAGAC.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ACTAAGAC-GTCCTCAT LB:LN_ACTAAGACGTCCTCAT SM:SA_ACTAAGACGTCCTCAT CN:BI
+HiMom:1:1101:17324:1480 589 * 0 0 * * 0 0 TCTCTGTGTTTTTTTTTTTTTTACT >111>333 at 11111A000///A/1A RG:Z:HiMom.1
+HiMom:1:1101:17324:1480 653 * 0 0 * * 0 0 CTTTTTTTTCTTCTCTTTCCTTCCT 1>>1111>00 at 333133331AA101 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AGGTCGCA.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AGGTCGCA.sam
new file mode 100644
index 0000000..03219df
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AGGTCGCA.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.AGGTCGCA-TTCCTTTC LB:LN_AGGTCGCATTCCTTTC SM:SA_AGGTCGCATTCCTTTC CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AGGTGCGA.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AGGTGCGA.sam
new file mode 100644
index 0000000..bae890f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AGGTGCGA.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.AGGTGCGA-GACATTAA LB:LN_AGGTGCGAGACATTAA SM:SA_AGGTGCGAGACATTAA CN:BI
+HiMom:1:1101:15634:1526 589 * 0 0 * * 0 0 TTTTTTTTTTCTTTGGTTATTTTAT 1>>>>>AA00>11B100A1BBAB2A RG:Z:HiMom.1
+HiMom:1:1101:15634:1526 653 * 0 0 * * 0 0 CCTCTCTTCTTTTTTTCTCCTTTTT 111>1>131 at 131110A1B1ABBA1 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AGGTTATC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AGGTTATC.sam
new file mode 100644
index 0000000..cb41e6a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AGGTTATC.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.AGGTTATC-TTAGCCAG LB:LN_AGGTTATCTTAGCCAG SM:SA_AGGTTATCTTAGCCAG CN:BI
+HiMom:1:1101:17862:1503 589 * 0 0 * * 0 0 TTTTTTTCCTACTTTGCTTTAGTTT >1>1>1>1133113A11A1A1133A RG:Z:HiMom.1
+HiMom:1:1101:17862:1503 653 * 0 0 * * 0 0 TCTTCCCCTTCTTTATTTATTTGCT 1>1111111>1 at AA3A3B33AA333 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AGTTGCTT.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AGTTGCTT.sam
new file mode 100644
index 0000000..2948939
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/AGTTGCTT.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.AGTTGCTT-TGACTTGG LB:LN_AGTTGCTTTGACTTGG SM:SA_AGTTGCTTTGACTTGG CN:BI
+HiMom:1:1101:14369:1492 589 * 0 0 * * 0 0 TTTCTTCTTTCTTTTTGTAAAGTTT 1>>11333 at B3BB31111333333B RG:Z:HiMom.1
+HiMom:1:1101:14369:1492 653 * 0 0 * * 0 0 TCCTTCTTTTTCTCTTTTTTTTCTT 1>11>@1131111AAAAA1100011 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ATAGCGTC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ATAGCGTC.sam
new file mode 100644
index 0000000..efd072d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ATAGCGTC.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ATAGCGTC-TTGGTCTG LB:LN_ATAGCGTCTTGGTCTG SM:SA_ATAGCGTCTTGGTCTG CN:BI
+HiMom:1:1101:17049:1423 589 * 0 0 * * 0 0 CTCTTTTCTTTCTTTCTCTTCCTCT 1>111 at 13@3333A33A3331111A RG:Z:HiMom.1
+HiMom:1:1101:17049:1423 653 * 0 0 * * 0 0 TTTTCTCCTCCTCTTCCTCTTTTTT 1111113111111111111113110 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ATTATCAA.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ATTATCAA.sam
new file mode 100644
index 0000000..422b7c7
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ATTATCAA.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ATTATCAA-CACCATAC LB:LN_ATTATCAACACCATAC SM:SA_ATTATCAACACCATAC CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ATTGTCTG.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ATTGTCTG.sam
new file mode 100644
index 0000000..fec0fd0
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/ATTGTCTG.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.ATTGTCTG-GATTCACA LB:LN_ATTGTCTGGATTCACA SM:SA_ATTGTCTGGATTCACA CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CAATAGTC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CAATAGTC.sam
new file mode 100644
index 0000000..6fa6e2d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CAATAGTC.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CAATAGTC-CGACTCTC LB:LN_CAATAGTCCGACTCTC SM:SA_CAATAGTCCGACTCTC CN:BI
+HiMom:1:1101:15479:1337 589 * 0 0 * * 0 0 CTCTCTTTTTTTTCTTTTTTATTCT 1111113311110013311001222 RG:Z:HiMom.1
+HiMom:1:1101:15479:1337 653 * 0 0 * * 0 0 TTTTCCTTCCTTTCTCTTCCCTCCT 111111 at 311133133331111111 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CAGCAAGG.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CAGCAAGG.sam
new file mode 100644
index 0000000..04b4be8
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CAGCAAGG.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CAGCAAGG-GCGATATT LB:LN_CAGCAAGGGCGATATT SM:SA_CAGCAAGGGCGATATT CN:BI
+HiMom:1:1101:17475:1506 589 * 0 0 * * 0 0 TCTTTTTTTTTCTCTCGTGTGTTGG >111>B11>0>013310A0A0BB## RG:Z:HiMom.1
+HiMom:1:1101:17475:1506 653 * 0 0 * * 0 0 CCTTTTTCTTTTCTCTCCTCTTTCC 11111111 at 33131331111A1331 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CAGCGGTA.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CAGCGGTA.sam
new file mode 100644
index 0000000..3b2ed89
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CAGCGGTA.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CAGCGGTA-AGTACTGC LB:LN_CAGCGGTAAGTACTGC SM:SA_CAGCGGTAAGTACTGC CN:BI
+HiMom:1:1101:13678:1483 589 * 0 0 * * 0 0 TCTTTTCTTTTTTTTTTTCTTTTTT >1>>>131331111000A01AB### RG:Z:HiMom.1
+HiMom:1:1101:13678:1483 653 * 0 0 * * 0 0 TTTTTTTTCTTTCCTCTCTTTTTTT 11111111013331A########## RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CATGCTTA.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CATGCTTA.sam
new file mode 100644
index 0000000..e53745f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CATGCTTA.sam
@@ -0,0 +1,6 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CATGCTTA-TAGCATTT LB:LN_CATGCTTATAGCATTT SM:SA_CATGCTTATAGCATTT CN:BI
+HiMom:1:1101:13947:1464 589 * 0 0 * * 0 0 CTCCTTTTCTTCTTCTTCTCTTTTT 1>11113 at 313331331331A3311 RG:Z:HiMom.1
+HiMom:1:1101:13947:1464 653 * 0 0 * * 0 0 TTTTTTTTTCCCTCCCCTTTCCCTT 1111111100111000000111111 RG:Z:HiMom.1
+HiMom:1:1101:17987:1524 589 * 0 0 * * 0 0 CCTCTTTTTCTGTTTTTTTTGCTGG 111>11 at 111133331110001B11 RG:Z:HiMom.1
+HiMom:1:1101:17987:1524 653 * 0 0 * * 0 0 TCTTCTTTTCTTTCTTCTTTATTTG 111>13131313A3A33A1A33A33 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CATGCTTT.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CATGCTTT.sam
new file mode 100644
index 0000000..bf025ee
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CATGCTTT.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CATGCTTT-TAGCATTG LB:LN_CATGCTTTTAGCATTG SM:SA_CATGCTTTTAGCATTG CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CATGTTCG.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CATGTTCG.sam
new file mode 100644
index 0000000..ecd136d
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CATGTTCG.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CATGTTCG-CGCCTTTT LB:LN_CATGTTCGCGCCTTTT SM:SA_CATGTTCGCGCCTTTT CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCAGAGCT.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCAGAGCT.sam
new file mode 100644
index 0000000..ab66e3a
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCAGAGCT.sam
@@ -0,0 +1,6 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CCAGAGCT-CAACTGAT LB:LN_CCAGAGCTCAACTGAT SM:SA_CCAGAGCTCAACTGAT CN:BI
+HiMom:1:1101:16357:1518 589 * 0 0 * * 0 0 GTCTTCTGCTTCGCTCACGCTGGGT 1>>>>3 at 113B311AA1111A0000 RG:Z:HiMom.1
+HiMom:1:1101:16357:1518 653 * 0 0 * * 0 0 TCCTTCTCTCTTTTTTTTTAATTCT >1111111B at BB311AA0001ABAB RG:Z:HiMom.1
+HiMom:1:1101:17387:1497 589 * 0 0 * * 0 0 CCCCTTTTTTGTTGTGCTTTAGCCT 111>>111111111A01B3311111 RG:Z:HiMom.1
+HiMom:1:1101:17387:1497 653 * 0 0 * * 0 0 CTTTTTGTCTTTCTTCCCCCTGCTT 111>11113@@@3333111AA0011 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCCGATTT.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCCGATTT.sam
new file mode 100644
index 0000000..6245307
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCCGATTT.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CCCGATTT-TCTCTCCC LB:LN_CCCGATTTTCTCTCCC SM:SA_CCCGATTTTCTCTCCC CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTATGCC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTATGCC.sam
new file mode 100644
index 0000000..79bf0d7
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTATGCC.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CCTATGCC-AATTGGCC LB:LN_CCTATGCCAATTGGCC SM:SA_CCTATGCCAATTGGCC CN:BI
+HiMom:1:1101:17516:1540 589 * 0 0 * * 0 0 CTTTCGTTTTTCTTTCCTATACATC 1>>1111B>1>1B3331B3A11333 RG:Z:HiMom.1
+HiMom:1:1101:17516:1540 653 * 0 0 * * 0 0 TTCTTTTTTTTCCCTTTCCCTTTTC 1>111 at B@11>0111B11AA1A112 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTATTCT.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTATTCT.sam
new file mode 100644
index 0000000..0d02f5f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTATTCT.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CCTATTCT-TCGTTTTC LB:LN_CCTATTCTTCGTTTTC SM:SA_CCTATTCTTCGTTTTC CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTCTTCT.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTCTTCT.sam
new file mode 100644
index 0000000..bdf0d9e
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTCTTCT.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CCTCTTCT-CTCGCTTT LB:LN_CCTCTTCTCTCGCTTT SM:SA_CCTCTTCTCTCGCTTT CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTCTTTC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTCTTTC.sam
new file mode 100644
index 0000000..8024be1
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTCTTTC.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CCTCTTTC-TTCTGCTC LB:LN_CCTCTTTCTTCTGCTC SM:SA_CCTCTTTCTTCTGCTC CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTTCGCA.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTTCGCA.sam
new file mode 100644
index 0000000..95ea56b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTTCGCA.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CCTTCGCA-GAATCGAC LB:LN_CCTTCGCAGAATCGAC SM:SA_CCTTCGCAGAATCGAC CN:BI
+HiMom:1:1101:15248:1531 589 * 0 0 * * 0 0 CCCTACCTGTCTGCTATCCATCCCC 111>11111B1311313A13B111A RG:Z:HiMom.1
+HiMom:1:1101:15248:1531 653 * 0 0 * * 0 0 TTCTCCTTCTATTTCTCTTGTCTTC 11111@@B@@3333333331A1333 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTTCTTT.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTTCTTT.sam
new file mode 100644
index 0000000..b2904b4
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTTCTTT.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CCTTCTTT-TATCATTT LB:LN_CCTTCTTTTATCATTT SM:SA_CCTTCTTTTATCATTT CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CGCTATGT.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CGCTATGT.sam
new file mode 100644
index 0000000..af2e6f7
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CGCTATGT.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CGCTATGT-TTCACCTT LB:LN_CGCTATGTTTCACCTT SM:SA_CGCTATGTTTCACCTT CN:BI
+HiMom:1:1101:17615:1538 589 * 0 0 * * 0 0 CTTTTTTTTTTTTCCTTTTTTTCTT >>>>11110000A011AA1A//0A1 RG:Z:HiMom.1
+HiMom:1:1101:17615:1538 653 * 0 0 * * 0 0 TTCTTTCCTTTTCTTTTTTCTGTTT 11>1133133 at 131331111A3333 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CTACCAGG.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CTACCAGG.sam
new file mode 100644
index 0000000..6297e7e
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CTACCAGG.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CTACCAGG-TTCTTGGC LB:LN_CTACCAGGTTCTTGGC SM:SA_CTACCAGGTTCTTGGC CN:BI
+HiMom:1:1101:14790:1540 589 * 0 0 * * 0 0 TTCTCTCTTTTCTCTTTCTTGTTGT A>1>13113313A3AAAAAB11B1B RG:Z:HiMom.1
+HiMom:1:1101:14790:1540 653 * 0 0 * * 0 0 CTCTGTATTTTCCTTTTTCTTCTTT 11111 at 33@@33133A1BB1A3A1B RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CTCCCTCT.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CTCCCTCT.sam
new file mode 100644
index 0000000..26105ec
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CTCCCTCT.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CTCCCTCT-TCCTTCTT LB:LN_CTCCCTCTTCCTTCTT SM:SA_CTCCCTCTTCCTTCTT CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CTGTAATC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CTGTAATC.sam
new file mode 100644
index 0000000..235ef32
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/CTGTAATC.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.CTGTAATC-CTATTAGC LB:LN_CTGTAATCCTATTAGC SM:SA_CTGTAATCCTATTAGC CN:BI
+HiMom:1:1101:15029:1349 589 * 0 0 * * 0 0 CTTCTCCTTTTCTTTTTTTTTTTTT 1>11111113 at 313A########## RG:Z:HiMom.1
+HiMom:1:1101:15029:1349 653 * 0 0 * * 0 0 TTTCTTTTTCTTTTTTCTTTCTTTT 1111>3 at 111133111113333331 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GACCAGGA.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GACCAGGA.sam
new file mode 100644
index 0000000..f333f4f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GACCAGGA.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GACCAGGA-CCATCACA LB:LN_GACCAGGACCATCACA SM:SA_GACCAGGACCATCACA CN:BI
+HiMom:1:1101:16241:1505 589 * 0 0 * * 0 0 CTTCTTTTTTTTCTTCCCTTTGCTC 11>1113 at 11100A331011A1111 RG:Z:HiMom.1
+HiMom:1:1101:16241:1505 653 * 0 0 * * 0 0 CTGTGGTTTTTTTCTTGTCTTTTCC 111>11111111001A111333AA1 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GCCGTCGA.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GCCGTCGA.sam
new file mode 100644
index 0000000..4b1178c
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GCCGTCGA.sam
@@ -0,0 +1,6 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GCCGTCGA-TGGTACCC LB:LN_GCCGTCGATGGTACCC SM:SA_GCCGTCGATGGTACCC CN:BI
+HiMom:1:1101:13789:1486 589 * 0 0 * * 0 0 CTTTTTTCTTCCTCTTTCTTTTTCT 1111111113311AAB33333A10A RG:Z:HiMom.1
+HiMom:1:1101:13789:1486 653 * 0 0 * * 0 0 TTTTTCTCTCCTTCTCTTCTCCTTC 1111111331111111331311111 RG:Z:HiMom.1
+HiMom:1:1101:14791:1400 589 * 0 0 * * 0 0 TTTTTTTCTTTTTCTTTTTTTCTTT >>1>>111 at 3@@11A3B1BA001A1 RG:Z:HiMom.1
+HiMom:1:1101:14791:1400 653 * 0 0 * * 0 0 TCCTTTTTCTTTCCTTTTCTTTTTT 111>131 at 1133313331313311A RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GCCTAGCC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GCCTAGCC.sam
new file mode 100644
index 0000000..58acb3b
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GCCTAGCC.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GCCTAGCC-CTTGAATC LB:LN_GCCTAGCCCTTGAATC SM:SA_GCCTAGCCCTTGAATC CN:BI
+HiMom:1:1101:14517:1469 589 * 0 0 * * 0 0 TTTCTTTTTTTTCCCTTTCCTCTTT >111133111>001111111B1111 RG:Z:HiMom.1
+HiMom:1:1101:14517:1469 653 * 0 0 * * 0 0 CCTCCTTTTTCTTCTTTTCCTTTTT 11111113111133AA3A313331A RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GCTATCCA.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GCTATCCA.sam
new file mode 100644
index 0000000..efa1bfc
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GCTATCCA.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GCTATCCA-CCTCCCCC LB:LN_GCTATCCACCTCCCCC SM:SA_GCTATCCACCTCCCCC CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GTATAACA.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GTATAACA.sam
new file mode 100644
index 0000000..9b3ff62
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GTATAACA.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GTATAACA-TATTCAAC LB:LN_GTATAACATATTCAAC SM:SA_GTATAACATATTCAAC CN:BI
+HiMom:1:1101:14857:1542 589 * 0 0 * * 0 0 TTTTCTCTTTTTGTTTTTTTCTTCT 1>>>1 at 33B3111ABB11AA01333 RG:Z:HiMom.1
+HiMom:1:1101:14857:1542 653 * 0 0 * * 0 0 TCTTCCTTTTTTTTTTTTCTTTCTT 111111133@@110000/AB1122A RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GTCTGATG.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GTCTGATG.sam
new file mode 100644
index 0000000..f45a307
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/GTCTGATG.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.GTCTGATG-TCACTTCC LB:LN_GTCTGATGTCACTTCC SM:SA_GTCTGATGTCACTTCC CN:BI
+HiMom:1:1101:16578:1461 589 * 0 0 * * 0 0 TTTTTTCTCTTTTTTTTGTTTCTGC >1>111113@@31A0A0000B2B21 RG:Z:HiMom.1
+HiMom:1:1101:16578:1461 653 * 0 0 * * 0 0 CTTTTTCTTTCTTTTTCTCTCTTCT 111111>133333311113A11313 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/N.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/N.sam
new file mode 100644
index 0000000..473afc5
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/N.sam
@@ -0,0 +1,40 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.N-N LB:LN_N SM:SA_N CN:BI
+HiMom:1:1101:13743:1511 589 * 0 0 * * 0 0 TCCTTCTTTTCCCTCCCCTTTCCTT >11>111@@@3111A111ABA1133 BC:Z:ATTATCAA-CACCATAC RG:Z:HiMom.1
+HiMom:1:1101:13743:1511 653 * 0 0 * * 0 0 CCCCCTTCCCTCTTTTTTCCTTCCC 1111111111 at 11131100133100 BC:Z:ATTATCAA-CACCATAC RG:Z:HiMom.1
+HiMom:1:1101:13844:1536 589 * 0 0 * * 0 0 TTTCTTTTTTCTTTTCCCTTTATTT 1111>3311111331311B111333 BC:Z:TCCCCGTT-CCAACTTC RG:Z:HiMom.1
+HiMom:1:1101:13844:1536 653 * 0 0 * * 0 0 TCTTCTTTTTTTTTTTTCTTTTCCT 111113131111A############ BC:Z:TCCCCGTT-CCAACTTC RG:Z:HiMom.1
+HiMom:1:1101:14281:1532 589 * 0 0 * * 0 0 CTTTTTTCCTTTTTTTCTTTTTTCT 1>>11111133 at 1A00013311A01 BC:Z:CCTTCTTT-TATCATTT RG:Z:HiMom.1
+HiMom:1:1101:14281:1532 653 * 0 0 * * 0 0 TTTCTCTTTTTTTTTCTCCCTTCCT >111133331111000121001001 BC:Z:CCTTCTTT-TATCATTT RG:Z:HiMom.1
+HiMom:1:1101:14340:1451 589 * 0 0 * * 0 0 TTTTTTCCTTCTCCCCTTTTTCCTT >11111113311111111111013A BC:Z:TTCCTCCT-CACCATCC RG:Z:HiMom.1
+HiMom:1:1101:14340:1451 653 * 0 0 * * 0 0 TCCCTTCCTCCCCTCCTTCTTTTTC 1111111111111111111113110 BC:Z:TTCCTCCT-CACCATCC RG:Z:HiMom.1
+HiMom:1:1101:14809:1476 589 * 0 0 * * 0 0 TTTTTCCCTTTCTCTTTTCTTTTCT >1>>111111113333313AAA131 BC:Z:GCTATCCA-CCTCCCCC RG:Z:HiMom.1
+HiMom:1:1101:14809:1476 653 * 0 0 * * 0 0 TCTCTTTTTCTTTTTTCTCCTTTCT >111133111133111113111313 BC:Z:GCTATCCA-CCTCCCCC RG:Z:HiMom.1
+HiMom:1:1101:14852:1366 589 * 0 0 * * 0 0 TTCTCTCCCTCTTTTTTTCTTCTTT 111>1311111113A1AA0133313 BC:Z:AGGTCGCA-TTCCTTTC RG:Z:HiMom.1
+HiMom:1:1101:14852:1366 653 * 0 0 * * 0 0 TCCTTTTTCTTTTCTTTTCTTTTCC 1111131111331313313133131 BC:Z:AGGTCGCA-TTCCTTTC RG:Z:HiMom.1
+HiMom:1:1101:14927:1516 589 * 0 0 * * 0 0 CTCCTTTTCTCTTTTCCCCCTGTGC 11111 at 3131333313111111111 BC:Z:GTCTGATG-TCACTTCC RG:Z:HiMom.1
+HiMom:1:1101:14927:1516 653 * 0 0 * * 0 0 TTCCTCCCCCTCCTCCCCCTCCCTC 11111111>1111111100000A00 BC:Z:GTCTGATG-TCACTTCC RG:Z:HiMom.1
+HiMom:1:1101:14943:1353 589 * 0 0 * * 0 0 TTTTTTTTTCTTTTTTTTTTTTTTT 1>1>111100 at 33A########### BC:Z:CTCCCTCT-TCCTTCTT RG:Z:HiMom.1
+HiMom:1:1101:14943:1353 653 * 0 0 * * 0 0 CTCCCTTTTTTTTTTCTTCCTCTCT 1111111111110000112111101 BC:Z:CTCCCTCT-TCCTTCTT RG:Z:HiMom.1
+HiMom:1:1101:15334:1365 589 * 0 0 * * 0 0 TTTTTTTCTTCTCTTTCTTTTCTTT 111>111113331333333B13133 BC:Z:TGTATCTC-TTACTCTT RG:Z:HiMom.1
+HiMom:1:1101:15334:1365 653 * 0 0 * * 0 0 TCTCTCTTTCTTCTCTTTTTTTTTT 1111111333333313331110000 BC:Z:TGTATCTC-TTACTCTT RG:Z:HiMom.1
+HiMom:1:1101:15424:1475 589 * 0 0 * * 0 0 CTTTTTTCTTTTTCTTTTTTTTTCT 1>>11 at 1113311113311000001 BC:Z:CCTCTTCT-CTCGCTTT RG:Z:HiMom.1
+HiMom:1:1101:15424:1475 653 * 0 0 * * 0 0 TTCCTTCTTTCCTTCTCTCTTTCTT 1111131113313311131133333 BC:Z:CCTCTTCT-CTCGCTTT RG:Z:HiMom.1
+HiMom:1:1101:15736:1478 589 * 0 0 * * 0 0 CCTCTCTTTTTTCCTTTCCCTGCCT 1111111 at 3B1111A33111A1001 BC:Z:ATTGTCTG-GATTCACA RG:Z:HiMom.1
+HiMom:1:1101:15736:1478 653 * 0 0 * * 0 0 CTCTTCCCTTTCCCCCTCTTCTTCT 111>111111111111A11113A33 BC:Z:ATTGTCTG-GATTCACA RG:Z:HiMom.1
+HiMom:1:1101:15785:1528 589 * 0 0 * * 0 0 CTTTTTTTTTTCTCTCTTTTTTTTT 11>111>100001221B######## BC:Z:CCCGATTT-TCTCTCCC RG:Z:HiMom.1
+HiMom:1:1101:15785:1528 653 * 0 0 * * 0 0 TCTTCTCTTTCTCTTTTTCTTTTCT 1111131 at 3@3333331A1133131 BC:Z:CCCGATTT-TCTCTCCC RG:Z:HiMom.1
+HiMom:1:1101:15865:1540 589 * 0 0 * * 0 0 GCTTTCCTTGTTTTCTGTCCCCTTC 11111113311BB13A33A111B10 BC:Z:TTCCCCAG-TGCTTTTA RG:Z:HiMom.1
+HiMom:1:1101:15865:1540 653 * 0 0 * * 0 0 CTTTTTTATTTTCCTTTTGCATCCT 11111111333 at 31333B1133301 BC:Z:TTCCCCAG-TGCTTTTA RG:Z:HiMom.1
+HiMom:1:1101:15987:1510 589 * 0 0 * * 0 0 CTTTTTTTTTTTCCCTTTTTACCTT ######################### BC:Z:CCTCTTTC-TTCTGCTC RG:Z:HiMom.1
+HiMom:1:1101:15987:1510 653 * 0 0 * * 0 0 TTCCCCTTCCCTTCTCTTTTCTTCT 111111>1111 at 1111333131333 BC:Z:CCTCTTTC-TTCTGCTC RG:Z:HiMom.1
+HiMom:1:1101:15998:1432 589 * 0 0 * * 0 0 TTCTTCCTCTTCTTCTTCTTCCTTT 111>131111113133133A31133 BC:Z:CATGTTCG-CGCCTTTT RG:Z:HiMom.1
+HiMom:1:1101:15998:1432 653 * 0 0 * * 0 0 CTTTTTTTCTTTTCTCCTCCTTTTT 11111 at 111@3313A31A000131A BC:Z:CATGTTCG-CGCCTTTT RG:Z:HiMom.1
+HiMom:1:1101:16070:1386 589 * 0 0 * * 0 0 TTTTTTTTTTTTTTTTCCTTCCTTT ######################### BC:Z:TGTCGGTT-TTTTGCTT RG:Z:HiMom.1
+HiMom:1:1101:16070:1386 653 * 0 0 * * 0 0 TTTTTTTTCTCTCTTTTTTTTTTTT 11111111013311331A####### BC:Z:TGTCGGTT-TTTTGCTT RG:Z:HiMom.1
+HiMom:1:1101:16085:1467 589 * 0 0 * * 0 0 TTTTTTCCTTTTCTTTTCCTCTTCT 1>>11>113B31313A13131111A BC:Z:ACCTACTG-CTTCCCTT RG:Z:HiMom.1
+HiMom:1:1101:16085:1467 653 * 0 0 * * 0 0 TTTTTTTTTTTTCCTCTTTTTTTCC ######################### BC:Z:ACCTACTG-CTTCCCTT RG:Z:HiMom.1
+HiMom:1:1101:16098:1529 589 * 0 0 * * 0 0 TTTTTTTTTTCTCTCCCTTTCTCTT 1>1>>11100012210001112222 BC:Z:TTCTCATC-TTCCTTCC RG:Z:HiMom.1
+HiMom:1:1101:16098:1529 653 * 0 0 * * 0 0 CCCTCTCCACTTTTCTTTCCTCCCT 11111>1111111331333131110 BC:Z:TTCTCATC-TTCCTTCC RG:Z:HiMom.1
+HiMom:1:1101:16530:1425 589 * 0 0 * * 0 0 TTTTTTTTTTTTTTCTTTTTTTTTT 1111>>110000A############ BC:Z:CCTATTCT-TCGTTTTC RG:Z:HiMom.1
+HiMom:1:1101:16530:1425 653 * 0 0 * * 0 0 TTCTTTCCCTTTTCTTTTCCTTCTC 1111133111111313313133111 BC:Z:CCTATTCT-TCGTTTTC RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TACTTAGC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TACTTAGC.sam
new file mode 100644
index 0000000..20b89bb
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TACTTAGC.sam
@@ -0,0 +1,6 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TACTTAGC-GTCTGCAC LB:LN_TACTTAGCGTCTGCAC SM:SA_TACTTAGCGTCTGCAC CN:BI
+HiMom:1:1101:13898:1519 589 * 0 0 * * 0 0 CCTTCTCTACTTTTTTTTCTATTTT 111>111B31 at 33311A0A1333BA RG:Z:HiMom.1
+HiMom:1:1101:13898:1519 653 * 0 0 * * 0 0 TTTTTTCTTTTCTCTTCCTCTTTTC 11>11111 at 3131A3A111A11313 RG:Z:HiMom.1
+HiMom:1:1101:14983:1536 589 * 0 0 * * 0 0 CCTTCTTCTTGTTCCCTCGCCAGGC 11>>1113 at B11133AA111A0000 RG:Z:HiMom.1
+HiMom:1:1101:14983:1536 653 * 0 0 * * 0 0 TCCTTATCCTTTTTACTGCCCTGTA 1111>331@@331A11A311111B3 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TCCCCGTT.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TCCCCGTT.sam
new file mode 100644
index 0000000..44a3c3c
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TCCCCGTT.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TCCCCGTT-CCAACTTC LB:LN_TCCCCGTTCCAACTTC SM:SA_TCCCCGTTCCAACTTC CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TCCTTGGT.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TCCTTGGT.sam
new file mode 100644
index 0000000..84531c8
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TCCTTGGT.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TCCTTGGT-GCTGCACT LB:LN_TCCTTGGTGCTGCACT SM:SA_TCCTTGGTGCTGCACT CN:BI
+HiMom:1:1101:17106:1463 589 * 0 0 * * 0 0 TTTCTTTTTTTTCTTTTCTCTTCCT 11>113 at 1111>0A3A131333111 RG:Z:HiMom.1
+HiMom:1:1101:17106:1463 653 * 0 0 * * 0 0 TTCATTTTCTTCTTTTTCTTCCTCT 1111133331333131111331111 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TCGCCTTG.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TCGCCTTG.sam
new file mode 100644
index 0000000..070cfe7
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TCGCCTTG.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TCGCCTTG-CCAACGCT LB:LN_TCGCCTTGCCAACGCT SM:SA_TCGCCTTGCCAACGCT CN:BI
+HiMom:1:1101:15287:1512 589 * 0 0 * * 0 0 CCTCCTCCTTTTATTTCTTTTCCCT 111111>1B131333333331A111 RG:Z:HiMom.1
+HiMom:1:1101:15287:1512 653 * 0 0 * * 0 0 CTTTTTTCTTTTTTTCGTCTTTCTT 1111111113 at 111000000A2221 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGCAAGTA.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGCAAGTA.sam
new file mode 100644
index 0000000..149c745
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGCAAGTA.sam
@@ -0,0 +1,6 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TGCAAGTA-CGAACTTC LB:LN_TGCAAGTACGAACTTC SM:SA_TGCAAGTACGAACTTC CN:BI
+HiMom:1:1101:13416:1538 589 * 0 0 * * 0 0 TTTTGTCTATCACTTTGTTTATTCA >11>11333333311A13113BBA3 RG:Z:HiMom.1
+HiMom:1:1101:13416:1538 653 * 0 0 * * 0 0 TTTTCTTCCCTTTCTTTCTCTGTTT 111111331111B133A33333D33 RG:Z:HiMom.1
+HiMom:1:1101:16315:1534 589 * 0 0 * * 0 0 TTTCTGTTTTATTCTTTTCTTATGT >1>113333B333333AB31A331D RG:Z:HiMom.1
+HiMom:1:1101:16315:1534 653 * 0 0 * * 0 0 TTTTTCTCCTCCTTTTTTTGTTCCT 111111131 at 11A1A111000B333 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGCTCGAC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGCTCGAC.sam
new file mode 100644
index 0000000..966ff62
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGCTCGAC.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TGCTCGAC-TTCACAGT LB:LN_TGCTCGACTTCACAGT SM:SA_TGCTCGACTTCACAGT CN:BI
+HiMom:1:1101:15028:1491 589 * 0 0 * * 0 0 TTTTTTTTTTTTTTTTTTTTTTTTT >1>>111>>000/A########### RG:Z:HiMom.1
+HiMom:1:1101:15028:1491 653 * 0 0 * * 0 0 TTCTTTTTTTTCTTTTTTTTTCTCT 1111131111001331100//0A22 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGTAATCA.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGTAATCA.sam
new file mode 100644
index 0000000..a3ec1f7
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGTAATCA.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TGTAATCA-CCTCTAAC LB:LN_TGTAATCACCTCTAAC SM:SA_TGTAATCACCTCTAAC CN:BI
+HiMom:1:1101:15439:1540 589 * 0 0 * * 0 0 CTTCTTTCATATTCTTAAATTTGCA 1>>11B333B333ABA331ABA333 RG:Z:HiMom.1
+HiMom:1:1101:15439:1540 653 * 0 0 * * 0 0 TTTTGTTTGAGTGTTATAGAAACAG 111>11BB111113B3333313110 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGTATCTC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGTATCTC.sam
new file mode 100644
index 0000000..696634f
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGTATCTC.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TGTATCTC-TTACTCTT LB:LN_TGTATCTCTTACTCTT SM:SA_TGTATCTCTTACTCTT CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGTCGGTT.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGTCGGTT.sam
new file mode 100644
index 0000000..b7b00bc
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGTCGGTT.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TGTCGGTT-TTTTGCTT LB:LN_TGTCGGTTTTTTGCTT SM:SA_TGTCGGTTTTTTGCTT CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGTTCCGA.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGTTCCGA.sam
new file mode 100644
index 0000000..fc9e0d9
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGTTCCGA.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TGTTCCGA-AACCTCTT LB:LN_TGTTCCGAAACCTCTT SM:SA_TGTTCCGAAACCTCTT CN:BI
+HiMom:1:1101:16256:1385 589 * 0 0 * * 0 0 TTTCTCTTTTTTTTTCCTTTTTTTT >>11>3 at 3@@11AAA01A22AA0/A RG:Z:HiMom.1
+HiMom:1:1101:16256:1385 653 * 0 0 * * 0 0 TCTTTTTCTTTTTTCTTTTCTCTTT 11111111 at 33111113A13A3A33 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTAATCAG.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTAATCAG.sam
new file mode 100644
index 0000000..1d4b2b6
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTAATCAG.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TTAATCAG-CTGGTATT LB:LN_TTAATCAGCTGGTATT SM:SA_TTAATCAGCTGGTATT CN:BI
+HiMom:1:1101:17703:1479 589 * 0 0 * * 0 0 TTTTTTTTTTCCTCCTTTTTTTCCT 111111110001110012A1//01A RG:Z:HiMom.1
+HiMom:1:1101:17703:1479 653 * 0 0 * * 0 0 TCTTTTTTCCTTCTCTTTTTTCTTT 11111 at 1111331113331100133 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTATATCT.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTATATCT.sam
new file mode 100644
index 0000000..8629fa0
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTATATCT.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TTATATCT-TCATGTCT LB:LN_TTATATCTTCATGTCT SM:SA_TTATATCTTCATGTCT CN:BI
+HiMom:1:1101:16819:1536 589 * 0 0 * * 0 0 TTTTTTTGTTTTGTCCTTTCTTCCT >1>111>1111>0A3AA33AAB31B RG:Z:HiMom.1
+HiMom:1:1101:16819:1536 653 * 0 0 * * 0 0 TTTTTTTTTCATCCCTCTCTTCCCT 1>1>>>>>>0333A010A0A2A101 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTCCCCAG.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTCCCCAG.sam
new file mode 100644
index 0000000..a651187
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTCCCCAG.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TTCCCCAG-TGCTTTTA LB:LN_TTCCCCAGTGCTTTTA SM:SA_TTCCCCAGTGCTTTTA CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTCCTCCT.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTCCTCCT.sam
new file mode 100644
index 0000000..67c6e54
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTCCTCCT.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TTCCTCCT-CACCATCC LB:LN_TTCCTCCTCACCATCC SM:SA_TTCCTCCTCACCATCC CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTCTCATC.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTCTCATC.sam
new file mode 100644
index 0000000..9294d00
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTCTCATC.sam
@@ -0,0 +1,2 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TTCTCATC-TTCCTTCC LB:LN_TTCTCATCTTCCTTCC SM:SA_TTCTCATCTTCCTTCC CN:BI
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTGAATAG.sam b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTGAATAG.sam
new file mode 100644
index 0000000..ce84c28
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTGAATAG.sam
@@ -0,0 +1,4 @@
+ at HD VN:1.4 SO:queryname
+ at RG ID:HiMom.1 PL:illumina PU:HiMom.1.TTGAATAG-ATATCCGA LB:LN_TTGAATAGATATCCGA SM:SA_TTGAATAGATATCCGA CN:BI
+HiMom:1:1101:16891:1545 589 * 0 0 * * 0 0 CTTTTGCCTGTGTTTTTTCTCTCAT 1>1>>11111B1BABA11AAA3A13 RG:Z:HiMom.1
+HiMom:1:1101:16891:1545 653 * 0 0 * * 0 0 CTTTTTTCTGACTTTCTTCTAGACT 11>1>1>>13311A3AB3AB33313 RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/25T8B8B25T/sams/barcode_double.params b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/barcode_double.params
new file mode 100644
index 0000000..a291ce1
--- /dev/null
+++ b/testdata/net/sf/picard/illumina/25T8B8B25T/sams/barcode_double.params
@@ -0,0 +1,65 @@
+BARCODE_1 BARCODE_2 SAMPLE_ALIAS LIBRARY_NAME
+AACTTGAC GCTCTCTT SA_AACTTGACGCTCTCTT LN_AACTTGACGCTCTCTT
+AAGACACT AGTCTCCT SA_AAGACACTAGTCTCCT LN_AAGACACTAGTCTCCT
+ACAGGTAT CACTTCAT SA_ACAGGTATCACTTCAT LN_ACAGGTATCACTTCAT
+ACAGTTGA ATCTTCTC SA_ACAGTTGAATCTTCTC LN_ACAGTTGAATCTTCTC
+ACCAACTG CATCACTT SA_ACCAACTGCATCACTT LN_ACCAACTGCATCACTT
+ACCTACTG CTTCCCTT SA_ACCTACTGCTTCCCTT LN_ACCTACTGCTTCCCTT
+ACTAAGAC GTCCTCAT SA_ACTAAGACGTCCTCAT LN_ACTAAGACGTCCTCAT
+AGGTCGCA TTCCTTTC SA_AGGTCGCATTCCTTTC LN_AGGTCGCATTCCTTTC
+AGGTGCGA GACATTAA SA_AGGTGCGAGACATTAA LN_AGGTGCGAGACATTAA
+AGGTTATC TTAGCCAG SA_AGGTTATCTTAGCCAG LN_AGGTTATCTTAGCCAG
+AGTTGCTT TGACTTGG SA_AGTTGCTTTGACTTGG LN_AGTTGCTTTGACTTGG
+ATAGCGTC TTGGTCTG SA_ATAGCGTCTTGGTCTG LN_ATAGCGTCTTGGTCTG
+ATTATCAA CACCATAC SA_ATTATCAACACCATAC LN_ATTATCAACACCATAC
+ATTGTCTG GATTCACA SA_ATTGTCTGGATTCACA LN_ATTGTCTGGATTCACA
+CAGCAAGG GCGATATT SA_CAGCAAGGGCGATATT LN_CAGCAAGGGCGATATT
+CAGCGGTA TGTACTGC SA_CAGCGGTATGTACTGC LN_CAGCGGTATGTACTGC
+CATGCTTA TAGCATTT SA_CATGCTTATAGCATTT LN_CATGCTTATAGCATTT
+CATGCTTT TAGCATTG SA_CATGCTTTTAGCATTG LN_CATGCTTTTAGCATTG
+CATGTTCG CGCCTTTT SA_CATGTTCGCGCCTTTT LN_CATGTTCGCGCCTTTT
+CCAGAGCT CAACTGAT SA_CCAGAGCTCAACTGAT LN_CCAGAGCTCAACTGAT
+CCCGATTT TCTCTCCC SA_CCCGATTTTCTCTCCC LN_CCCGATTTTCTCTCCC
+CCTATGCC AATTGGCC SA_CCTATGCCAATTGGCC LN_CCTATGCCAATTGGCC
+CCTATTCT TCGTTTTC SA_CCTATTCTTCGTTTTC LN_CCTATTCTTCGTTTTC
+CCTCTTCT CTCGCTTT SA_CCTCTTCTCTCGCTTT LN_CCTCTTCTCTCGCTTT
+CCTCTTTC TTCTGCTC SA_CCTCTTTCTTCTGCTC LN_CCTCTTTCTTCTGCTC
+CCTTCGCA GAATCGAC SA_CCTTCGCAGAATCGAC LN_CCTTCGCAGAATCGAC
+CCTTCTTT TATCATTT SA_CCTTCTTTTATCATTT LN_CCTTCTTTTATCATTT
+CGCTATGT TTCTCCTT SA_CGCTATGTTTCTCCTT LN_CGCTATGTTTCTCCTT
+CTACCAGG TTCTTGGC SA_CTACCAGGTTCTTGGC LN_CTACCAGGTTCTTGGC
+CTCCCTCT TCCTTCTT SA_CTCCCTCTTCCTTCTT LN_CTCCCTCTTCCTTCTT
+CTGTAATC CTATTAGC SA_CTGTAATCCTATTAGC LN_CTGTAATCCTATTAGC
+GACCAGGA CCATCACA SA_GACCAGGACCATCACA LN_GACCAGGACCATCACA
+GCCGTCGA AGGTACCC SA_GCCGTCGAAGGTACCC LN_GCCGTCGAAGGTACCC
+GCCGTCGA TGGTACCC SA_GCCGTCGATGGTACCC LN_GCCGTCGATGGTACCC
+GCCTAGCC CTTGAATC SA_GCCTAGCCCTTGAATC LN_GCCTAGCCCTTGAATC
+GCTATCCA CCTCCCCC SA_GCTATCCACCTCCCCC LN_GCTATCCACCTCCCCC
+GTATAACA TATTCAAC SA_GTATAACATATTCAAC LN_GTATAACATATTCAAC
+GTCTGATG GAACTTCG SA_GTCTGATGGAACTTCG LN_GTCTGATGGAACTTCG
+GTCTGATG TCACTTCC SA_GTCTGATGTCACTTCC LN_GTCTGATGTCACTTCC
+TACTTAGC GTCTGCAC SA_TACTTAGCGTCTGCAC LN_TACTTAGCGTCTGCAC
+TCCCCGTT CCAACTTC SA_TCCCCGTTCCAACTTC LN_TCCCCGTTCCAACTTC
+TCCTTGGT GCTGCACT SA_TCCTTGGTGCTGCACT LN_TCCTTGGTGCTGCACT
+TCGCCTTG CCAACGCT SA_TCGCCTTGCCAACGCT LN_TCGCCTTGCCAACGCT
+TGCAAGTA CGAACTTC SA_TGCAAGTACGAACTTC LN_TGCAAGTACGAACTTC
+TGCTCGAC TTCACAGT SA_TGCTCGACTTCACAGT LN_TGCTCGACTTCACAGT
+TGTAATCA CCTCTAAC SA_TGTAATCACCTCTAAC LN_TGTAATCACCTCTAAC
+TGTATCTC TTACTCTT SA_TGTATCTCTTACTCTT LN_TGTATCTCTTACTCTT
+TGTCGGTT TTTTGCTT SA_TGTCGGTTTTTTGCTT LN_TGTCGGTTTTTTGCTT
+TGTTCCGA AACCTCTT SA_TGTTCCGAAACCTCTT LN_TGTTCCGAAACCTCTT
+TTAATCAG CTGGTATT SA_TTAATCAGCTGGTATT LN_TTAATCAGCTGGTATT
+TTATATCT TCATGTCT SA_TTATATCTTCATGTCT LN_TTATATCTTCATGTCT
+TTCCCCAG TGCTTTTA SA_TTCCCCAGTGCTTTTA LN_TTCCCCAGTGCTTTTA
+TTCCTCCT CACCATCC SA_TTCCTCCTCACCATCC LN_TTCCTCCTCACCATCC
+TTCTCATC TTCCTTCC SA_TTCTCATCTTCCTTCC LN_TTCTCATCTTCCTTCC
+TTGAATAG ATATCCGA SA_TTGAATAGATATCCGA LN_TTGAATAGATATCCGA
+CAATAGTC CGACTCTC SA_CAATAGTCCGACTCTC LN_CAATAGTCCGACTCTC
+GCCGTCGA AGGTACCA SA_GCCGTCGAAGGTACCA LN_GCCGTCGAAGGTACCA
+CATGCTTA TAGCATTG SA_CATGCTTATAGCATTG LN_CATGCTTATAGCATTG
+CAGCGGTA AGTACTGC SA_CAGCGGTAAGTACTGC LN_CAGCGGTAAGTACTGC
+TGCTCGAC TTCACAGA SA_TGCTCGACTTCACAGA LN_TGCTCGACTTCACAGA
+AAGACACT AGTCACCT SA_AAGACACTAGTCACCT LN_AAGACACTAGTCACCT
+CGCTATGT TTCACCTT SA_CGCTATGTTTCACCTT LN_CGCTATGTTTCACCTT
+GTATAACA AATTCAAC SA_GTATAACAAATTCAAC LN_GTATAACAAATTCAAC
+N N SA_N LN_N
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl
deleted file mode 100644
index 7a1fe42..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C1.1/s_1_1201.bcl b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C1.1/s_1_1201.bcl
deleted file mode 100644
index 49e7507..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C1.1/s_1_1201.bcl and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C1.1/s_1_2101.bcl b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C1.1/s_1_2101.bcl
deleted file mode 100644
index d7257f8..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C1.1/s_1_2101.bcl and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl
deleted file mode 100644
index 4024466..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl and /dev/null differ
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diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_1_1101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_1_1101_qseq.txt
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--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_1_1101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 1 1101 1075 1001 0 1 .GTGTGAAGTTCAAGAAGCAGACAA BPYcccc^aeegecfegeghdg]_[ 1
-SL-HAR 281 1 1101 1131 1008 0 1 .TTTTCTTAAAATATTAATTTCATG BOVW]\^_Y][[\__^^BBBBBBBB 0
-SL-HAR 281 1 1101 1184 1010 0 1 .GTGAACAAACTGGTTTTATCTGGT BP\ccceegggggihiiidgghhif 1
-SL-HAR 281 1 1101 1018 1020 0 1 .TTGTGGAAGTGGAAGAGGCT...A BOWX_[ZXP^XY^Y[]][_BBBBBB 0
-SL-HAR 281 1 1101 1242 1021 0 1 AACCTAGGCAATCAGGAAGGAGGAG BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 1 1101 1036 1021 0 1 .ATTTCCATTTTATTCACGTAA.AA BOVX_Z]^_\^\]__Y^__\[_BBB 0
-SL-HAR 281 1 1101 1127 1026 0 1 CTAGAAAAGCCTAGAAACAGCTCCT ___ccccc^^^`cfX[f]de_dYJ` 1
-SL-HAR 281 1 1101 1067 1028 0 1 TAAACCCTTCTCCTGCCCTCATATA ^\_P`ca^^b`eeddbed[d_R[[^ 1
-SL-HAR 281 1 1101 1103 1030 0 1 TAAAGTAGAATAATTTCATGGTATT _b_eeedcgfgegihiigghid_gg 1
-SL-HAR 281 1 1101 1225 1040 0 1 TATGATATTGATCTCTATTTGCTTG _^^cceeeggegghhhhhihhghii 1
-SL-HAR 281 1 1101 1175 1044 0 1 CGGTCAGCAAAGGCTATTCTCATCT bbbeeeeeggggghiihiihhbgeg 1
-SL-HAR 281 1 1101 1080 1053 0 1 AATTCAAGAATTCTGTGGCATATGC _bbeeeeeggggfihiihihiiiii 1
-SL-HAR 281 1 1101 1209 1058 0 1 TGGGGTGTGGAGGGAGACCCAGGGC ___cc`ccegegehegghhh\gghZ 1
-SL-HAR 281 1 1101 1135 1062 0 1 GTATAGTCATGAGCGGCGCTTTCTT bbbeeeeefgfggiiifgdgghggh 1
-SL-HAR 281 1 1101 1012 1069 0 1 .TAAAACGGAGTATGTACAT..... BOZ\_^[[^Y_\]^_]_^]^BBBBB 0
-SL-HAR 281 1 1101 1153 1081 0 1 CCTGATGAACAAACAGACTAAGATT ___ceecacgeggihiifhhhihgh 1
-SL-HAR 281 1 1101 1099 1084 0 1 CACTGTATTTGGTGCTGGGTCATTT bbbeeeeeggggfiiiiiigfhghi 1
-SL-HAR 281 1 1101 1134 1088 0 1 CTGCCATTCAAAACTCATCCTTCTT \Y\PJJ[JQ[Q[]_``V`]JRK_`B 0
-SL-HAR 281 1 1101 1006 1090 0 1 .ACC.CTCAGGAGCAGAGTG..... BGGQBQ[LL[]^Z^[^^^BBBBBBB 0
-SL-HAR 281 1 1101 1018 1110 0 1 .GAGGTTTTCTCCAGCACCCA...C BOO\_[^^^^^^^_^_^^_^^BBBB 0
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_1_1201_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_1_1201_qseq.txt
deleted file mode 100644
index 6494d92..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_1_1201_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 1 1201 1134 1002 0 1 .ACCTGCGTGTCAGCAACATCCGCC BP\`acccggge^ec[Z`ef_d`gh 1
-SL-HAR 281 1 1201 1224 1012 0 1 .ATAATGACCTGGGGCTACTGAATC BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 1 1201 1154 1019 0 1 AATAGTAATAGTGGTTGTAGTTATC ^__ccccce[beeabdcdghhhhhS 1
-SL-HAR 281 1 1201 1093 1020 0 1 ATAC...AAACAGGCCGCTTCCTAG [[[^BBBQQ\]Z^_^[^_^^^^^^^ 0
-SL-HAR 281 1 1201 1197 1023 0 1 TGCTAGAGGAGTGCAGGAAGGGGGA BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 1 1201 1134 1032 0 1 TCATCTTTTTTCTTCTGACGTTCTT PP\cYS`K\`caccdhhhS_`bWWb 1
-SL-HAR 281 1 1201 1207 1033 0 1 TGATTGAATACTATAAGAATGGGGA ^_\acccaegge]ef]eggdeda^b 1
-SL-HAR 281 1 1201 1171 1035 0 1 TGGACGAAAGAGTGAGACTCTGCCT ___ccccccg^e`defYegfhhhhh 1
-SL-HAR 281 1 1201 1113 1036 0 1 AGGA.GCTTCTCAGCAGAGTCTCCA _bbcBQ`ceggegghiiiidggfhf 1
-SL-HAR 281 1 1201 1215 1054 0 1 AGTAACCTTCCTTCATGAAATTTAC ab_eeeddgggggfghifhihhihe 1
-SL-HAR 281 1 1201 1177 1062 0 1 ATCCTTCAGCCCACCTGCTGCATGC ___ececcca]ccZYeagff_fegg 1
-SL-HAR 281 1 1201 1128 1076 0 1 GTATGGATTTGGGGAGTAAATGGCT ___eee`cgggfgh\fYbe^efggh 1
-SL-HAR 281 1 1201 1199 1080 0 1 TAATCACTTTGCTTTTTCCCGTCTT OGO\GHXH\^HHQU_^]^BBBBBBB 0
-SL-HAR 281 1 1201 1229 1085 0 1 AAGATAAGCCTTTGGAAGTAAAGAT b_beeeeegggggiighh_iiihhh 1
-SL-HAR 281 1 1201 1176 1085 0 1 TCACAAACTAATTTAATCCAAAAAC _[_ccecceegggggggghihhddg 1
-SL-HAR 281 1 1201 1149 1085 0 1 CATGAGACAGGCATATGTTGAATGA ___ececegggeggffhhfggfgif 1
-SL-HAR 281 1 1201 1113 1097 0 1 GGAA.GGAACATTGGGAAAGTCCCC ^_^cBQ`\bccc[edfdffhhdbgf 1
-SL-HAR 281 1 1201 1188 1109 0 1 AATTTCTTCCGGTTCCAACCCTTTT BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 1 1201 1136 1112 0 1 AGGAATGGCTTGCTTAAGACTTGCC bbbeeeeefggP`dedgcbfhgbeg 1
-SL-HAR 281 1 1201 1201 1117 0 1 CCTCAGTTTCGGGAGATCATCCACA [__cacccggggc_^ac`b`g][eX 1
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_1_2101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_1_2101_qseq.txt
deleted file mode 100644
index 3478ff9..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_1_2101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 1 2101 1100 1002 0 1 .ACC...AGCACTTACCTCGT..TC BOZ]BBBQR\W_^^^^^^^_^BBBB 0
-SL-HAR 281 1 2101 1145 1006 0 1 .CCGTG.GGCACACCGAGGTGAGGG BOZ___BQ\_\^^_^^]^^]_]_^^ 0
-SL-HAR 281 1 2101 1126 1012 0 1 .TATG..TATCGGCCCAAGAAGGAC BOV\\BBQQ[_\^^^W\R^UY]^R[ 0
-SL-HAR 281 1 2101 1104 1024 0 1 TTCTA..TGTGTGCTGAATGCTTCA [[[^^BBQ[___^^^_^[_^^_^\] 0
-SL-HAR 281 1 2101 1239 1031 0 1 GTGCTGTCCAGCCAGACCGCCAGCT ZZ[^[^_BBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 1 2101 1066 1031 0 1 C.CA...TCCTTCAGGGTCACCAAG [BO_BBBQQ]_^_____^^]_^__^ 0
-SL-HAR 281 1 2101 1193 1035 0 1 CATCTGCCTATGAAGATTATGACAT bbbeeeeegggggfhfgihiihigh 1
-SL-HAR 281 1 2101 1218 1037 0 1 CCGGACCCTGGGCTCAGCCCTGATG _bbeeceegfgggiiiiihihifhh 1
-SL-HAR 281 1 2101 1135 1041 0 1 AGTCC..GCTGGCATGTCTTTAAGA GZZ\^BBQQ\^^Y^^_^]_^_^_^] 0
-SL-HAR 281 1 2101 1154 1042 0 1 GCGTGGTCCTTGGGGAGACCCCACC _bbeeecdggegghhfh`fhhhhff 1
-SL-HAR 281 1 2101 1231 1076 0 1 TTATTGTTTTCAGCAGCGACCCCCT bbbeeeeegggfghiighhiiiiii 1
-SL-HAR 281 1 2101 1201 1078 0 1 ATAAAGAAATGTGTTATGTATGTTG _aaeeeeegggcghhfhhiiiiiih 1
-SL-HAR 281 1 2101 1136 1088 0 1 CTGTA..CAGGTTTACAATATAGTA ZZW_^BBGQQ\W]]X][_\__\WXX 0
-SL-HAR 281 1 2101 1178 1091 0 1 GAGGGCCCCTCGCACCATCTGGCCC ___ccH\c^ccc_P_`be^fee[c` 1
-SL-HAR 281 1 2101 1162 1100 0 1 GCCCAAGGTTATGTTTGATCCCTCT ___ecaccggceehhfhhhbdgghh 1
-SL-HAR 281 1 2101 1069 1101 0 1 G.TT...TTAAACATGGTGCTTAGT [BO\BBBQRY]^_^^___^__^^_^ 0
-SL-HAR 281 1 2101 1209 1106 0 1 CAAATCTGATTGCATTATTCACCTG bbbeeceeggggghhihhifhihii 1
-SL-HAR 281 1 2101 1133 1107 0 1 TTTTA..TTTAACCTAGAGATTTTA [[[^^BBQY_X^^^^]^^_\_^__\ 0
-SL-HAR 281 1 2101 1191 1112 0 1 TAAAGGGAAGTCCTAATTCACTTTG ___ccc`Rbag[eddcfg`aeeggh 1
-SL-HAR 281 1 2101 1103 1112 0 1 ACCA...TGCCCCGGTGGGGGCTGC Z[[_BBBBBBBBBBBBBBBBBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_2101_barcode.txt.gz b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_2101_barcode.txt.gz
deleted file mode 100644
index 239ae54..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_2101_barcode.txt.gz and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_2_1101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_2_1101_qseq.txt
deleted file mode 100644
index 5e00636..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_2_1101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 1 1101 1075 1001 0 2 .GGTCGCA BP\aceee 1
-SL-HAR 281 1 1101 1131 1008 0 2 .GGTCGCA BP\cceec 0
-SL-HAR 281 1 1101 1184 1010 0 2 .GGTCGCA BP\cceee 1
-SL-HAR 281 1 1101 1018 1020 0 2 .GGTCGCA BP\`ccee 0
-SL-HAR 281 1 1101 1242 1021 0 2 .GGTCGCA BP\`ccec 0
-SL-HAR 281 1 1101 1036 1021 0 2 .GGTCGCA BP\aceee 0
-SL-HAR 281 1 1101 1127 1026 0 2 .GGTCGCA BP\accec 1
-SL-HAR 281 1 1101 1067 1028 0 2 .GGTCGCA BP\`cccc 1
-SL-HAR 281 1 1101 1103 1030 0 2 .GGTCGCA BP\aceec 1
-SL-HAR 281 1 1101 1225 1040 0 2 .GGTCGCA BP\`ccec 1
-SL-HAR 281 1 1101 1175 1044 0 2 .GGTCGCA BP\`ceee 1
-SL-HAR 281 1 1101 1080 1053 0 2 .GGTCGCA BP\accee 1
-SL-HAR 281 1 1101 1209 1058 0 2 .GGTCGCA BS\`ceec 1
-SL-HAR 281 1 1101 1135 1062 0 2 .GGTCGCA BS\aceee 1
-SL-HAR 281 1 1101 1012 1069 0 2 .GGTCGCA BP\cceee 0
-SL-HAR 281 1 1101 1153 1081 0 2 .GGTCGCA BP\cceee 1
-SL-HAR 281 1 1101 1099 1084 0 2 .GGTCGCA BP\aceee 1
-SL-HAR 281 1 1101 1134 1088 0 2 .GGTTGCA BP\aYace 0
-SL-HAR 281 1 1101 1006 1090 0 2 ..GTCGC. BBPS`ceB 0
-SL-HAR 281 1 1101 1018 1110 0 2 .GGTCGCA BP\accec 0
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_2_1201_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_2_1201_qseq.txt
deleted file mode 100644
index 04a452d..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_2_1201_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 1 1201 1134 1002 0 2 .GGTCGCA BP\aceec 1
-SL-HAR 281 1 1201 1224 1012 0 2 .GGTCGCA BS\`ccee 0
-SL-HAR 281 1 1201 1154 1019 0 2 .GGTCGCA BS\aceee 1
-SL-HAR 281 1 1201 1093 1020 0 2 .GGTCGCA BP\accee 0
-SL-HAR 281 1 1201 1197 1023 0 2 .GGTCGCA BP\aceee 0
-SL-HAR 281 1 1201 1134 1032 0 2 .GGTCGCA BP\aceee 1
-SL-HAR 281 1 1201 1207 1033 0 2 .GGTCGCA BP\aceee 1
-SL-HAR 281 1 1201 1171 1035 0 2 .GGTCGCA BP\accee 1
-SL-HAR 281 1 1201 1113 1036 0 2 .GGTCGCA BP\`ccee 1
-SL-HAR 281 1 1201 1215 1054 0 2 .GGTCGCA BP\aceee 1
-SL-HAR 281 1 1201 1177 1062 0 2 .GGTCGCA BP\aceee 1
-SL-HAR 281 1 1201 1128 1076 0 2 .GGTCGCA BP\cceee 1
-SL-HAR 281 1 1201 1199 1080 0 2 .GGTCGCA BP\aceee 0
-SL-HAR 281 1 1201 1229 1085 0 2 .GGTCGCA BP\accee 1
-SL-HAR 281 1 1201 1176 1085 0 2 .GGTCGCA BP\accec 1
-SL-HAR 281 1 1201 1149 1085 0 2 .GGTCGCA BP\aceee 1
-SL-HAR 281 1 1201 1113 1097 0 2 .GGTCGCA BP\`ccee 1
-SL-HAR 281 1 1201 1188 1109 0 2 .GGTCGCA BP\`ccee 0
-SL-HAR 281 1 1201 1136 1112 0 2 .GGTCGCA BP\accee 1
-SL-HAR 281 1 1201 1201 1117 0 2 .GGTCGCA BP\accee 1
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_2_2101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_2_2101_qseq.txt
deleted file mode 100644
index 78be415..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_2_2101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 1 2101 1100 1002 0 2 .GGTCGCA BP\accee 0
-SL-HAR 281 1 2101 1145 1006 0 2 .GGTCGCA BP\`ceee 0
-SL-HAR 281 1 2101 1126 1012 0 2 .GGTCGCA BP\`ceee 0
-SL-HAR 281 1 2101 1104 1024 0 2 .GGTCGCA BS\aceee 0
-SL-HAR 281 1 2101 1239 1031 0 2 .GGTCGCA BP\accee 0
-SL-HAR 281 1 2101 1066 1031 0 2 .GGTCGCA BP\accce 0
-SL-HAR 281 1 2101 1193 1035 0 2 .GGTCGCA BP\aceee 1
-SL-HAR 281 1 2101 1218 1037 0 2 .GGTCGCA BP\accee 1
-SL-HAR 281 1 2101 1135 1041 0 2 .GGTCGCA BP\aceee 0
-SL-HAR 281 1 2101 1154 1042 0 2 .GGTCGCA BP\aceee 1
-SL-HAR 281 1 2101 1231 1076 0 2 .GGTCGCA BS\aceee 1
-SL-HAR 281 1 2101 1201 1078 0 2 .GGTCGCA BP\aceee 1
-SL-HAR 281 1 2101 1136 1088 0 2 .GGTCGCA BP\`ccec 0
-SL-HAR 281 1 2101 1178 1091 0 2 .GGTCGCA BP\aceee 1
-SL-HAR 281 1 2101 1162 1100 0 2 .GGTCGCA BP\aceee 1
-SL-HAR 281 1 2101 1069 1101 0 2 .GGTCGCA BP\aceee 0
-SL-HAR 281 1 2101 1209 1106 0 2 .GGTCGCA BP\aceee 1
-SL-HAR 281 1 2101 1133 1107 0 2 .GGTCGCA BP\aceee 0
-SL-HAR 281 1 2101 1191 1112 0 2 .GGTCGCA BS\`ceee 1
-SL-HAR 281 1 2101 1103 1112 0 2 .GGTCGCA BS\aceee 0
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_3_1101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_3_1101_qseq.txt
deleted file mode 100644
index 7cca850..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_3_1101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 1 1101 1075 1001 0 3 AACTGA..AAAAACACTCCAAATAA [__c^aBBQQbee[bc^dgfJQ[[b 1
-SL-HAR 281 1 1101 1131 1008 0 3 CTAGTTGGGGAATCTATTGTGTGCA __^c\acc`ecbc^a^`dcg_`ebX 0
-SL-HAR 281 1 1101 1184 1010 0 3 CCCTATCAGTTTGTTGTCACTTCCA aabe`ccdggggghihiiiggfggi 1
-SL-HAR 281 1 1101 1018 1020 0 3 T....A..AAAAAACCTAGAGCTAA _BBBBQBBQQ`^aefdgXXQ^^^bd 0
-SL-HAR 281 1 1101 1242 1021 0 3 GTGGGTTGGGAGGGGCCATGGAGGG ^Z_J\`ccgUbecUfUbZbccI^c] 0
-SL-HAR 281 1 1101 1036 1021 0 3 AG..CACCCCAGTAACATTGTCCAA ^[BBSQQ`e`egcg_e[d[bbaS`b 0
-SL-HAR 281 1 1101 1127 1026 0 3 CCCAGCGGTCGCCGCTAGCCCCCTC _aaeceeec_^[^dd_H^[^c`ac` 1
-SL-HAR 281 1 1101 1067 1028 0 3 TTTTCATGCACTCTGACTCAGGATA ___^c^`c^eg`egh`fdd]e]`be 1
-SL-HAR 281 1 1101 1103 1030 0 3 GGGTTACCACTTTGAATCATCATCC _bbeeecefaeegfdghfghddfd] 1
-SL-HAR 281 1 1101 1225 1040 0 3 CCTTCAGTGCACTCCACTGCCTCAT _bbeeeecegggghifffihgfihi 1
-SL-HAR 281 1 1101 1175 1044 0 3 GTCCCAGGGAGGAGTCCCTGTGGGA _abceccegcee^eefiiiihhhh_ 1
-SL-HAR 281 1 1101 1080 1053 0 3 TCACCTACTTCCTGGAAAATGTCAT ___cecccgggggiiihiihiefdg 1
-SL-HAR 281 1 1101 1209 1058 0 3 GTCCCTGCCTCCGTCCTGATCCCAG _bbeeeeeggaeghfhaa_ggiihh 1
-SL-HAR 281 1 1101 1135 1062 0 3 AATACCAAGGTTGTTCTACATGACG b_bece^cgggggfhhhffeghd]f 1
-SL-HAR 281 1 1101 1012 1069 0 3 .....C...CCTGGCTG.CCTCAC. BBBBBQBBBQQ`cfhfgBRQ`e\fB 0
-SL-HAR 281 1 1101 1153 1081 0 3 CGCCGGTTATCCGGTAGTTCTCCGA ___ceeeefggggidffhf^dceeY 1
-SL-HAR 281 1 1101 1099 1084 0 3 TATGTATGTATGTGTAGGGAATCTA _aaeceeegggggiiihhiefghhg 1
-SL-HAR 281 1 1101 1134 1088 0 3 ATCAATTCATCACGGGTTGGTGCGG PJJJJQ\JQb`QJ[PHHQ_HQ`I^W 0
-SL-HAR 281 1 1101 1006 1090 0 3 ............CACCA.....TC. BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 1 1101 1018 1110 0 3 C....G..GCCAGACCAGGTAGTTC aBBBBQBBQQ`eefhiifiabfegh 0
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_3_1201_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_3_1201_qseq.txt
deleted file mode 100644
index b494712..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_3_1201_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 1 1201 1134 1002 0 3 A.GGGC..CATCACAGGAGCCTGCC _BPS`cBBR[beecgfghhhfb`bf 1
-SL-HAR 281 1 1201 1224 1012 0 3 GCCTTTACTTATGATCACAGTTTAT BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 1 1201 1154 1019 0 3 AGTAGGCTCTCCTTCCTTGGACTGT _bbaceeegfecegfgihhibcgfi 1
-SL-HAR 281 1 1201 1093 1020 0 3 GTATTCCTGAGAAAAATCACACTCT _^aeeeeeg`eagf``ghhgfffdg 0
-SL-HAR 281 1 1201 1197 1023 0 3 TAGCCTTTTCTGCCCTAATGTACCA BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 1 1201 1134 1032 0 3 GGTTAATCCAATGTCTCAGCAGAAT PJP``Q`K`JQbcfKKb_iXd^BBB 1
-SL-HAR 281 1 1201 1207 1033 0 3 ATTGAGCCTATCATCAAATGTCACT ^^_PSQ`Zb[c`e`c[_]``ibS`g 1
-SL-HAR 281 1 1201 1171 1035 0 3 TCCTCATATTCCCCCAAAGAGGCCA aa_cecccegeegiidhihhihihf 1
-SL-HAR 281 1 1201 1113 1036 0 3 AGGCGCATGAGTCAGGAGGGTGAGT [aaeeeeegggeghhhdgfhWbbee 1
-SL-HAR 281 1 1201 1215 1054 0 3 AAATTTGGGGGGTAATTTGTTATGT _^[ccecefggcEU`bcccbcbdcd 1
-SL-HAR 281 1 1201 1177 1062 0 3 TTTTCATATTAACCTGGCTACCCAT __beecdcegeeehghabfb`Zf]Z 1
-SL-HAR 281 1 1201 1128 1076 0 3 GAGCCCAGAAGGTGCTGCAGGCCTG bb_eeeeegggggiiiicfffadff 1
-SL-HAR 281 1 1201 1199 1080 0 3 TCAGCACCTAGTACAGCCTGGGCGA PYJ\YJQY\J`cS[KbJJ`bBBBBB 0
-SL-HAR 281 1 1201 1229 1085 0 3 ATTTTCTTTCCTGCATTAGGTATTT aabeeeeegggfgighiiii`eghi 1
-SL-HAR 281 1 1201 1176 1085 0 3 CTTCAGCCACTTCATCATCCGTCAG ___^ccdcgegg`egYbfbgg\fgi 1
-SL-HAR 281 1 1201 1149 1085 0 3 ATGGCCTTAAGGATATGGACACGTG __beeeeegfggghigifhhfghih 1
-SL-HAR 281 1 1201 1113 1097 0 3 AGCCTGTGATTCTCCACCCCTGCCT W\\ccceeage`gdg[`fggbghfd 1
-SL-HAR 281 1 1201 1188 1109 0 3 AAGCCTCTTGCAAGTACTTGTTAAT BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 1 1201 1136 1112 0 3 TATCCAAAATCAAAATGAAATGCAG _bbeeeeeggggghihhhihiihdg 1
-SL-HAR 281 1 1201 1201 1117 0 3 CTCAATACTAAATCTCAAGATTGAT ^__eccd]eccga_ef_YYJ`hcag 1
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_3_2101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_3_2101_qseq.txt
deleted file mode 100644
index 9cc9604..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_1_3_2101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 1 2101 1100 1002 0 3 ....A...GCTTTCCTATT..CCCT BBBBSBBBQQ`eghiifhiBBQ[ee 0
-SL-HAR 281 1 2101 1145 1006 0 3 A...C..CCCTGCCCCCTCCTGCAG _BBBSBBQQ`cechiiiifgiihhh 0
-SL-HAR 281 1 2101 1126 1012 0 3 C.TGAC.TTTTTTCACTCTTCTGGG _BP``cBQ`ceegfghhhhhfdgih 0
-SL-HAR 281 1 2101 1104 1024 0 3 TTTGTCACTGTCAACATCATCCAGC _bbeceeegggeghifhihihicgh 0
-SL-HAR 281 1 2101 1239 1031 0 3 ACTGTGCTCCCATTTCTCAGTACTG JYYJS`^^^RJQ`bgc[ea[[b[^_ 0
-SL-HAR 281 1 2101 1066 1031 0 3 GCCAAAGTTCAGGTAACAGAGTTCA b_beeeeegggggghiiiighggfh 0
-SL-HAR 281 1 2101 1193 1035 0 3 ATTTAAACACAGGTCATTTTAAGTC bbbeeeeegggggghhhiiiihihi 1
-SL-HAR 281 1 2101 1218 1037 0 3 TGCTGGACTGTTTGTGCAGGCGGCA b__eeeeefggeehfhihhhihiga 1
-SL-HAR 281 1 2101 1135 1041 0 3 GAAGCGGAGGTTGCGGTGAGCCAAG __aeeeecggggghfifhcdfXaeg 0
-SL-HAR 281 1 2101 1154 1042 0 3 CCACAGATGCTCTTCACTCCAGCCC ___eeeeegggegihiiiiiihfgi 1
-SL-HAR 281 1 2101 1231 1076 0 3 TGGGTAGAGAAAGGAAAAAGAAAAT abbeceecgeeggihhiiihhhiih 1
-SL-HAR 281 1 2101 1201 1078 0 3 ACTCTAAGGTCAACGGCCCATGTGG a_aeeeeegggggiiiiiiiiiiii 1
-SL-HAR 281 1 2101 1136 1088 0 3 CCAATTTTCTTTTTATAGTGATGGT a__ZaccceeggghbfY``gfgcb` 0
-SL-HAR 281 1 2101 1178 1091 0 3 GCCCCTCTCCACTCAGTCCCCTTCC __ae`ccdZ`[cefgfdfddfZea_ 1
-SL-HAR 281 1 2101 1162 1100 0 3 CACCTACTGTACATTTATTTGGTTT ___eecccggcg`fhhdghhiigih 1
-SL-HAR 281 1 2101 1069 1101 0 3 AATTCCCCCTCCCCCATCTATAATT _a_eccdeeggggiihhfhhfbaeh 0
-SL-HAR 281 1 2101 1209 1106 0 3 AGCTTGTTTGGGGGTCTGCTGTAGT aabeeeceggggfieghiiiighhh 1
-SL-HAR 281 1 2101 1133 1107 0 3 CTTTTGGGAAGTTGGTTCAACACAG abbeeeeegeecggdgihhidhffh 0
-SL-HAR 281 1 2101 1191 1112 0 3 AACCTGCAATTTTAAAAAAATGAAG _^_ceecaaccee_egffddefh`e 1
-SL-HAR 281 1 2101 1103 1112 0 3 AGGAGGGGGGGGGGTGAGGGAACCG Y^BBBBBBBBBBBBBBBBBBBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_1_1101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_1_1101_qseq.txt
deleted file mode 100644
index d4a2aff..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_1_1101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 2 1101 1178 1003 0 1 .CAA...CACCTCCCAGAGTCGTGG BOZ_BBBQQ\\]^^_^^]^^^^_BB 0
-SL-HAR 281 2 1101 1237 1017 0 1 TGTATAAAGGGAAGGTTGTCATGTG PY\Q^KK]QJ[[`Q`\_]`aXRR^Q 0
-SL-HAR 281 2 1101 1185 1039 0 1 CCAA...TTAATAGGCTAACACTAT ZTZ^BBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 2 1101 1228 1040 0 1 TAGGATCTCATTCAGTTTCTTGATA ___ececc`aegeggghgedhf`hg 1
-SL-HAR 281 2 1101 1159 1042 0 1 TT.G...AAGTTCTTCAAAGCCACA Z[BQBBBQLYX\^^^^^_[^W[V]^ 0
-SL-HAR 281 2 1101 1191 1056 0 1 AAAAGGCAAATTTGTATATGTAGAG _bbeeeeegggggiggghhhgihgi 1
-SL-HAR 281 2 1101 1239 1067 0 1 GTACATCTTGGGGTCCTGGGCTTGG GOZ\W_BBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 2 1101 1178 1070 0 1 TC.C...TGGTGTCACCCATGATAG [ZBQBBBQQ_^^_Y^PSZ_XX^Z\^ 0
-SL-HAR 281 2 1101 1215 1071 0 1 AGGGATTTCAGTTGGTGGTGGGGCA ^__`cccc`Wc^bfd[`f[befd`e 1
-SL-HAR 281 2 1101 1189 1093 0 1 CCACCGTGAGAATGCGCCATCTGCA \PV[PW``JQ\QQ^S`U^H[J_[\_ 0
-SL-HAR 281 2 1101 1171 1103 0 1 GT.G...GGAGATGTACTGGTGAAA BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 2 1101 1199 1108 0 1 TGTATCCCTCAGTGTGGCCTGAACT \\\``S^JJQ_`aa^bPR\J^BBBB 0
-SL-HAR 281 2 1101 1159 1119 0 1 CT.C...AAAGTTGTACTAGGCAAA [[BQBBBLQL_LZ]XW]^[_^X_^^ 0
-SL-HAR 281 2 1101 1216 1120 0 1 CGGCTTTGGGTTGGAGCCAGGCCTG P\^cc^YYbPcaYbdedWbf`ehhV 1
-SL-HAR 281 2 1101 1248 1124 0 1 AATTTTTCTAGGCACCAGAAAATGA ___eeeeegggggbghhihhifhid 1
-SL-HAR 281 2 1101 1179 1142 0 1 CAGC...AGCCGTGAGATAACTGAG [[[^BBBQ[__^^_[_^^_^___^_ 0
-SL-HAR 281 2 1101 1220 1145 0 1 GTTTTAACTTTGAGGAGAGGAAAAA ZZZ^^W]_BBBBBBBBBBBBBBBBB 0
-SL-HAR 281 2 1101 1236 1152 0 1 TTTTTCAGCTCTGGGGAAAATGACA Z[G_\S]_[_BBBBBBBBBBBBBBB 0
-SL-HAR 281 2 1101 1200 1155 0 1 CCTGAGCACAGCTGGCATGGAGGTC ___cceeecgecehhfhaghfcg`b 1
-SL-HAR 281 2 1101 1163 1173 0 1 GG.C...CTTTCCAAAGCATTTTAC [[BQBBBQS_^^^^^_^^_^^^_^^ 0
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_1_1201_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_1_1201_qseq.txt
deleted file mode 100644
index f750588..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_1_1201_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 2 1201 1162 1003 0 1 .AAT...CTCACCACAATTCTGTTC BOZ_BBBQS_\__^^]^^_^_^_^^ 0
-SL-HAR 281 2 1201 1228 1012 0 1 .TGGTCATCTGCAGGTTTCTGAGAT BPYacaScccecefeccfdehbgae 1
-SL-HAR 281 2 1201 1175 1029 0 1 GGCA.TTTTTTACCAGCATAAATAA bb_eBQ`cggggghhhihiiiifhh 1
-SL-HAR 281 2 1201 1229 1034 0 1 CCTGTTGTACGTCCCAGTATGGAGC bbbeeeeefgggghfggihhiiX_b 1
-SL-HAR 281 2 1201 1194 1053 0 1 AGATCTCATATCGTCGCTCGTCATG ___eeccecegggfhfhhiiidbdd 1
-SL-HAR 281 2 1201 1221 1074 0 1 ACTCTTGTAACACAGCAATGGGTTT _bbacceeccc`cghhffhhheghh 1
-SL-HAR 281 2 1201 1187 1076 0 1 AAAAAAGCAAACACCTATACTGCCC ___cZ_cZRc`b^\e`YbS`dggeh 1
-SL-HAR 281 2 1201 1175 1093 0 1 CATG.AGACACGCGCCCTGGCATGT ___^BQ`acggc`efghhifhdhid 1
-SL-HAR 281 2 1201 1156 1097 0 1 ACCT...GACTCGGCTTTGCCTCCC BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 2 1201 1232 1099 0 1 TGCGGAGTCTTGCTGGGGGGGGCTA [__acYccegeaghhafhf__BBBB 1
-SL-HAR 281 2 1201 1218 1104 0 1 AGGCTCCTCAAAACCTCAAGATGTG BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 2 1201 1193 1115 0 1 AAAAGAATTATTTTTGCATATGAAA [[_cccaegcegfiiiiegihifhh 1
-SL-HAR 281 2 1201 1152 1116 0 1 G.AA...ACACTGGAATGCATGTCC [BOWBBBQQW^^_^^^^^[[_^]_^ 0
-SL-HAR 281 2 1201 1248 1122 0 1 TGACTTGTGCACTTAAGTGTATTTT ^_^ceeeegagfghhihefgfgiii 1
-SL-HAR 281 2 1201 1220 1129 0 1 TTCACTTTCTCACTTGAGTGTTGAA __\^cccdceec^cfbdeegghdga 1
-SL-HAR 281 2 1201 1206 1151 0 1 TGAACTTCCTGTGACCTGTGGTGAG ^^ZYaccaYbccede`eehhhhhad 1
-SL-HAR 281 2 1201 1190 1155 0 1 AGTTAGGTTTGTGCTTTGTAATCTT \\Z`[``[]``baX`aaaaSR^K^` 0
-SL-HAR 281 2 1201 1173 1158 0 1 ACGC.GGCAATGATGGCGTCTCGCA _^_cBQ``eeeeehhhhhhhhhffb 1
-SL-HAR 281 2 1201 1226 1160 0 1 CTGAGATTGGGGCAGGGGCAGCAGA _bbceacdgfgggiiiiha`gf[cB 1
-SL-HAR 281 2 1201 1199 1178 0 1 ATGCCAGTTTCACATCACAGTAGAC W^_c^acceg^cghfh_dgfdcdhh 1
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_1_2101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_1_2101_qseq.txt
deleted file mode 100644
index d187d90..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_1_2101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 2 2101 1139 1012 0 1 .GTATCATTTTGTTAAAAGTCCTAC BPP`acZceec^bfeeeaedghec_ 1
-SL-HAR 281 2 2101 1225 1019 0 1 TCCTTTAGCTTCAGATGGAAAGACC ___eeeccggggghghhi`eghbgd 1
-SL-HAR 281 2 2101 1115 1023 0 1 AGAGCCCGGGACAATGGGGCCGCGG bbbeeeeeggcggiiiihhiihhfe 1
-SL-HAR 281 2 2101 1161 1028 0 1 AATTATTTATCATTATTAGAAATAA RGZ\^_^^P_BBBBBBBBBBBBBBB 0
-SL-HAR 281 2 2101 1247 1036 0 1 TTCTTTCTACAGTGTAGTCAACCCA bbaeeeeeggggghiiiiiihiiih 1
-SL-HAR 281 2 2101 1178 1039 0 1 GCAAAGCTGGGGACCTGCGAACTCT ^[J`accac[ccbc_adR[_e_bPb 1
-SL-HAR 281 2 2101 1199 1041 0 1 GCGGGGCCATCTACTACTTTAAGAT _V_cccccgeeeeha[^c]ffeg^a 1
-SL-HAR 281 2 2101 1219 1041 0 1 TAGTAATTTTTAAGACTAGGATGCT abbcececgggggihhihhiiiiii 1
-SL-HAR 281 2 2101 1155 1045 0 1 TCCCATTCTTGCCCAACAAGCATTT ___eeeeegggeghiihiifffgii 1
-SL-HAR 281 2 2101 1123 1045 0 1 CAGGGGTGGTGACAGTAAACAGCCC ___eee_`e[c^edgegffhbffhf 1
-SL-HAR 281 2 2101 1092 1048 0 1 TGTCA.ATGTGCCCCTACACAACTC _bbeeBQ`ebeggiiiiihhhbhhf 1
-SL-HAR 281 2 2101 1177 1057 0 1 AAGAGAACACGTTATAGGACATTTT _[^cc^cccegeefgdggbdffghh 1
-SL-HAR 281 2 2101 1198 1058 0 1 AGGGCAGCTTCATAATACACATCCA JY\P\JH_J^]JQ[K[K[`a]`BBB 0
-SL-HAR 281 2 2101 1070 1062 0 1 A.TA...CAGGGATAACTCAA..GC [BO_BBBSQ_^_^^^^^^^^^BBBB 0
-SL-HAR 281 2 2101 1110 1066 0 1 CAATCAAGGGAGCTGGCGTGCGTGG _b_eeeeegg`eghhhcfeghfdce 1
-SL-HAR 281 2 2101 1130 1071 0 1 CCGACAACAGATCTCCCTATTAAGG ___c^ccZ^ceJ[b_fhdX`ed_gd 1
-SL-HAR 281 2 2101 1152 1075 0 1 ACACACATATATAATATAGAACTTA bbbeeeeeggggghihhihghihhf 1
-SL-HAR 281 2 2101 1086 1080 0 1 CAGA...CCAATCAACAGTCTGATG [[[_BBBQ[_^_^_^^^^^___^^^ 0
-SL-HAR 281 2 2101 1208 1082 0 1 CACTCGGCATGGGCCGAGGTGCCTC bbbeeeeeggggghihhhhbegiih 1
-SL-HAR 281 2 2101 1246 1085 0 1 TCTTCCCATGAGGGCACAGTTTGAC bbbeeeeeggggghgghhgfghigh 1
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_2_1101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_2_1101_qseq.txt
deleted file mode 100644
index 48a25e3..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_2_1101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 2 1101 1178 1003 0 2 AGGTCGCA aabeeeec 0
-SL-HAR 281 2 1101 1237 1017 0 2 AGGTCGCA _bbeeeee 0
-SL-HAR 281 2 1101 1185 1039 0 2 AGGTCGCA abbeeeee 0
-SL-HAR 281 2 1101 1228 1040 0 2 AGGTCGCA aabeeeee 1
-SL-HAR 281 2 1101 1159 1042 0 2 AGGTCGCA a_aceeee 0
-SL-HAR 281 2 1101 1191 1056 0 2 AGGTCGCA a_beeeee 1
-SL-HAR 281 2 1101 1239 1067 0 2 AGGTCGCA __bceeee 0
-SL-HAR 281 2 1101 1167 1070 0 2 AGGTCGCA _abceeee 0
-SL-HAR 281 2 1101 1215 1071 0 2 AGGTCGCA a_beeeee 1
-SL-HAR 281 2 1101 1189 1093 0 2 AGGTCGCA aaaeeeee 0
-SL-HAR 281 2 1101 1171 1103 0 2 AGGTCGCA __bcceee 0
-SL-HAR 281 2 1101 1199 1108 0 2 AGGTCGCA _abceeee 0
-SL-HAR 281 2 1101 1159 1119 0 2 AGGTAGCA _abccdee 0
-SL-HAR 281 2 1101 1216 1120 0 2 AGGTCGCA _bbceeee 1
-SL-HAR 281 2 1101 1248 1124 0 2 AGGTCGCA aabceeee 1
-SL-HAR 281 2 1101 1179 1142 0 2 AGGTCGCA bbbeeeee 0
-SL-HAR 281 2 1101 1220 1145 0 2 AGGTCGCA _abeeeee 0
-SL-HAR 281 2 1101 1236 1152 0 2 AGGTCGCA _abceeec 0
-SL-HAR 281 2 1101 1200 1155 0 2 AGGTCGCA _abeeeee 1
-SL-HAR 281 2 1101 1163 1173 0 2 AGGTCGCA bbbeeeee 0
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_2_1201_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_2_1201_qseq.txt
deleted file mode 100644
index d666b1f..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_2_1201_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 2 1201 1162 1003 0 2 .GGTCGCA BP\accee 0
-SL-HAR 281 2 1201 1228 1012 0 2 .GGTCGCA BPY\\a_W 1
-SL-HAR 281 2 1201 1175 1029 0 2 .GGTCGCA BP\cceee 1
-SL-HAR 281 2 1201 1229 1034 0 2 .GGTCGCA BP\`ccee 1
-SL-HAR 281 2 1201 1194 1053 0 2 .ATTAGAT BPPa\c`a 1
-SL-HAR 281 2 1201 1221 1074 0 2 .GGTCGCA BS\cceee 1
-SL-HAR 281 2 1201 1187 1076 0 2 .GGTCGCA BPYcaccc 1
-SL-HAR 281 2 1201 1175 1093 0 2 .GGTCGCA BP\accee 1
-SL-HAR 281 2 1201 1156 1097 0 2 .GGTCGCA BS\aceec 0
-SL-HAR 281 2 1201 1232 1099 0 2 .GGTCGCA BP\`ceee 1
-SL-HAR 281 2 1201 1218 1104 0 2 .GGTCGCA BS\aceec 0
-SL-HAR 281 2 1201 1193 1115 0 2 .GGTCGCA BP\accee 1
-SL-HAR 281 2 1201 1152 1116 0 2 .GGTCGCA BP\aceec 0
-SL-HAR 281 2 1201 1248 1122 0 2 .GGTCGCA BP\accee 1
-SL-HAR 281 2 1201 1220 1129 0 2 .GGTCGCA BS\aceee 1
-SL-HAR 281 2 1201 1206 1151 0 2 .GGTCGCA BP\`ccec 1
-SL-HAR 281 2 1201 1190 1155 0 2 .GGTCGCA BS\accce 0
-SL-HAR 281 2 1201 1173 1158 0 2 .GGTCGCA BP\cceee 1
-SL-HAR 281 2 1201 1226 1160 0 2 .GGTCGCA BP\accee 1
-SL-HAR 281 2 1201 1199 1178 0 2 .GGTCGCA BS\accee 1
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_2_2101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_2_2101_qseq.txt
deleted file mode 100644
index 37451c4..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_2_2101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 2 2101 1139 1012 0 2 .GGTCGCA BP\cceee 1
-SL-HAR 281 2 2101 1225 1019 0 2 .GGTCGCA BS\cceee 1
-SL-HAR 281 2 2101 1115 1023 0 2 .GGTCGCA BP\cccec 1
-SL-HAR 281 2 2101 1161 1028 0 2 .GGTCGCA BP\ccccc 0
-SL-HAR 281 2 2101 1247 1036 0 2 .GGTCGCA BP\accee 1
-SL-HAR 281 2 2101 1178 1039 0 2 .GGTCGCA BS\cccec 1
-SL-HAR 281 2 2101 1199 1041 0 2 .GGTCGCA BP\cceee 1
-SL-HAR 281 2 2101 1219 1041 0 2 .GGTCGCA BP\cceee 1
-SL-HAR 281 2 2101 1155 1045 0 2 .GGTCGCA BS\cceee 1
-SL-HAR 281 2 2101 1123 1045 0 2 .GGTCGCA BS\cceee 1
-SL-HAR 281 2 2101 1092 1048 0 2 .GGTCGCA BP\accec 1
-SL-HAR 281 2 2101 1177 1057 0 2 .GGTCGCA BP\cceee 1
-SL-HAR 281 2 2101 1198 1058 0 2 .GGTCGCA BP\cceee 0
-SL-HAR 281 2 2101 1070 1062 0 2 .GGTCGCA BS\cceec 0
-SL-HAR 281 2 2101 1110 1066 0 2 .GGTCGCA BP\cceee 1
-SL-HAR 281 2 2101 1130 1071 0 2 .GGTCGCA BS\cceee 1
-SL-HAR 281 2 2101 1152 1075 0 2 .GGTCGCA BS\cceec 1
-SL-HAR 281 2 2101 1086 1080 0 2 .GGTCGCA BP\cceee 0
-SL-HAR 281 2 2101 1208 1082 0 2 .GGTCGCA BP\cceee 1
-SL-HAR 281 2 2101 1246 1085 0 2 .GGTCGCA BP\accee 1
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_3_1101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_3_1101_qseq.txt
deleted file mode 100644
index d62fa8f..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_3_1101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 2 1101 1178 1003 0 3 AG.GACCAGAAGCTCTCTGAGTTAG _aBS`cceggfgghhifhibgghhi 0
-SL-HAR 281 2 1101 1237 1017 0 3 CCCAGGATGTTGGAATTGATTGGGG JJYSY`RJ\b[bceJJQ`J[Y`dBB 0
-SL-HAR 281 2 1101 1185 1039 0 3 TGACAAGAAAATTCGTTTCTGGGAC \JPSSa`cgRY`e^f[JQJRbg_eB 0
-SL-HAR 281 2 1101 1228 1040 0 3 TGGTTAAGGTGAGGGTTTCAGAGGT ___cccacgegceghffhgdg_egf 1
-SL-HAR 281 2 1101 1159 1042 0 3 CCAGAACTACCACCAGGACTCAGAG J\a\J\ccb^`ae^efhhfgaa[`a 0
-SL-HAR 281 2 1101 1191 1056 0 3 TTCACAAAATCTTAGAAAGAGGAAG bb_eeeeeggggghhihhihiiddh 1
-SL-HAR 281 2 1101 1239 1067 0 3 GCATTAAGAGGAGACTAAAGTATCC BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 2 1101 1167 1070 0 3 AATAAATGTGTATTTGTGAATAACA ^__cc^acgcegghiii_^hihh[[ 0
-SL-HAR 281 2 1101 1215 1071 0 3 GAACATATTTGTCTCAGAGAGACTT ___cccaYc^ge`beeghh]f\c_e 1
-SL-HAR 281 2 1101 1189 1093 0 3 AAAACAGAACCCAGTTAGCAGTATG PWJ`^J``RJ[bPJQ[KK`bgBBBB 0
-SL-HAR 281 2 1101 1171 1103 0 3 TCTTTGGCTTGCTAAATTTTATTTA PJY`JQJJ`a_^^Y^BBBBBBBBBB 0
-SL-HAR 281 2 1101 1199 1108 0 3 GGTAGGGAAGCACCATCCAGATCTC \PJJ`ccJ[JQJQYZd`BBBBBBBB 0
-SL-HAR 281 2 1101 1159 1119 0 3 AAGCAGTTTCCACCCAGCTCCATCC ^^_Za``cegbbbZYabZeYJ[^aa 0
-SL-HAR 281 2 1101 1216 1120 0 3 AGAGGCTCCAGCATCTCTAGTACTA JYJ``JJaJ`eggd^^XY[bYb^bY 1
-SL-HAR 281 2 1101 1248 1124 0 3 AGAGGCGTGTGAAGGGCTGGAGGAG ^__eeeeeBBBBBBBBBBBBBBBBB 1
-SL-HAR 281 2 1101 1179 1142 0 3 ACTGGGTAAGTTGTTCTCCATCCTT _abeeecdgggggiifhhhhiihii 0
-SL-HAR 281 2 1101 1220 1145 0 3 ACCAAATACTTTTGATTCCCAACTA JJJ\JQ\`[``ccf_egd]c^dY`` 0
-SL-HAR 281 2 1101 1236 1152 0 3 TGTATACCTTGGATGCAATTCCTTC Z^_c^a]]Yb\YJ[`_XJ`eSR[b` 0
-SL-HAR 281 2 1101 1200 1155 0 3 TGTCTTCTATGAAGACGGACTCTTC __acc`cc]cK[`d`gag^begfg[ 1
-SL-HAR 281 2 1101 1163 1173 0 3 CTAGGATGTAAATTTTTTATGTTGC __^ce`deceggghiiiidghhhhf 0
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_3_1201_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_3_1201_qseq.txt
deleted file mode 100644
index 9d7b87e..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_3_1201_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 2 1201 1162 1003 0 3 TCTACCCTTCTACCTGCATGAAGCT a__cccedgffcghffhhiiiiifh 0
-SL-HAR 281 2 1201 1228 1012 0 3 TTTCTTATAGAAACATCTTTTATTT _a_ceeccaeeggihiegihheggb 1
-SL-HAR 281 2 1201 1175 1029 0 3 TTGTAGACAGGTTTGCCCGTAAGTA abbeeeeefggfgihiiihhiihgb 1
-SL-HAR 281 2 1201 1229 1034 0 3 CTCTATCCCAGACCCTTCTCAGGCA ___ccecc[bcgcgcegfhdgfggh 1
-SL-HAR 281 2 1201 1194 1053 0 3 TGTCGATTATCGCACTGGTGCGAAT ___eecceegge^gaddgdggf^^^ 1
-SL-HAR 281 2 1201 1221 1074 0 3 AGCTTTTAGCTATAATGCATAGAAA ___eeeeeeggbcghhhiiihi_]_ 1
-SL-HAR 281 2 1201 1187 1076 0 3 ATCAGAAATAGTCATTATTCTATTT \^\accZ\QJ[Q`^`face^eYhd^ 1
-SL-HAR 281 2 1201 1175 1093 0 3 AAATAGAGATCGCGTTACATTCCAT ___eceeeeeeegghg`_ggggggg 1
-SL-HAR 281 2 1201 1156 1097 0 3 AACTATAACTCCTGCTCGAGGAGAG \^Z\S\KK`\\[`d]aafcbBBBBB 0
-SL-HAR 281 2 1201 1232 1099 0 3 CATCCAGAATGTACCCGCTGCTGGG ^^_aZ^aceggecfefcfYcdgXdf 1
-SL-HAR 281 2 1201 1218 1104 0 3 TCGAGTGAAAAGAAGGCGAACATGA ^\_c`^ace^[^cef_R_^[beS^B 0
-SL-HAR 281 2 1201 1193 1115 0 3 GTGACATGGGACAGCACCACGCAGG _^_ccceefggcegggiheffg[eg 1
-SL-HAR 281 2 1201 1152 1116 0 3 GTTGGAACACTCAAAGAGCCGGGGG ab_eeeedcggfghiihgdgghfii 0
-SL-HAR 281 2 1201 1248 1122 0 3 CTCAACAAAAGCGATTTTAACCTAC __beeeccgggggghhiihgghifh 1
-SL-HAR 281 2 1201 1220 1129 0 3 CAGTTAAACTTACTTCAGGAAGAGA _^_^a^ccega[eehhaegf]ebef 1
-SL-HAR 281 2 1201 1206 1151 0 3 CTAAACAGTATGCTATCTGTGTGGA [^acce`ceeeaeaeedfgbcdffi 1
-SL-HAR 281 2 1201 1190 1155 0 3 TCAGCAGAGTCAAGCATGGCGTCCC _[_ac^c`egc^cgdfg^eZH[_W^ 0
-SL-HAR 281 2 1201 1173 1158 0 3 TGCATCGACTGCCCTATTTTGTCTA a__^cccc^egeefefgfb]dfgif 1
-SL-HAR 281 2 1201 1226 1160 0 3 AGCAGTAACCATCCTACAGCTCCCC ___eeeeeggggehhhihhehiihi 1
-SL-HAR 281 2 1201 1199 1178 0 3 ATGTGCTATGGTGGCAGTGTGCTTG ^__ca`c`cgeceg`efYb`eegfi 1
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_3_2101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_3_2101_qseq.txt
deleted file mode 100644
index 8cd7b30..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_2_3_2101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 2 2101 1139 1012 0 3 CAAAAT.ATGCTCAAGAGTGCCCAG [^ZcccBQQ`[^bfgaffhgb]_ed 1
-SL-HAR 281 2 2101 1225 1019 0 3 TTAACGCCAGAAGCCCGCAAGACGT BBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-HAR 281 2 2101 1115 1023 0 3 GTCTCCCCTCGGCGTCCCTCCGCCC a_beeeeeggggfhhiihihhffgh 1
-SL-HAR 281 2 2101 1161 1028 0 3 TATTAAGTGTGGTATGGTAAAAAGC WYJ`cKa\\\bZcff`BBBBBBBBB 0
-SL-HAR 281 2 2101 1247 1036 0 3 TTTGTACATGGCTCACTATTAATGA bbbeeeeegggggiiiiiiifggif 1
-SL-HAR 281 2 2101 1178 1039 0 3 TTATGGAAATAATGGGGGGGTGGGG _WP`ccc]`cecef]bcfacBBBBB 1
-SL-HAR 281 2 2101 1199 1041 0 3 CCATCTCAAAAAACAAAAAAGAAAA _^[ccccceegg_dcf_f`agabcc 1
-SL-HAR 281 2 2101 1219 1041 0 3 CCCAAGACAAAACACAGCAAGAAGT abbccecefgggfghii\fhiiifg 1
-SL-HAR 281 2 2101 1155 1045 0 3 GGGAATGGCTGCTTTTGATATGTTC abbceeeefggaghihf_ddgfdgf 1
-SL-HAR 281 2 2101 1123 1045 0 3 GCCCCGCCCCTCGTCCCCCTGCTGT babeeeeeggfe`fegffhcVec_c 1
-SL-HAR 281 2 2101 1092 1048 0 3 GACAACTGGACATAAAGAAGTCAAG babeeeeegggggiiiiiiigiiii 1
-SL-HAR 281 2 2101 1177 1057 0 3 AGGCCAAGTGCCCCTCTTGGTGTCT ___cc`ecgg`ec^dfdfgidfdXb 1
-SL-HAR 281 2 2101 1198 1058 0 3 AGGTTTTTTCACTGCATTTTCCAGG PP^cc^J\bbYK`eRJ[[eBBBBBB 0
-SL-HAR 281 2 2101 1070 1062 0 3 AACTCAGACTACAGGTGCAGAAAAC __bccaeeeggggihegfffgdgff 0
-SL-HAR 281 2 2101 1110 1066 0 3 ACGCCCCCAAACCCGCCTGCCAACT ___eeeeegggfgehhffhhfhabf 1
-SL-HAR 281 2 2101 1130 1071 0 3 TTCCAGCCCTCGATTTTGCTTTTTT _^_c^^YaeagcPbeeXKRR`^edf 1
-SL-HAR 281 2 2101 1152 1075 0 3 AGCTCGAGGAAATGTTATCGTTCCA _a_eeecegegggighgighifhih 1
-SL-HAR 281 2 2101 1086 1080 0 3 TAATTTAGTCATGTGGGTAAAGTTA aa_ceeeeggggghhhiehhihiii 0
-SL-HAR 281 2 2101 1208 1082 0 3 AGTAAAAATAAAGAACAACAGCTCA baaeeeeegggggihihhifihhhi 1
-SL-HAR 281 2 2101 1246 1085 0 3 AGTCGAATTGTAATTCCATTTGCCC bbbeeeeeggggghiighiiiihih 1
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_1_1101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_1_1101_qseq.txt
deleted file mode 100644
index 34625ec..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_1_1101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 3 1101 1224 1003 0 1 .CCAATTACATTTTCTCTCTATCAC BPYacceeggggghfhghhhgghhh 1
-SL-HAR 281 3 1101 1193 1020 0 1 AG.T...CCTACCTACAAAGAAAAA [[BQBBBQQZZ__^^^^__^]^[_V 0
-SL-HAR 281 3 1101 1199 1042 0 1 CAAA..CAAACCCACATACCCATCT [[[^BBQ[]^____^^^^^^^^[^^ 0
-SL-HAR 281 3 1101 1225 1047 0 1 AGTGTCTGTCCTCTTTCCTCCATAC ^_\ccZcccbQQbdfa`ddc]RbgX 1
-SL-HAR 281 3 1101 1218 1072 0 1 ATGAC.AGGGGGAAGTAGTCGTCAA Z^VZZBQQ`cP_HH[[Q_Yb^YH^^ 1
-SL-HAR 281 3 1101 1193 1087 0 1 TC.T...TAGTTTTTAGGAATCAAC [[BGBBBQQL_XW]Z___^]^Z^]] 0
-SL-HAR 281 3 1101 1229 1094 0 1 CAAAGTTACATGGCCAAGATAAGCT a_aeeeea`cgeghhidhhhhihhi 1
-SL-HAR 281 3 1101 1247 1112 0 1 AATCGTGTTTTTTTTAGTGTAACTT Z[[[^[_P\H[Z\_^BBBBBBBBBB 0
-SL-HAR 281 3 1101 1195 1128 0 1 TC.T..CTCTGCGCTCCCTCTCGCT [ZBQBBQQ_^X^\^^^[^^[_V\^^ 0
-SL-HAR 281 3 1101 1232 1155 0 1 AAACCCAATGATCAGGTATGTACCC bbbeeeeeggagehhidgfgghihh 1
-SL-HAR 281 3 1101 1240 1185 0 1 CCAGCAGGCGGGGGCAGGGGGGCAG BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 3 1101 1198 1204 0 1 ATGA..ACGACAGCAAAGATGACCC [[[^BBQ[__^^^^_^^^__^__]_ 0
-SL-HAR 281 3 1101 1221 1216 0 1 AAGAGCATCCCCTTGTCCATCAAGA __beeeeeggfffiihfgiiihghh 1
-SL-HAR 281 3 1101 1243 1225 0 1 CATCATGCTGCCAGCAGTCTAGCTG [_[ccccccegegbgghdghhbghX 1
-SL-HAR 281 3 1101 1208 1250 0 1 CCAT..TTAAAGGAAAGACTCAAAA Z[[_BBQ[\]^_^^^^[^]_^^[^^ 0
-SL-HAR 281 3 1101 1352 1005 0 1 .GGGAGTGATGGTGCCCAGCTGGTA BP\cccccggggcfghhfghhhfdg 1
-SL-HAR 281 3 1101 1497 1006 0 1 .ATACTATTTAAGCACCGGGTTGTC BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 3 1101 1435 1006 0 1 .CTGCTGGGCTGAAGAAGAGGAGCA BP\cceccgfggefhefhagh`ffg 1
-SL-HAR 281 3 1101 1260 1009 0 1 .TGCCTCTTCCCGCCAACCCTGGCG BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 3 1101 1306 1020 0 1 GGCACTGTACCTGATGACTCATCTA ^_\`Y`caecYbbYbed`b`^bgg] 1
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_1_1201_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_1_1201_qseq.txt
deleted file mode 100644
index 3b99015..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_1_1201_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 3 1201 1238 1015 0 1 .AAGGCCCGCCACGATGACTATCAT BP\ccccc[begehff_cbdefgeb 1
-SL-HAR 281 3 1201 1178 1023 0 1 C.TG...GACAAAGCGAAACTCCAT ZBOWBBBQQ\Z^^__^_^^_^__^^ 0
-SL-HAR 281 3 1201 1208 1031 0 1 CTGC.CAGGCATTCACAATGGAGGC ___cBQ\`ea^ee[bd[Ybgd`ef[ 1
-SL-HAR 281 3 1201 1178 1044 0 1 A.AT...ATTGATGCAATTGTTCAC BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 3 1201 1214 1051 0 1 CTCCTCCGGCGTTGACTTTCCTGGG BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 3 1201 1234 1085 0 1 TTACTGTGAAAAAGAACATAAGTCT Y^J\aca\cc]Sc_\dXZcd`b[Y` 1
-SL-HAR 281 3 1201 1225 1098 0 1 CTTGAGCTCAGTAATGGTGAGTATT ^__c[c^aQ^RQ`[a[b^dhe[[eg 1
-SL-HAR 281 3 1201 1194 1109 0 1 ACTG.CTGATAGTGGAATACCTGGA ___cBQ`c[caecdgfgdgffhhh` 1
-SL-HAR 281 3 1201 1182 1130 0 1 A.TA...ATAACATCCTGGACTAGG [BO\BBBQQW\]^^_]_[[^[_^^^ 0
-SL-HAR 281 3 1201 1210 1133 0 1 CACA.GCTGCTTTCAAAAACAAGAG bbbeBQ`ceggggfihihiihigdf 1
-SL-HAR 281 3 1201 1180 1154 0 1 G.TG...CAGCTGCTGCTTATGGAG VBOLBBBGLQG\P_S[[]_^^[_W[ 0
-SL-HAR 281 3 1201 1227 1155 0 1 CCAAAACCCTTCTGGAACATGGGAG V^[c`ccccaae^fdaeZYd^fedf 1
-SL-HAR 281 3 1201 1211 1159 0 1 AATCTTGATCAAAGCGAGGTTGAAA ___eceecggggghffafhffhZed 1
-SL-HAR 281 3 1201 1227 1176 0 1 GGAAACCCCCAACCAAGAAGCTCCT ___cc^ccg`ecad^e^^eeaeX^a 1
-SL-HAR 281 3 1201 1186 1185 0 1 A.AA...TCAAAAACAGTCATGGCT [BO\BBBSQ_]__Y^^^^]^^]^[^ 0
-SL-HAR 281 3 1201 1202 1195 0 1 CAAG.CAAGTGAAGATGTGTAAGGT _^_cBQ\`b`ccghaegfgedgggg 1
-SL-HAR 281 3 1201 1242 1201 0 1 ATCTGCCGCACCTCTGACTTTGTAC __[ccccc``eeeaR^[debg[b[X 1
-SL-HAR 281 3 1201 1220 1217 0 1 AGACCGGCGGAGATGTGAACGTGGG ^^^cccccccYc^Za^cSaWcNabB 1
-SL-HAR 281 3 1201 1243 1246 0 1 ATGGGTGAGGGGCATCCCTTTGGGA _bbeeceegggggiiiiiiiiiihg 1
-SL-HAR 281 3 1201 1364 1001 0 1 .TTTAAACCCCAACAATTAATTTTA BJPV```_`J^\`b[```bVV_a^^ 0
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_1_2101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_1_2101_qseq.txt
deleted file mode 100644
index 73b2df1..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_1_2101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 3 2101 1125 1003 0 1 .GTCTGGCCTTGCTGCTGTCCCTGG BP\ccceegggggiifhhhhihhii 1
-SL-HAR 281 3 2101 1099 1006 0 1 .TGCTGTTTCACAGCCTCTTCAATC BP\cceccgeggfihhhhhihghhh 1
-SL-HAR 281 3 2101 1198 1014 0 1 .CCAGATGTTACATGGTGAGCCAGA BP\ccceegggggiiifhghhihgg 1
-SL-HAR 281 3 2101 1078 1021 0 1 GCAAA.GATGAGATCGCTGGGCCTG bbbeeBQ`eggggfehhhhhhghhh 1
-SL-HAR 281 3 2101 1245 1032 0 1 GCGACACTTTGCAGCCCATGAGCGT ___cccccgggggfdhfiihii]ee 1
-SL-HAR 281 3 2101 1098 1037 0 1 TTCCTATAATCCTGGTAGGAGTCAC bbbeeeeegggggiieghiegeggh 1
-SL-HAR 281 3 2101 1051 1039 0 1 T.AT...AAAATCAGACTCA...CG [BO\BBBQR]^^]^^^^_^^BBBBB 0
-SL-HAR 281 3 2101 1133 1044 0 1 CAGGGGTGCAGGTGGAGTCAAAGCT _aaeeeccggggegiehgghhihhh 1
-SL-HAR 281 3 2101 1211 1050 0 1 TGAATGTACAAGAATGCCATGCGGT bbbeeeeegggggiiiiiiiihiih 1
-SL-HAR 281 3 2101 1077 1055 0 1 GGAAA.TCAGCAAAATAGTAATCAC bbbeeBQ`egggghiiiihdegfhi 1
-SL-HAR 281 3 2101 1176 1056 0 1 AAAGACCCTTTCAAAGCCAAATCGT _bbeeeeegggggiiiiiiiiifii 1
-SL-HAR 281 3 2101 1242 1062 0 1 GTGTGCTGTTCCCCTCCCTGTGTCT ___cccccggggghgYdghh[b[^g 1
-SL-HAR 281 3 2101 1147 1067 0 1 GTGCAGTGCGCACATATCACATGCT aaaeeeeeggegghhhighhiihhi 1
-SL-HAR 281 3 2101 1208 1075 0 1 CCCTGCACCCCCACAGCCTGGCTTC _bbeeeeegggggiegeghiiihih 1
-SL-HAR 281 3 2101 1105 1085 0 1 AAAAAATGAGAAAGAAATTACCCTA bbbeeeeefggggiiiiiiihfhie 1
-SL-HAR 281 3 2101 1076 1087 0 1 GAGTT.AAGAAAACCCAACAGATGT a__eeBQ`ccggghiiiiiiffghi 1
-SL-HAR 281 3 2101 1212 1092 0 1 GAGTGTGAAGTTACGGGAACACCTC \JY``__^S^Q[_a``W[RRJ_\\b 0
-SL-HAR 281 3 2101 1237 1093 0 1 AGTCCTGGTTTTCAGAGCGACTGGC _b_eeeeegggggihhihiiiiiii 1
-SL-HAR 281 3 2101 1138 1094 0 1 AAACTACTACAGCTGCAGCAGAATC __beeeeegeceghehaefaegffh 1
-SL-HAR 281 3 2101 1188 1095 0 1 TTTTACAGGGGATTCACATAACAGG \\\`\`Z`JJ[[H[[K^bb^a`aaa 0
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_2_1101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_2_1101_qseq.txt
deleted file mode 100644
index b37b3ae..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_2_1101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 3 1101 1224 1003 0 2 AGGTCGCA _abceeee 1
-SL-HAR 281 3 1101 1193 1020 0 2 AGGTCGCA abbcceee 0
-SL-HAR 281 3 1101 1199 1042 0 2 AGGTCGCA _bbceeee 0
-SL-HAR 281 3 1101 1225 1047 0 2 AGGTCGCA Y\^SS_O_ 1
-SL-HAR 281 3 1101 1218 1072 0 2 AGGTCGCA aabcceee 1
-SL-HAR 281 3 1101 1193 1087 0 2 AGGTCGCA aabceeee 0
-SL-HAR 281 3 1101 1229 1094 0 2 AGGTCGCA _abcceee 1
-SL-HAR 281 3 1101 1247 1112 0 2 AGGTCGCA bbbceeee 0
-SL-HAR 281 3 1101 1195 1128 0 2 AGGTCGCA bb_eeeee 0
-SL-HAR 281 3 1101 1232 1155 0 2 AGGTCGCA bbbceeee 1
-SL-HAR 281 3 1101 1240 1185 0 2 AGGTCGCA _abceeee 0
-SL-HAR 281 3 1101 1198 1204 0 2 AGGTCGCA bbbceeee 0
-SL-HAR 281 3 1101 1221 1216 0 2 AGGTCGCA a_bceeee 1
-SL-HAR 281 3 1101 1243 1225 0 2 AGGTCGCA _bbceeee 1
-SL-HAR 281 3 1101 1208 1250 0 2 ACGAATAG BBBBBBBB 0
-SL-HAR 281 3 1101 1352 1005 0 2 AGGTCGCA _bbceeee 1
-SL-HAR 281 3 1101 1497 1006 0 2 AGGTCGCA abbaceee 0
-SL-HAR 281 3 1101 1435 1006 0 2 AGGTCGCA _bbcceee 1
-SL-HAR 281 3 1101 1260 1009 0 2 AGGTCGCA abbceeee 0
-SL-HAR 281 3 1101 1306 1020 0 2 AGGTCGCA _abcceee 1
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_2_1201_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_2_1201_qseq.txt
deleted file mode 100644
index c3bff61..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_2_1201_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 3 1201 1238 1015 0 2 .GGTCGCA BP\`ccee 1
-SL-HAR 281 3 1201 1178 1023 0 2 .GGTCGCA BP\accee 0
-SL-HAR 281 3 1201 1208 1031 0 2 .GGTCGCA BP\`ccec 1
-SL-HAR 281 3 1201 1178 1044 0 2 .GGTCGCA BS\aceee 0
-SL-HAR 281 3 1201 1214 1051 0 2 .GGTCGCA BP\`ccce 0
-SL-HAR 281 3 1201 1234 1085 0 2 .GGTCGCA BP\`ccee 1
-SL-HAR 281 3 1201 1225 1098 0 2 .GGTCGCA BP\`ccee 1
-SL-HAR 281 3 1201 1194 1109 0 2 .GGTCGCA BS\aceee 1
-SL-HAR 281 3 1201 1182 1130 0 2 .GGTCGCA BP\aceee 0
-SL-HAR 281 3 1201 1210 1133 0 2 .GGTCGCA BS\cceee 1
-SL-HAR 281 3 1201 1180 1154 0 2 .GGTCGCA BP\cceee 0
-SL-HAR 281 3 1201 1227 1155 0 2 .GGTCGCA BP\accee 1
-SL-HAR 281 3 1201 1211 1159 0 2 .GGTCGCA BS\accec 1
-SL-HAR 281 3 1201 1227 1176 0 2 .GGTCGCA BP\`ccee 1
-SL-HAR 281 3 1201 1186 1185 0 2 .GGTCGCA BP\`ccee 0
-SL-HAR 281 3 1201 1202 1195 0 2 .GGTCGCA BP\`ccee 1
-SL-HAR 281 3 1201 1242 1201 0 2 .GGTCGCA BS\aceec 1
-SL-HAR 281 3 1201 1220 1217 0 2 .GGTCGCA BP\accee 1
-SL-HAR 281 3 1201 1243 1246 0 2 .GGTCGCA BP\accee 1
-SL-HAR 281 3 1201 1364 1001 0 2 .GGTCGCA BP\aceee 0
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_2_2101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_2_2101_qseq.txt
deleted file mode 100644
index 0207102..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_2_2101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 3 2101 1125 1003 0 2 AGGTCGCA _bbceeee 1
-SL-HAR 281 3 2101 1099 1006 0 2 AGGTCGCA bbbeeeee 1
-SL-HAR 281 3 2101 1198 1014 0 2 AGGTCGCA bbbeeeee 1
-SL-HAR 281 3 2101 1078 1021 0 2 AGGTCGCA _abceeee 1
-SL-HAR 281 3 2101 1245 1032 0 2 AGGTCGCA a__eaccc 1
-SL-HAR 281 3 2101 1098 1037 0 2 AGGTCGCA bbbeeeee 1
-SL-HAR 281 3 2101 1051 1039 0 2 AGGTCGCA __^eccce 0
-SL-HAR 281 3 2101 1133 1044 0 2 AGGTCGCA bbbeeeee 1
-SL-HAR 281 3 2101 1211 1050 0 2 AGGTCGCA bbbeeeee 1
-SL-HAR 281 3 2101 1077 1055 0 2 AGGTCGCA _abceece 1
-SL-HAR 281 3 2101 1176 1056 0 2 AGGTCGCA bbbeeeee 1
-SL-HAR 281 3 2101 1242 1062 0 2 AGGTCGCA aabcccee 1
-SL-HAR 281 3 2101 1147 1067 0 2 CATTAGAT __beeecd 1
-SL-HAR 281 3 2101 1208 1075 0 2 AGGTCGCA bbbceeee 1
-SL-HAR 281 3 2101 1105 1085 0 2 AGGTCGCA bbbeeeee 1
-SL-HAR 281 3 2101 1076 1087 0 2 AGGTCGCA _a_ceeee 1
-SL-HAR 281 3 2101 1212 1092 0 2 AGGTCGCA bbbeeeee 0
-SL-HAR 281 3 2101 1237 1093 0 2 AGGTCGCA bbbeeeee 1
-SL-HAR 281 3 2101 1138 1094 0 2 AGGTCGCA _bbceeee 1
-SL-HAR 281 3 2101 1188 1095 0 2 AGGTCGCA bbbeeeee 0
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_3_1101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_3_1101_qseq.txt
deleted file mode 100644
index 98b0931..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_3_1101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 3 1101 1224 1003 0 3 TTTTCTTGGTTGGGTCTCGGGCTTG bbbeeeeeggggghghiiiihffdg 1
-SL-HAR 281 3 1101 1193 1020 0 3 GACTCTTTCCTTCTCCCTTCTCCCA Z\^c^ccecY`eJ^b[`ddbgXeBB 0
-SL-HAR 281 3 1101 1199 1042 0 3 TTTTATGTGGAAGGCTTACCTGAGG abbeeeeegfgegiihiffhiigfh 0
-SL-HAR 281 3 1101 1225 1047 0 3 AACTGTGGATAAACCTCAGGTAAGT _[_ccee`g[egacedaefhefhfd 1
-SL-HAR 281 3 1101 1218 1072 0 3 GCCCAACTACTTAACTCCTTGGCAC JW^aJ\`ceaS`Y^d_ge[hegdg_ 1
-SL-HAR 281 3 1101 1193 1087 0 3 TCTGGAGCACGTTTTGGGGCCTAAA a^_eeccaWbee`dgffcdaacfhb 0
-SL-HAR 281 3 1101 1229 1094 0 3 AGAAGCCCAGAGTGAACAGAAAGAG bb_ceeeefggfghhiffhhhhdff 1
-SL-HAR 281 3 1101 1247 1112 0 3 AAGGCCAAGAACCCAGAGCCACAGA abbcceeeg^cggihhafffdfhfg 0
-SL-HAR 281 3 1101 1195 1128 0 3 ACCAGGAGGAAAGTGTGGGGCCAGA _^aacc^cebceghfaffdf`^dbe 0
-SL-HAR 281 3 1101 1232 1155 0 3 CTTACCTAGTTTCCAGCAGTCTGCT bbbeeeecggeggiihihiihiibg 1
-SL-HAR 281 3 1101 1240 1185 0 3 ACAGTAGGCACTCACTACATGCGGC aJJ`aYcc^cZQ``da^J[bSJ[_e 0
-SL-HAR 281 3 1101 1198 1204 0 3 TGCTCCTGGCCCTGCCTGTCTTACT abbeeeeegggggiiiiiiiiifgg 0
-SL-HAR 281 3 1101 1221 1216 0 3 GGGACGCGCACTCTGCCTGGCTTCA _bbceeee`gecehhhi_eg]cgff 1
-SL-HAR 281 3 1101 1243 1225 0 3 CAGGAGGGGACGGGCACGCAGCAGG _[aecc`eeeegff[cgfeggf]cf 1
-SL-HAR 281 3 1101 1208 1250 0 3 TATGGTAGGGGGGATGATAGGGGTT BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 3 1101 1352 1005 0 3 CTCACTACTCCATGAACAGGACGAT b_beeeeegggfgiiiiiiihhhfh 1
-SL-HAR 281 3 1101 1497 1006 0 3 ATGAGTAATTCAAACAGGTTAAGGG BBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 3 1101 1435 1006 0 3 GCAGAAGACTAGGACCATATATCAA a__ccde^ecgeghhhhh]gbgfif 1
-SL-HAR 281 3 1101 1260 1009 0 3 CGCGGCAGCCTCCGAGGAGGGGGGA aBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 3 1101 1306 1020 0 3 CATAACTGCTCACGATCCAGACGAA \[aZc`ccRbY``bdcd^^bbJ__^ 1
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_3_1201_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_3_1201_qseq.txt
deleted file mode 100644
index d527609..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_3_1201_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 3 1201 1238 1015 0 3 CCATGGCCCCTGTGACCAGGGCACC a^_cceee`^cggf^fd[egf\cWd 1
-SL-HAR 281 3 1201 1178 1023 0 3 TGTGCCCCTGCAGATACTCGCAGGC aa_ccceegggegfdgbefhedghh 0
-SL-HAR 281 3 1201 1208 1031 0 3 TGCTGGGATTACAGGCGTGGGGACT a_^ce`e^eg^cadfaeg^BBBBBB 1
-SL-HAR 281 3 1201 1178 1044 0 3 TCGGATGCTGCTGGAAGTCACCTTT ^WW`J\H\`eeaJQ[`[[[[``acb 0
-SL-HAR 281 3 1201 1214 1051 0 3 TGCTGTGACTACGGGGGGTGAGCCG Y^ZJSQ`BBBBBBBBBBBBBBBBBB 0
-SL-HAR 281 3 1201 1234 1085 0 3 CTCTGCCTGTACTACCCCCAGATGC a_[`cW^c[eacY^efZ_b_eJJ[a 1
-SL-HAR 281 3 1201 1225 1098 0 3 CTGCATACTTGGGTCCCAGGCTCAC a__a\c]cbeae`YbfgX`dRb`_e 1
-SL-HAR 281 3 1201 1194 1109 0 3 CAGCCCAGGTATTTAAACACTTGAG a_^cccccgeeegfcffadgghdgg 1
-SL-HAR 281 3 1201 1182 1130 0 3 CTGGCTCATGCTGTCAGTCTGACCA a__ceeceef`eYd^eac]egagbg 0
-SL-HAR 281 3 1201 1210 1133 0 3 CCAACTTTGTGATATATTTGTAGAA a__eeeeefggeghfggiiiefhhi 1
-SL-HAR 281 3 1201 1180 1154 0 3 CCAAAACTAGTAGTTTTCTTACCTG _\a`Vac``ecY`ebfgK`dRb]gg 0
-SL-HAR 281 3 1201 1227 1155 0 3 GTAAAGTATAAGACCTGTCAGTTAC \a_`ccK\ba^^aafgaf^gdgfhb 1
-SL-HAR 281 3 1201 1211 1159 0 3 CTATCGCTTCGCAGAACCTACTCAG _bbececefgg`efffcghhhicgf 1
-SL-HAR 281 3 1201 1227 1176 0 3 CTGTAGGCACCTTTGTCATCAGTAA ^_^ccee^cceeehfhcceabdgha 1
-SL-HAR 281 3 1201 1186 1185 0 3 CACCTGCATTGGGCTCCAGTGAAAC bbbeeeeeeeggefhhhfh^eeghh 0
-SL-HAR 281 3 1201 1202 1195 0 3 CCACAAACAGGATGATGGAGGCAGA bbbeeeeeggf^egfhhha`dfdfd 1
-SL-HAR 281 3 1201 1242 1201 0 3 GGAAAGGGTAATAAGTATGACTTGA Z^^c`cWcJ`aecghSbeighfggg 1
-SL-HAR 281 3 1201 1220 1217 0 3 TGGGAAGTGCTGCAGGCTCACTGCG _bbeeeecegfcghghfhifffghh 1
-SL-HAR 281 3 1201 1243 1246 0 3 ATGCTGATGGCATGGATGTCAATGT _bbeeeeegggggiiffhiiiehhi 1
-SL-HAR 281 3 1201 1364 1001 0 3 TG..GAAGTGCAGTTAGATCCTTCA \aBBSJ\`Q`JQQ[SbeJR``bSJ` 0
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_3_2101_qseq.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_3_2101_qseq.txt
deleted file mode 100644
index ec6bbfa..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_3_3_2101_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-HAR 281 3 2101 1125 1003 0 3 CCCAGATTTTTTATCACAGAGTTGA ___eecdeggggehgfhfgfhgghg 1
-SL-HAR 281 3 2101 1099 1006 0 3 ATTTTACTATTCTTTCAGGCTTTCA ___eedceeggggiiiiihhihige 1
-SL-HAR 281 3 2101 1198 1014 0 3 TCAGTCTCTCACTGTGCTGTGTCCT bbbeeeeegegggiiiiiihiiiii 1
-SL-HAR 281 3 2101 1078 1021 0 3 GCACTCGGCCTCGAGTATCCTTTAG bbbeeeeegegfghiihfhighh]e 1
-SL-HAR 281 3 2101 1245 1032 0 3 TCAACGTGCATCCCAGGCACCCCAT _bbcceeeeggggiaghhhifghff 1
-SL-HAR 281 3 2101 1098 1037 0 3 ATAGAATATGTGATATAGTATTACT bbbeeeeeggggghhhhigfihhhi 1
-SL-HAR 281 3 2101 1051 1039 0 3 CATTTC.GCAAATACTCTTGCCCTG ___eecBQ`ceeghghhfhhhhfhi 0
-SL-HAR 281 3 2101 1133 1044 0 3 ACACTCTGATTACAAAGCATTGGGT bbbeeeeeeggffhhihiihiiiih 1
-SL-HAR 281 3 2101 1211 1050 0 3 CGCCTTTGGCGAGAGGACAGTTTCT _bbeeeeegegggcghegghefhdg 1
-SL-HAR 281 3 2101 1077 1055 0 3 TGTTTCATACTTTTTTTCCTATAGC abbeeeeegggggiiiighifhhif 1
-SL-HAR 281 3 2101 1176 1056 0 3 CATTTCTGAATGAGAGCTGTGTAGA ___eeeeeggggehghhiiiidfih 1
-SL-HAR 281 3 2101 1242 1062 0 3 CTACTGGGAAAGCAAAATCAGAATA ___eeeeeaecgfhdghhhhhhhhb 1
-SL-HAR 281 3 2101 1147 1067 0 3 ATAGCGCAGAGCGTGATCATGACTA _bbeceeegcgegghghihhifhih 1
-SL-HAR 281 3 2101 1208 1075 0 3 TACTTACCTGCAGGGTTGTAGACTG bbbeeccegggggiibefgehbgfg 1
-SL-HAR 281 3 2101 1105 1085 0 3 TGTAAATGTATCTAAGTGTGACTGT ab_eeeeegggegffhfgihghhii 1
-SL-HAR 281 3 2101 1076 1087 0 3 GTCCTCGCCATTCTGCGATGCCACA ___eeeeefggggihhihiiiiabg 1
-SL-HAR 281 3 2101 1212 1092 0 3 ACTGGTATTCCCCAGTGTCTGAAGG P\^c^SY\``cccYbYQ``bggXR` 0
-SL-HAR 281 3 2101 1237 1093 0 3 ACTAAATTGTCTTTGGTACCAATTG abbeeeeegggggihihhiihiiii 1
-SL-HAR 281 3 2101 1138 1094 0 3 ATTGGCATTGACTTTTTATCAAAAA \a_eeddcgg^bbfgdgfhcfef[e 1
-SL-HAR 281 3 2101 1188 1095 0 3 TGGAGAGTGCCATCCTTCAGACGGC JPYSJQJQJQSJYJ[`dJ[`[eBBB 0
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_9_1101_barcode.txt.gz b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_9_1101_barcode.txt.gz
deleted file mode 100644
index a8cd656..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_9_1101_barcode.txt.gz and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_9_2101_barcode.txt.gz b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_9_2101_barcode.txt.gz
deleted file mode 100644
index 239ae54..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/s_9_2101_barcode.txt.gz and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L001/s_1_1101.clocs b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L001/s_1_1101.clocs
deleted file mode 100644
index f538fb1..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L001/s_1_1101.clocs and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L001/s_1_1201.clocs b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L001/s_1_1201.clocs
deleted file mode 100644
index 1852c84..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L001/s_1_1201.clocs and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L001/s_1_2101.clocs b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L001/s_1_2101.clocs
deleted file mode 100644
index 346a99a..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L001/s_1_2101.clocs and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L003/s_3_1101.clocs b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L003/s_3_1101.clocs
deleted file mode 100644
index d00eb48..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L003/s_3_1101.clocs and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L003/s_3_1201.clocs b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L003/s_3_1201.clocs
deleted file mode 100644
index 4d90d4c..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L003/s_3_1201.clocs and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L003/s_3_2101.clocs b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L003/s_3_2101.clocs
deleted file mode 100644
index 3f0f9b8..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L003/s_3_2101.clocs and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L009/s_1_1101.clocs b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L009/s_1_1101.clocs
deleted file mode 100644
index f538fb1..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L009/s_1_1101.clocs and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L009/s_1_1201.clocs b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L009/s_1_1201.clocs
deleted file mode 100644
index 1852c84..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L009/s_1_1201.clocs and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L009/s_1_2101.clocs b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L009/s_1_2101.clocs
deleted file mode 100644
index 346a99a..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/L009/s_1_2101.clocs and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_1_1101_pos.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_1_1101_pos.txt
deleted file mode 100644
index c303b46..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_1_1101_pos.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-7.50 0.10
-13.10 0.80
-18.40 1.00
-1.80 2.00
-24.20 2.10
-3.60 2.10
-12.70 2.60
-6.70 2.80
-10.30 3.00
-22.50 4.00
-17.50 4.40
-8.00 5.30
-20.90 5.80
-13.50 6.20
-1.20 6.90
-15.30 8.10
-9.90 8.40
-13.40 8.80
-0.60 9.00
-1.80 11.00
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_1_1201_pos.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_1_1201_pos.txt
deleted file mode 100644
index 1991526..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_1_1201_pos.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-13.40 0.20
-22.40 1.20
-15.40 1.90
-9.30 2.00
-19.70 2.30
-13.40 3.20
-20.70 3.30
-17.10 3.50
-11.30 3.60
-21.50 5.40
-17.70 6.20
-12.80 7.60
-19.90 8.00
-22.90 8.50
-17.60 8.50
-14.90 8.50
-11.30 9.70
-18.80 10.90
-13.60 11.20
-20.10 11.70
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_1_2101_pos.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_1_2101_pos.txt
deleted file mode 100644
index f07c82b..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_1_2101_pos.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-10.00 0.20
-14.50 0.60
-12.60 1.20
-10.40 2.40
-23.90 3.10
-6.60 3.10
-19.30 3.50
-21.80 3.70
-13.50 4.10
-15.40 4.20
-23.10 7.60
-20.10 7.80
-13.60 8.80
-17.80 9.10
-16.20 10.00
-6.90 10.10
-20.90 10.60
-13.30 10.70
-19.10 11.20
-10.30 11.20
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_2_1101_pos.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_2_1101_pos.txt
deleted file mode 100644
index b687e4a..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_2_1101_pos.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-17.80 0.30
-23.70 1.70
-18.50 3.90
-22.80 4.00
-15.90 4.20
-19.10 5.60
-23.90 6.70
-16.70 7.00
-21.50 7.10
-18.90 9.30
-17.10 10.30
-19.90 10.80
-15.90 11.90
-21.60 12.00
-24.80 12.40
-17.90 14.20
-22.00 14.50
-23.60 15.20
-20.00 15.50
-16.30 17.30
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_2_1201_pos.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_2_1201_pos.txt
deleted file mode 100644
index 2ed1292..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_2_1201_pos.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-16.20 0.30
-22.80 1.20
-17.50 2.90
-22.90 3.40
-19.40 5.30
-22.10 7.40
-18.70 7.60
-17.50 9.30
-15.60 9.70
-23.20 9.90
-21.80 10.40
-19.30 11.50
-15.20 11.60
-24.80 12.20
-22.00 12.90
-20.60 15.10
-19.00 15.50
-17.30 15.80
-22.60 16.00
-19.90 17.80
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_2_2101_pos.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_2_2101_pos.txt
deleted file mode 100644
index d0a851f..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_2_2101_pos.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-13.90 1.20
-22.50 1.90
-11.50 2.30
-16.10 2.80
-24.70 3.60
-17.80 3.90
-19.90 4.10
-21.90 4.10
-15.50 4.50
-12.30 4.50
-9.20 4.80
-17.70 5.70
-19.80 5.80
-7.00 6.20
-11.00 6.60
-13.00 7.10
-15.20 7.50
-8.60 8.00
-20.80 8.20
-24.60 8.50
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_3_1101_pos.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_3_1101_pos.txt
deleted file mode 100644
index 4774b9b..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_3_1101_pos.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-22.40 0.30
-19.30 2.00
-19.90 4.20
-22.50 4.70
-21.80 7.20
-19.30 8.70
-22.90 9.40
-24.70 11.20
-19.50 12.80
-23.20 15.50
-24.00 18.50
-19.80 20.40
-22.10 21.60
-24.30 22.50
-20.80 25.00
-35.20 0.50
-49.70 0.60
-43.50 0.60
-26.00 0.90
-30.60 2.00
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_3_1201_pos.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_3_1201_pos.txt
deleted file mode 100644
index e764fe8..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_3_1201_pos.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-23.80 1.50
-17.80 2.30
-20.80 3.10
-17.80 4.40
-21.40 5.10
-23.40 8.50
-22.50 9.80
-19.40 10.90
-18.20 13.00
-21.00 13.30
-18.00 15.40
-22.70 15.50
-21.10 15.90
-22.70 17.60
-18.60 18.50
-20.20 19.50
-24.20 20.10
-22.00 21.70
-24.30 24.60
-36.40 0.10
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_3_2101_pos.txt b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_3_2101_pos.txt
deleted file mode 100644
index 9bc2afb..0000000
--- a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_3_2101_pos.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-12.50 0.30
-9.90 0.60
-19.80 1.40
-7.80 2.10
-24.50 3.20
-9.80 3.70
-5.10 3.90
-13.30 4.40
-21.10 5.00
-7.70 5.50
-17.60 5.60
-24.20 6.20
-14.70 6.70
-20.80 7.50
-10.50 8.50
-7.60 8.70
-21.20 9.20
-23.70 9.30
-13.80 9.40
-18.80 9.50
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_4_1101_pos.txt.gz b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_4_1101_pos.txt.gz
deleted file mode 100644
index 46821d5..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_4_1101_pos.txt.gz and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_4_1201_pos.txt.gz b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_4_1201_pos.txt.gz
deleted file mode 100644
index e33bb5f..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_4_1201_pos.txt.gz and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_4_2101_pos.txt.gz b/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_4_2101_pos.txt.gz
deleted file mode 100644
index 74bd41c..0000000
Binary files a/testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/s_4_2101_pos.txt.gz and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/barcodeData.4 b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/barcodeData.4
deleted file mode 100644
index 7b6341c..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/barcodeData.4
+++ /dev/null
@@ -1,2 +0,0 @@
-barcode_sequence_1 barcode_sequence_2 barcode_name library_name
-ACAGGTAT GCTTCCTA tagged_109_809_revcmp Solexa-74830
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/barcodeData.5 b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/barcodeData.5
deleted file mode 100644
index 56a33dd..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/barcodeData.5
+++ /dev/null
@@ -1,2 +0,0 @@
-barcode_sequence_1 barcode_sequence_2 barcode_name library_name
-ACAGGTAT GCTTCC tagged_109_809_revcmp Solexa-74830
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/barcodeData.6 b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/barcodeData.6
deleted file mode 100755
index 7b6341c..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/barcodeData.6
+++ /dev/null
@@ -1,2 +0,0 @@
-barcode_sequence_1 barcode_sequence_2 barcode_name library_name
-ACAGGTAT GCTTCCTA tagged_109_809_revcmp Solexa-74830
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/barcodeData.7 b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/barcodeData.7
deleted file mode 100755
index 7b6341c..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/barcodeData.7
+++ /dev/null
@@ -1,2 +0,0 @@
-barcode_sequence_1 barcode_sequence_2 barcode_name library_name
-ACAGGTAT GCTTCCTA tagged_109_809_revcmp Solexa-74830
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/barcodeData.8 b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/barcodeData.8
deleted file mode 100755
index df6728a..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/barcodeData.8
+++ /dev/null
@@ -1,2 +0,0 @@
-barcode_sequence_1 barcode_sequence_2 barcode_sequence_3 barcode_sequence_4 barcode_name library_name
-ACAG GTAT GCTT CCTA tagged_109_809_revcmp Solexa-74830
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_4_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_4_1_0001_qseq.txt
deleted file mode 100644
index 3006f6d..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_4_1_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 4 10 16396 1438 0 1 GAACCTCTCT ___cceecgg 1
-SL-MAD 15 4 10 14002 1439 0 1 AAAACGAATC ___eeceegg 1
-SL-MAD 15 4 10 15760 1439 0 1 CACACACACG \[YY\`_a_^ 1
-SL-MAD 15 4 10 15149 1439 0 1 CCATGGGATT ___eccccgg 1
-SL-MAD 15 4 10 15580 1439 0 1 TTCCTGGGGT ^__ccaYYWc 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_4_2_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_4_2_0001_qseq.txt
deleted file mode 100644
index e980b60..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_4_2_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 4 10 16396 1438 0 2 ACAGGTAT BP\ac\`a 1
-SL-MAD 15 4 10 14002 1439 0 2 CCAGGTAT BP\cc`^a 1
-SL-MAD 15 4 10 15760 1439 0 2 ACAGGTAT BBBBBBBB 1
-SL-MAD 15 4 10 15149 1439 0 2 GCAGGTAT BPYaccde 1
-SL-MAD 15 4 10 15580 1439 0 2 ACAGGTAT BPJQ[`\` 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_4_3_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_4_3_0001_qseq.txt
deleted file mode 100644
index df2e2e5..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_4_3_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 4 10 16396 1438 0 3 GCTTCC BBBBBB 1
-SL-MAD 15 4 10 14002 1439 0 3 GCTTCC BBBBBB 1
-SL-MAD 15 4 10 15760 1439 0 3 GCTTCC BBBBBB 1
-SL-MAD 15 4 10 15149 1439 0 3 GCTTCC BBBBBB 1
-SL-MAD 15 4 10 15580 1439 0 3 GCTTCC BBBBBB 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_4_4_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_4_4_0001_qseq.txt
deleted file mode 100644
index 9cf1b0e..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_4_4_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 4 10 16396 1438 0 4 .ACTCAATCA BP\\`ac`e] 1
-SL-MAD 15 4 10 14002 1439 0 4 .CTTGAATGT BP\ceceegg 1
-SL-MAD 15 4 10 15760 1439 0 4 .GTGACATTG BPP`cecceg 1
-SL-MAD 15 4 10 15149 1439 0 4 .CCACAAAAA BP\ceeeegg 1
-SL-MAD 15 4 10 15580 1439 0 4 .CCGGTCACC BP\``ccPcg 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_5_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_5_1_0001_qseq.txt
deleted file mode 100644
index 7bdfce9..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_5_1_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 5 10 16396 1438 0 1 GAACCTCTCT ___cceecgg 1
-SL-MAD 15 5 10 14002 1439 0 1 AAAACGAATC ___eeceegg 1
-SL-MAD 15 5 10 15760 1439 0 1 CACACACACG \[YY\`_a_^ 1
-SL-MAD 15 5 10 15149 1439 0 1 CCATGGGATT ___eccccgg 1
-SL-MAD 15 5 10 15580 1439 0 1 TTCCTGGGGT ^__ccaYYWc 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_5_2_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_5_2_0001_qseq.txt
deleted file mode 100644
index 154d45e..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_5_2_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 5 10 16396 1438 0 2 ACAGGTAT BP\ac\`a 1
-SL-MAD 15 5 10 14002 1439 0 2 CCAGGTAT BP\cc`^a 1
-SL-MAD 15 5 10 15760 1439 0 2 ACAGGTAT BBBBBBBB 1
-SL-MAD 15 5 10 15149 1439 0 2 GCAGGTAT BPYaccde 1
-SL-MAD 15 5 10 15580 1439 0 2 ACAGGTAT BPJQ[`\` 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_5_3_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_5_3_0001_qseq.txt
deleted file mode 100644
index b105603..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_5_3_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 5 10 16396 1438 0 3 GCTTCCTA BBBBBBBB 1
-SL-MAD 15 5 10 14002 1439 0 3 GCTTCCTA BBBBBBBB 1
-SL-MAD 15 5 10 15760 1439 0 3 GCTTCCTT BBBBBBBB 1
-SL-MAD 15 5 10 15149 1439 0 3 GCTTCCTG BBBBBBBB 1
-SL-MAD 15 5 10 15580 1439 0 3 GCTTCCGG BBBBBBBB 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_5_4_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_5_4_0001_qseq.txt
deleted file mode 100644
index c24e698..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_5_4_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 5 10 16396 1438 0 4 .ACTCAATCA BP\\`ac`e] 1
-SL-MAD 15 5 10 14002 1439 0 4 .CTTGAATGT BP\ceceegg 1
-SL-MAD 15 5 10 15760 1439 0 4 .GTGACATTG BPP`cecceg 1
-SL-MAD 15 5 10 15149 1439 0 4 .CCACAAAAA BP\ceeeegg 1
-SL-MAD 15 5 10 15580 1439 0 4 .CCGGTCACC BP\``ccPcg 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_6_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_6_1_0001_qseq.txt
deleted file mode 100755
index fcfd94a..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_6_1_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 6 10 16396 1438 0 1 GAACCTCTCT ___cceecgg 1
-SL-MAD 15 6 10 14002 1439 0 1 AAAACGAATC ___eeceegg 1
-SL-MAD 15 6 10 15760 1439 0 1 CACACACACG \[YY\`_a_^ 1
-SL-MAD 15 6 10 15149 1439 0 1 CCATGGGATT ___eccccgg 1
-SL-MAD 15 6 10 15580 1439 0 1 TTCCTGGGGT ^__ccaYYWc 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_6_2_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_6_2_0001_qseq.txt
deleted file mode 100755
index a6556a8..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_6_2_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 6 10 16396 1438 0 2 ACAGGTAT BP\ac\`a 1
-SL-MAD 15 6 10 14002 1439 0 2 CCAGGTAT BP\cc`^a 1
-SL-MAD 15 6 10 15760 1439 0 2 ACAGGTAT BBBBBBBB 1
-SL-MAD 15 6 10 15149 1439 0 2 GCAGGTAT BPYaccde 1
-SL-MAD 15 6 10 15580 1439 0 2 ACAGGTAT BPJQ[`\` 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_6_3_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_6_3_0001_qseq.txt
deleted file mode 100755
index 0e01453..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_6_3_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 6 10 16396 1438 0 3 GCTTCCTA BBBBBBBB 1
-SL-MAD 15 6 10 14002 1439 0 3 GCTTCCTA BBBBBBBB 1
-SL-MAD 15 6 10 15760 1439 0 3 GCTTCCTT BBBBBBBB 1
-SL-MAD 15 6 10 15149 1439 0 3 GCTTCCTG BBBBBBBB 1
-SL-MAD 15 6 10 15580 1439 0 3 GCTTCCGG BBBBBBBB 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_6_4_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_6_4_0001_qseq.txt
deleted file mode 100755
index 437efc9..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_6_4_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 6 10 16396 1438 0 4 .ACTCAATCA BP\\`ac`e] 1
-SL-MAD 15 6 10 14002 1439 0 4 .CTTGAATGT BP\ceceegg 1
-SL-MAD 15 6 10 15760 1439 0 4 .GTGACATTG BPP`cecceg 1
-SL-MAD 15 6 10 15149 1439 0 4 .CCACAAAAA BP\ceeeegg 1
-SL-MAD 15 6 10 15580 1439 0 4 .CCGGTCACC BP\``ccPcg 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_7_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_7_1_0001_qseq.txt
deleted file mode 100755
index 07faa87..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_7_1_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 7 10 16396 1438 0 2 ACAGGTAT BP\ac\`a 1
-SL-MAD 15 7 10 14002 1439 0 2 CCAGGTAT BP\cc`^a 1
-SL-MAD 15 7 10 15760 1439 0 2 ACAGGTAT BBBBBBBB 1
-SL-MAD 15 7 10 15149 1439 0 2 GCAGGTAT BPYaccde 1
-SL-MAD 15 7 10 15580 1439 0 2 ACAGGTAT BPJQ[`\` 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_7_2_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_7_2_0001_qseq.txt
deleted file mode 100755
index 4bd7d8b..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_7_2_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 7 10 16396 1438 0 1 GAACCTCTCT ___cceecgg 1
-SL-MAD 15 7 10 14002 1439 0 1 AAAACGAATC ___eeceegg 1
-SL-MAD 15 7 10 15760 1439 0 1 CACACACACG \[YY\`_a_^ 1
-SL-MAD 15 7 10 15149 1439 0 1 CCATGGGATT ___eccccgg 1
-SL-MAD 15 7 10 15580 1439 0 1 TTCCTGGGGT ^__ccaYYWc 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_7_3_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_7_3_0001_qseq.txt
deleted file mode 100755
index 9e360c5..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_7_3_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 7 10 16396 1438 0 4 .ACTCAATCA BP\\`ac`e] 1
-SL-MAD 15 7 10 14002 1439 0 4 .CTTGAATGT BP\ceceegg 1
-SL-MAD 15 7 10 15760 1439 0 4 .GTGACATTG BPP`cecceg 1
-SL-MAD 15 7 10 15149 1439 0 4 .CCACAAAAA BP\ceeeegg 1
-SL-MAD 15 7 10 15580 1439 0 4 .CCGGTCACC BP\``ccPcg 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_7_4_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_7_4_0001_qseq.txt
deleted file mode 100755
index c9c25dc..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_7_4_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 7 10 16396 1438 0 3 GCTTCCTA BBBBBBBB 1
-SL-MAD 15 7 10 14002 1439 0 3 GCTTCCTA BBBBBBBB 1
-SL-MAD 15 7 10 15760 1439 0 3 GCTTCCTT BBBBBBBB 1
-SL-MAD 15 7 10 15149 1439 0 3 GCTTCCTG BBBBBBBB 1
-SL-MAD 15 7 10 15580 1439 0 3 GCTTCCGG BBBBBBBB 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_1_0001_qseq.txt
deleted file mode 100755
index b185d8c..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_1_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 8 10 16396 1438 0 2 ACAG BP\a 1
-SL-MAD 15 8 10 14002 1439 0 2 CCAG BP\c 1
-SL-MAD 15 8 10 15760 1439 0 2 ACAG BBBB 1
-SL-MAD 15 8 10 15149 1439 0 2 GCAG BPYa 1
-SL-MAD 15 8 10 15580 1439 0 2 ACAG BPJQ 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_2_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_2_0001_qseq.txt
deleted file mode 100755
index 2879c98..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_2_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 8 10 16396 1438 0 1 GAACCTCTCT ___cceecgg 1
-SL-MAD 15 8 10 14002 1439 0 1 AAAACGAATC ___eeceegg 1
-SL-MAD 15 8 10 15760 1439 0 1 CACACACACG \[YY\`_a_^ 1
-SL-MAD 15 8 10 15149 1439 0 1 CCATGGGATT ___eccccgg 1
-SL-MAD 15 8 10 15580 1439 0 1 TTCCTGGGGT ^__ccaYYWc 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_3_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_3_0001_qseq.txt
deleted file mode 100755
index e40e918..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_3_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 8 10 16396 1438 0 2 GTAT c\`a 1
-SL-MAD 15 8 10 14002 1439 0 2 GTAT c`^a 1
-SL-MAD 15 8 10 15760 1439 0 2 GTAT BBBB 1
-SL-MAD 15 8 10 15149 1439 0 2 GTAT ccde 1
-SL-MAD 15 8 10 15580 1439 0 2 GTAT [`\` 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_4_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_4_0001_qseq.txt
deleted file mode 100755
index f362af4..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_4_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 8 10 16396 1438 0 3 GCTT BBBB 1
-SL-MAD 15 8 10 14002 1439 0 3 GCTT BBBB 1
-SL-MAD 15 8 10 15760 1439 0 3 GCTT BBBB 1
-SL-MAD 15 8 10 15149 1439 0 3 GCTT BBBB 1
-SL-MAD 15 8 10 15580 1439 0 3 GCTT BBBB 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_5_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_5_0001_qseq.txt
deleted file mode 100755
index 80a7aaf..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_5_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 8 10 16396 1438 0 4 .ACTCAATCA BP\\`ac`e] 1
-SL-MAD 15 8 10 14002 1439 0 4 .CTTGAATGT BP\ceceegg 1
-SL-MAD 15 8 10 15760 1439 0 4 .GTGACATTG BPP`cecceg 1
-SL-MAD 15 8 10 15149 1439 0 4 .CCACAAAAA BP\ceeeegg 1
-SL-MAD 15 8 10 15580 1439 0 4 .CCGGTCACC BP\``ccPcg 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_6_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_6_0001_qseq.txt
deleted file mode 100755
index c876ab4..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/dual/s_8_6_0001_qseq.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-SL-MAD 15 8 10 16396 1438 0 3 CCTA BBBB 1
-SL-MAD 15 8 10 14002 1439 0 3 CCTA BBBB 1
-SL-MAD 15 8 10 15760 1439 0 3 CCTT BBBB 1
-SL-MAD 15 8 10 15149 1439 0 3 CCTG BBBB 1
-SL-MAD 15 8 10 15580 1439 0 3 CCGG BBBB 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/qual/s_1_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/qual/s_1_1_0001_qseq.txt
deleted file mode 100644
index ed2e489..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/qual/s_1_1_0001_qseq.txt
+++ /dev/null
@@ -1 +0,0 @@
-SL-XAS 2 1 1 0 1598 0 1 ACAGTG.................................... [[[[[[BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/qual/s_2_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/qual/s_2_1_0001_qseq.txt
deleted file mode 100644
index 4bbca0c..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/qual/s_2_1_0001_qseq.txt
+++ /dev/null
@@ -1 +0,0 @@
-SL-XAS 2 2 1 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/qual/s_3_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/qual/s_3_1_0001_qseq.txt
deleted file mode 100644
index ca44739..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/qual/s_3_1_0001_qseq.txt
+++ /dev/null
@@ -1 +0,0 @@
-SL-XAS 2 3 1 0 1598 0 1 ACAGTG.................................... B[[[[[BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/qual/s_4_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/qual/s_4_1_0001_qseq.txt
deleted file mode 100644
index 8864e3b..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/qual/s_4_1_0001_qseq.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-SL-XAS 2 4 1 0 1598 0 1 ....................................ACAGTG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/qual/s_5_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/qual/s_5_1_0001_qseq.txt
deleted file mode 100644
index 9bec701..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/qual/s_5_1_0001_qseq.txt
+++ /dev/null
@@ -1 +0,0 @@
-SL-XAS 2 5 1 0 1598 0 1 ACAGTG.................................... B[[[[[BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_1_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_1_1_0001_qseq.txt
deleted file mode 100644
index e6f5534..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_1_1_0001_qseq.txt
+++ /dev/null
@@ -1 +0,0 @@
-SL-XAS 2 1 1 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
\ No newline at end of file
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_2_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_2_1_0001_qseq.txt
deleted file mode 100644
index 8e1eff8..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_2_1_0001_qseq.txt
+++ /dev/null
@@ -1 +0,0 @@
-SL-XAS 2 2 1 0 1598 0 1 ....................................ACAGTG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_2_1_0002_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_2_1_0002_qseq.txt
deleted file mode 100644
index 30fc4c2..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_2_1_0002_qseq.txt
+++ /dev/null
@@ -1,23 +0,0 @@
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 2 0 1598 1 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 2 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
\ No newline at end of file
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_2_1_0003_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_2_1_0003_qseq.txt
deleted file mode 100644
index 634a2e8..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_2_1_0003_qseq.txt
+++ /dev/null
@@ -1,23 +0,0 @@
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 3 0 1598 1 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAS 2 2 3 0 1598 0 1 ACAGTG.................................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
\ No newline at end of file
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_3_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_3_1_0001_qseq.txt
deleted file mode 100644
index 21c3158..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_3_1_0001_qseq.txt
+++ /dev/null
@@ -1 +0,0 @@
-SL-XAS 2 3 1 0 1598 0 1 ....................................ACAGTG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_3_2_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_3_2_0001_qseq.txt
deleted file mode 100644
index 7fca392..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_3_2_0001_qseq.txt
+++ /dev/null
@@ -1 +0,0 @@
-SL-XAS 2 3 1 0 1598 0 2 CGTTTGTTGGCCGTATTCTTGACTGGTACAAAGCGA a`bbb`bb``ba_bbb_O_b`aXaaab`Q`bbZHYb 0
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_4_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_4_1_0001_qseq.txt
deleted file mode 100644
index d8c2980..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_4_1_0001_qseq.txt
+++ /dev/null
@@ -1 +0,0 @@
-SL-XAS 2 4 1 0 1598 0 2 CGTTTGTTGGCCGTATTCTTGACTGGTACAAAGCGA a`bbb`bb``ba_bbb_O_b`aXaaab`Q`bbZHYb 0
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_4_2_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_4_2_0001_qseq.txt
deleted file mode 100644
index 012ffe0..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_4_2_0001_qseq.txt
+++ /dev/null
@@ -1 +0,0 @@
-SL-XAS 2 4 1 0 1598 0 1 ....................................ACAGTG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_5_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_5_1_0001_qseq.txt
deleted file mode 100644
index 39ac2d3..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_5_1_0001_qseq.txt
+++ /dev/null
@@ -1 +0,0 @@
-SL-XAS 2 5 1 0 1598 0 1 ....................................ACAGTG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_5_1_0002_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_5_1_0002_qseq.txt
deleted file mode 100644
index 9f8818f..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_5_1_0002_qseq.txt
+++ /dev/null
@@ -1 +0,0 @@
-SL-XAS 2 5 2 0 1598 0 1 ....................................TGACCT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_5_1_0003_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_5_1_0003_qseq.txt
deleted file mode 100644
index 9b860cd..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_5_1_0003_qseq.txt
+++ /dev/null
@@ -1 +0,0 @@
-SL-XAS 2 5 3 0 1598 0 1 ....................................TGACTT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_5_1_0004_qseq.txt b/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_5_1_0004_qseq.txt
deleted file mode 100644
index d9ee784..0000000
--- a/testdata/net/sf/picard/illumina/ExtractIlluminaBarcodes/s_5_1_0004_qseq.txt
+++ /dev/null
@@ -1 +0,0 @@
-SL-XAS 2 5 4 0 1598 0 1 ....................................ACAGTC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
diff --git a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_0001_barcode.txt b/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_0001_barcode.txt
deleted file mode 100644
index 5a716b7..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_0001_barcode.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-ACGTAC Y 000001
-ACGTAC N
-ACGTAC Y 000003
-ACGTAC N
-ACGTAC Y 000005
-ACGTAC N
-ACGTAC Y 000007
-ACGTAC N
-ACGTAC Y 000009
-ACGTAC N
-ACGTAC Y 000011
-ACGTAC N
-ACGTAC Y 000013
-ACGTAC N
-ACGTAC Y 000015
-ACGTAC N
-ACGTAC Y 000017
-ACGTAC N
-ACGTAC Y 000019
-ACGTAC N
diff --git a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_0002_barcode.txt b/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_0002_barcode.txt
deleted file mode 100644
index abe3d93..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_0002_barcode.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-ACGTAC Y 000021
-ACGTAC N
-ACGTAC Y 000023
-ACGTAC N
-ACGTAC Y 000025
-ACGTAC N
-ACGTAC Y 000027
-ACGTAC N
-ACGTAC Y 000029
-ACGTAC N
-ACGTAC Y 000031
-ACGTAC N
-ACGTAC Y 000033
-ACGTAC N
-ACGTAC Y 000035
-ACGTAC N
-ACGTAC Y 000037
-ACGTAC N
-ACGTAC Y 000039
-ACGTAC N
diff --git a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_0003_barcode.txt b/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_0003_barcode.txt
deleted file mode 100644
index 88534ac..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_0003_barcode.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-ACGTAC Y 000041
-ACGTAC N
-ACGTAC Y 000043
-ACGTAC N
-ACGTAC Y 000045
-ACGTAC N
-ACGTAC Y 000047
-ACGTAC N
-ACGTAC Y 000049
-ACGTAC N
-ACGTAC Y 000051
-ACGTAC N
-ACGTAC Y 000053
-ACGTAC N
-ACGTAC Y 000055
-ACGTAC N
-ACGTAC Y 000057
-ACGTAC N
-ACGTAC Y 000059
-ACGTAC N
diff --git a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_1_0001_qseq.txt
deleted file mode 100644
index aca5533..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_1_0001_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 6 1 1793 1420 0 1 G....................C.....................T.....................T.......... \DDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1441 0 1 C....................C.....................G.....................G.......... GDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDJDDDDDDDDDDDDDDDDDDDDDTDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1483 0 1 G....................G.....................A.....................A.......... YDDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDDNDDDDDDDDDDDDDDDDDDDDDWDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1495 0 1 G....................C.....................G.....................C.......... VDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1527 0 1 G....................G.....................G.....................T.......... MDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1545 0 1 C....................A.....................A.....................C.......... HDDDDDDDDDDDDDDDDDDDDHDDDDDDDDDDDDDDDDDDDDDHDDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1583 0 1 G....................G.....................G.....................A.......... YDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1596 0 1 G....................C.....................C.....................T.......... TDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDTDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1658 0 1 C....................C.....................T.....................A.......... GDDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1718 0 1 G....................C.....................C.....................C.......... YDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDHDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1745 0 1 C....................C.....................C.....................A.......... PDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDVDDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1777 0 1 G....................C.....................T.....................C.......... YDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDYDDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1813 0 1 G....................C.....................A.....................C.......... VDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1916 0 1 G....................T.....................T.....................C.......... [DDDDDDDDDDDDDDDDDDDDUDDDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1959 0 1 G....................C.....................T.....................C.......... [DDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 808 0 1 T....................C.....................C.....................T.......... YDDDDDDDDDDDDDDDDDDDD^DDDDDDDDDDDDDDDDDDDDD^DDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 6 1 1793 602 0 1 T....................A.....................A.....................A.......... [DDDDDDDDDDDDDDDDDDDD]DDDDDDDDDDDDDDDDDDDDDVDDDDDDDDDDDDDDDDDDDDDQDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1602 0 1 C....................G.....................G.....................A.......... [DDDDDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1681 0 1 C....................T.....................A.....................A.......... ^DDDDDDDDDDDDDDDDDDDDHDDDDDDDDDDDDDDDDDDDDDEDDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1011 0 1 A....................C.....................G.....................G.......... GDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDD 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_1_0002_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_1_0002_qseq.txt
deleted file mode 100644
index 66b4cad..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_1_0002_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 6 2 1793 1893 0 1 G.TCC.......A.TCCCCGTGGATGAAAATGCTGTACATGTTCTTGTTGATAACAATGGGCAAGGTCTAGGACAG ODZb[DDDDDDDHDXbb_G]^b_P\`VGOO\ab`aXU`][`^_b``a_``T]V`aPFU]V]aXMXaVaTHVZTa[] 0
-SL-XBA 1 6 2 1793 1909 0 1 G.CCT.......C.CTCACACCGCCCCCCTTCTCACCTGCCCTGCGTAACCTGTACTGACTGCCCACTCCTCACCC GD[_WDDDDDDDIDZGW_ZI]VZIMG[a]TGMT_NI]XRZGQ_\LYFT]HO\JPZFTYFZNGZP_I]KGZFZGGYH 0
-SL-XBA 1 6 2 1793 1931 0 1 G.CTA.......T.CACTGTCGACACCGCACACGGGGCATACCCACATCAAAGCAGTCCCCCAAGTCCCTGCGCAG [DWMFDDDDDDDEDMG[aIIG]RIVVTGIGZFMUFFJZFEPGXMHMIGVZTNFQGUS`VO]OMKQR_HODFT\[IF 0
-SL-XBA 1 6 2 1793 2004 0 1 G.GTT.......C.TACTGGCATTTACTGTTTAACATCACACACCAAGCCAGGTTATTTCACACTCCTGCTACTGG WDPR[DDDDDDDYD^bbaaa^G]bbbbba`_IXJ_J_b_JIP^ZW_JRI_IWbS_S]b]V_WPPT^HKbb[V_^Y` 0
-SL-XBA 1 6 2 1793 2038 0 1 G.GCG.......G.CACCTTGGTACTGGGTGATGGGGAGGCACTGAATGGGCTTCAAGTCCTCAAACGCCTGATCT ^DYLZDDDDDDDMD\H_bb`ba\W`aba^V_E]a^`b\^baXbS```]]U\\]]ZDT]RDYNYDKRMZ_OKXILPZ 0
-SL-XBA 1 6 2 1793 829 0 1 T.GGC.......C.TGGGCAAGCACCTGACCAGCAACAGCCCCCGCCTGGTGCAGCACTGCCTGTGGACCCTGCGC ZDZ]IDDDDDDD[DYa`a_OZaaaaaa_Z_a_`_ZI_I]aaaaa`aa`^_R__Z[GT_``a_Y]M\ZK[aaZ[a`a 0
-SL-XBA 1 6 2 1793 1117 0 1 G.GGG.......C.GGTCGTTAGCAAGTGATGGCTGTGTTCTGTATCTTTATTGTGGCGACACTTACATGACTGGA RDZaVDDDDDDD\DXbIFT_^aba][MX]^_a`H]]Ga[R_H_S^a[WHT]UV[U`TJTLOMGWSLWURVKVNVDH 0
-SL-XBA 1 6 2 1793 1478 0 1 T.TTT.......C.AATTTTACCTCATAAAATTTTTTGAGGTTTGATGTATGTCTCTGTCTTATCAATAATGAGGC \D^b^DDDDDDDIDJK_bba]abaa`_\VVWabababa^ab^ab`S`b_Z_b_babaa`b`YH\a]FZUS\]U\`b 0
-SL-XBA 1 6 2 1793 1354 0 1 T.GCT.......G.GGCGCCGCGAAGCGCACGGCGCCGACGCAGGGGGAAGGCGGGACATACACGACCCGCGAGCG PDZ`ZDDDDDDDWDGTZ_aVZGZIWZGW_Z_[XNWPGGVVI[GW_LR[FGT\ZGVGG[FHF[MOGNIGVNMQGX]P 0
-SL-XBA 1 6 2 1793 666 0 1 C.GAG.......T.GGGTAGGAAACACAGCCTTGCTCCACAGCGCACTGTCAGCAAGACGCTCCTTTCTTCGGAGA ^DXGXDDDDDDDDDVHXMM[YY]R]PZVV[aOT^^Ha]O\PQGQ`U\SYSXTU^NDTLDLZPZUTSQZNLEGQUKG 0
-SL-XBA 1 6 2 1793 2031 0 1 C.CCG.......G.GGTGCATGGGCTCCAACGTGGTGTCCTGTGGAGCTGTTGGGCCTGGGCAGGCGGCACAGATC YDFIYDDDDDDDYDYaZa_G[aa`aXa`R``aX`_KaPG\\`U_`N^^Z\T\^`RDQVR[S`KZVZY\ZJEENKNR 0
-SL-XBA 1 6 2 1793 1812 0 1 C.CTC.......C.GCATACTTAACAAGTCTGATCTTGCTTATAGAAATTGGATCTTACTACTTCATTCTCAGAAT GD^a]DDDDDDD^D]aV\L_aaZ\_OVa_baaT^baaaba^J]YaXSS^aa_P_baaXN\Va_`a\__aa_G]GW[ 0
-SL-XBA 1 6 2 1793 475 0 1 C.GGG.......C.CCCCCCTAGGCAATATGCTACTGCATATATATTTGGTCTAGATATATAACAAGTTACTACTG ^DX^RDDDDDDDOD[[DTZGQIV[_^GPFHU]V^KV\V_IHUHRTFVYVHDDKFRGMGJQJJSWQMYHHLDOLFFQ 0
-SL-XBA 1 6 2 1793 1329 0 1 C.TCT.......T.GATGCAGTAACTGGAAATATAGAAGATGCTGTGACTCCATTTGAATCTATAAAAAGCGTTGT WDWOTDDDDDDDRDX^IV^GPGXOFWOZSGY^^[[JXYTJN\`WTKN\^RH\FHULJIKT\NXOQLQLOJTLDKLO 0
-SL-XBA 1 6 2 1793 404 0 1 C.CCC.......T.CAATGCTATGCAGTATGTCTTCTTATCTCTGTCTTCAAGAGCATCCTCTGTCAGTCCTACAT YDH^ODDDDDDDXDINODKWMLL]]]]X_^\XVTG\SNDO^VSFNFFRXDL^WWQWKSSPQ\OPUWZQJX`YVSFT 0
-SL-XBA 1 6 2 1793 1455 0 1 C.TTC.......G.GACTGCAGTTGCTGTTGCCCATTAAGACCTTGAGAAAAGGCTTGCCTGCCCTTCGTCTGACT ^DW\^DDDDDDDYDXF\^_bI_QF\a[ZNGZ\D^KWXFWOG\aX\]VPSTMLGVaLHRWNTHF\DTL\YNTVHDUD 0
-SL-XBA 1 6 2 1793 1793 0 1 C.CCA.......C.GGGCCCTTTGTCTAAAGTCTGAATCAGCATTTGGATTTAGCCCTAATAGAGCCTGTTCATCC \D^DHDDDDDDD\DUW]aaaX^]_YaYHQGVY`WSFUV]TZ]NUVWWXFRWTKX_^\LJGRQVJR_]WVVV[NPT_ 0
-SL-XBA 1 6 2 1793 310 0 1 C.GGA.......T.GAACCTTTGGCAAGGCTGCTCTTACGAGTCCTCTCGCCCTGTTCCACCTATCCCCATAGCTA GDTZFDDDDDDDGDMIO_XX_`a]b`THY\Y`PZ`[RFYLFFMFRFZGFT]ab_a\`G`[]TPPGUa^KFFG[ELI 0
-SL-XBA 1 6 2 1793 1969 0 1 T.CGC.......A.CCCTGACTGGCAAGGCGGTGGCGGCTCCAGTGAAGGCTCCCCGTGTTCTTAAAGACTAGCGC TDWGGDDDDDDDPDZaaa]JHVaaa^L^PO_aVaaaX`__`RVXF^IRXa`S_]HZFTYFaa``Z]Q]`UJXJ_I[ 0
-SL-XBA 1 6 2 1794 490 0 1 C.TCC.......T.TATTTACTATTTTCTGATTTTTAAAATGACAGTGGCAATTACCATTTATACTGTGTTATTTG ^DWb^DDDDDDDXDUG\^YG\_a``__a_`[[[[\_\ZT^_XJ^`_Y^X_TEP\]`^JYUUUW\`X^V^X^\[X\U 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_1_0003_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_1_0003_qseq.txt
deleted file mode 100644
index 733b5ae..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_1_0003_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 6 3 1793 1282 0 1 G.TAG.......C.GGACTCTGGCGTCACCTTTGGCGCTGAGCGCCCCAGGCCCGCCAGCCCGCCCGCCCACTGCC [DZGMDDDDDDDGDMUMGZa_TTJX]IW_G]I_ZGMZ_VTFTFZZ_ZZIS[T[QI_ZN][_T]TGPUZPZVHFKMM 0
-SL-XBA 1 6 3 1793 1301 0 1 G.AGG.......T.CAGGGTTGAGGTATTCTTAGGTTAGCCGAGCTCTTTCCTCCTTTCCCCCCCCCTCTCCCCCA ^DIYRDDDDDDDGDZIXH]RJLIL_\HR^bba``ZH`W_QIQTZ`VKTQ\aZG\HSVH\abZJYb_HQ_O\a`XGX 0
-SL-XBA 1 6 3 1793 1311 0 1 G.TAT.......T.TTCCTTCAGTCTGCACAAAGATTAAGGTAATTTACAGTCAATCTGTGAATGAATGTTGAGAC [DGH[DDDDDDDVD[[ababbb`abbbb_baa^abbbbbab]``bb^I_Ma`aWI_bbbab_Y_^V^`a``^^aWa 0
-SL-XBA 1 6 3 1793 1326 0 1 G.CCA.......C.TCTTGGGCTCCACACCATTACCAGCATCAGAGGCAGGGGAACACAATCTGCTGCCTTATAAG ^D^_VDDDDDDD^DRb\JZM[_J__W`^`b__`aaa_aba^J^Z^LTL_a`XQLVa[^LQNKI_`Q^aaZ`T^PFS 0
-SL-XBA 1 6 3 1793 1389 0 1 G.GGG.......G.CGCAGGTGGGGATGGGCACCCTCACAGCTTCCCTGGACCTTAGTTTTGTTGGGGTTCAGTCC YD[aZDDDDDDDVDZ`_P_]M]aa_YZ`a``aaaaa[J[V^_W_aaaa`VQ_]Q[G]TJ\VXOU`[ZTIR[Q_LGS 0
-SL-XBA 1 6 3 1793 1405 0 1 G.TGG.......T.GCTGAGATGCTCTTTAACCAAAGGAGGAAAGAGAGGAGACCAAGGGCCAGCTGGTTGGTTGT VDPb\DDDDDDDWDWb`\Q_^`aaUa`aa`aabZY]aa]a_XGZ`\_^a]R^H_`^\TGV^_P]a\`ZG\__KP\R 0
-SL-XBA 1 6 3 1793 1507 0 1 G.GTG.......T.GTTGCCAGCCTGCTGCCCGCCATCCTGGTCTTCATTCTCATCTTCATGGAGACACAGATCAC \D\\WDDDDDDD^DT`a`aa`abbaabaabbbab_OX`ba\\Zbaa_OZ]`aaa`b`]^FX`\\]H_H^XZUR^T_ 0
-SL-XBA 1 6 3 1793 1557 0 1 G.GGA.......C.TCGAGCCATTCCACTCCCGCCCGGGCACCAACAGCCAAACGCACGCTCATCAAAAAGGCCGA GDZIGDDDDDDDZDT]NGS^`Z\UG][PI_PIL__]NIO_XHX^]QM\WF[KW[KPGGDYP[^JGMOWFJTTa^YD 0
-SL-XBA 1 6 3 1793 1570 0 1 G.TCT.......T.TCTCCACTCTGCTGCCCTACCTCTCGGAGTCTTCTACCGCGTCTAACTAGTCATATTTACAA UDRaUDDDDDDDKDFb__ab]P^a_bb^b_b`a_a_^UEa`b`SK^I[a_]PFPRK[aZH_aaRF^DHJY`_Zba_ 0
-SL-XBA 1 6 3 1793 1709 0 1 G.GGG.......T.CCATTGGTTTCTGAAAGTATTCACATCATTTGGGATACCAGATAGCTCAATACTCTCTGAGT WD]a[DDDDDDDYD^aWaaaa^aab`b^_U_PZ`a_I_[]aX]^__a^X[SaaW_WQH[b_b`Y^Wa_b_b_^N\F 0
-SL-XBA 1 6 3 1793 1738 0 1 G.GCC.......G.CTCTTGGGGAATATCTGAGGCTCTGTGGTCACCCACAGACCCGTTACTCCTTTAGGTGTCTG ^DYb^DDDDDDDWD\ab`aaaab^aababaaaaab_b^`P`aM^R^`QH_WWO__HODXU^X_aZ][J\]T_O]\_ 0
-SL-XBA 1 6 3 1793 1779 0 1 G.GCA.......C.TGCGTATATTTACAGATATATATACAGAATTGTTTGCTCTGAGCCATTTATAAGCACTTACT \DT`ODDDDDDD^DHXI]F\_YY]aaaYa_ZV```_V_\RNMIY^_WZK[IZaS\`aab^HM\S]GZa`\b`YL^Z 0
-SL-XBA 1 6 3 1793 1859 0 1 G.GAG.......A.CCAAGCATCTATCCCAGTGTGGGGGCTGAGGCTGCGAGAGGAAAGCGGGGACGGAAGACGGG [DGGZDDDDDDD[DGZ\[aXU[_aR^aaa\aPPG`ZaaNGO\LY^XH_L\KPQ[\Q]]Y_W_FYDW[\MTQGWQGJ 0
-SL-XBA 1 6 3 1793 1898 0 1 G.ACA.......G.AATATGGGCTTATCCAACCCAACCAAGATGGAGAGTGAGGGGGTTGTCCCTGGGCCCAAGGC YDN\GDDDDDDDYDIN[P\TZaaa```bb`W`ab``baZH_^aaaJaU^SaY`VZ^^PU_\a`^XTOXa^_LJWSS 0
-SL-XBA 1 6 3 1793 1143 0 1 T.GGG.......T.CATGGTGAGGAAGAGTCGGAAGCAGGCATGCGGCTGCAGGGAATGCAACTTCTTCTCCATCG YDGaRDDDDDDDYD\abbb[baaa[bbaRI_^aaa``I\a_X_^a^W[RZ]RZ`ZJQYX[SRY[Z^X]`YW[JD[D 0
-SL-XBA 1 6 3 1793 141 0 1 T.CTC.......C.CTTAGCAGTGCGCCCCCCGAGCGCGGCACAGGGGCCAGGGAGACAGAGGACACCGGGATCTC ZDZXKDDDDDDDKDTQGGGRMWGJNINa_P[PGG\MESJXJNGYYPPJGEVUOOJMJ`SFIDDDLDYNKDDKFXFa 0
-SL-XBA 1 6 3 1793 1617 0 1 C.GAA.......T.CGCCTTCTTCTTCAACTCGGAGCTGCTGAGCGCTGTGCGCTTCGCCCTGGGCAAGGGCCGCG YDVTFDDDDDDDRDZZa`][`Z\aZV_WS]FX]YXO[KV[KUPPRQDIWNNRSVPFRSXJUKRUJYEJSUQJMEMD 0
-SL-XBA 1 6 3 1793 1031 0 1 C.ACT.......G..GCATTGGAGAAGAACCAAGCTGGCTCTCTAAGGAAGTGCACACGAGTTGGAACACATATTC ^D[^GDDDDDDDYDD\aSV^a\U^\Q^NOO_WHK_aa\RK]HMFTOZYVQHHPHT\YH[PXDHJGDT^Y\ZVMHPF 0
-SL-XBA 1 6 3 1793 1793 0 1 C.TCT.......A..ATGGGCTTTCTACAGCCTGCTTACCACTAACAGTAAGGAATCTTTCATAAACACACCTCAG YDP_UDDDDDDDEDDFLZYHUQGX\H\]RHO`X]_TOP^^Y\TYTWRSUUMSTPKX_XTQ[KXSMQZWWJQ\WZRK 0
-SL-XBA 1 6 3 1793 456 0 1 C.TAT.......C..CGGGTACCACAGTTGAGGACTGACATTCTGAACCCTGATGTTTCTAAAGAAACGACAGTAT ^DU_WDDDDDDD^DD^_^_U```^^U[]]_UNV^`^^U][[W\_QTQZ]_WS[X]TW_^VMLUZVWZ[SFXL[YUW 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_2_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_2_0001_qseq.txt
deleted file mode 100644
index 31f9cf6..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_2_0001_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 6 1 1793 1420 0 2 C...A................A.....................C.....................T.......... ^DDDIDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1441 0 2 C...A................A.....................C.....................G.......... [DDDGDDDDDDDDDDDDDDDDFDDDDDDDDDDDDDDDDDDDDDYDDDDDDDDDDDDDDDDDDDDDEDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1483 0 2 G...A................A.....................T.....................C.......... [DDDDDDDDDDDDDDDDDDDDODDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDD]DDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1495 0 2 A...T................A.....................C.....................C.......... HDDDIDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDDYDDDDDDDDDDDDDDDDDDDDDSDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1527 0 2 C...C................C.....................C.....................G.......... YDDDIDDDDDDDDDDDDDDDDVDDDDDDDDDDDDDDDDDDDDDTDDDDDDDDDDDDDDDDDDDDDIDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1545 0 2 C...T................G.....................T.....................G.......... TDDDIDDDDDDDDDDDDDDDDQDDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1583 0 2 C...T................G.....................G.....................G.......... [DDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDEDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1596 0 2 C...C................G.....................C.....................C.......... [DDDJDDDDDDDDDDDDDDDDTDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDJDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1658 0 2 T...C................C.....................C.....................C.......... YDDDJDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1718 0 2 A...A................A.....................A.....................G.......... GDDDDDDDDDDDDDDDDDDDDNDDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1745 0 2 A...T................T.....................C.....................A.......... GDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDDSDDDDDDDDDDDDDDDDDDDDDODDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1777 0 2 A...A................C.....................C.....................C.......... HDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1813 0 2 C...C................C.....................T.....................C.......... [DDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDIDDDDDDDDDDDDDDDDDDDDDYDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1916 0 2 C...A................T.....................C.....................C.......... GDDDGDDDDDDDDDDDDDDDDODDDDDDDDDDDDDDDDDDDDDTDDDDDDDDDDDDDDDDDDDDDSDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1959 0 2 A...C................C.....................A.....................C.......... PDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 6 1 1793 808 0 2 C...A................A.....................G.....................G.......... [DDDDDDDDDDDDDDDDDDDDMDDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 602 0 2 C...A................T.....................T.....................G.......... ^DDDEDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDYDDDDDDDDDDDDDDDDDDDDDUDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1602 0 2 C...G................C.....................C.....................C.......... ZDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDWDDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1681 0 2 A...A................G.....................G.....................G.......... HDDDGDDDDDDDDDDDDDDDDVDDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDDDDDDDDDDDDDSDDDDDDDDDD 0
-SL-XBA 1 6 1 1793 1011 0 2 A...T................T.....................C.....................C.......... RDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDD^DDDDDDDDDDDDDDDDDDDDDIDDDDDDDDDD 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_2_0002_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_2_0002_qseq.txt
deleted file mode 100644
index 2a34617..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_2_0002_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 6 2 1793 1893 0 2 GGGCAGGGGGCTTTTTCTCACTCTCTCTCATATCTTCTAGGGTAACTACATGAACACACGCTTCTCTCCCCTTCCG `aaaS\aaaYH\a[``b^b]H^b_b^baaRZH[b_abXG]^`R_L_\H_U_\SF^SGSQTbX\a[b_ba_GOVGGY 0
-SL-XBA 1 6 2 1793 1909 0 2 CTCACACCCACACCCCCCCCAATCCCACCCCCGGACACCACACCCCTCCAACTTCCCCCCCCGAGCGCAGCCGGGG aPUJYERYGDJFSJEUZNQGDKNQXMFTKKLLKGFEMFFDDKEMPJDIYDDPDDDDKGGDFEGDGQSVLIDJPPED 0
-SL-XBA 1 6 2 1793 1931 0 2 CTGAAGCGCCACCGCCGCGGCGTGGCGGGCCCCGCGCACCACCTCTTCCCGTCCTCTACCGGCCCTGGCCACGCCC XJEFSPPFSPKOFPNMDFDEXGOKDKFLLDDLFDDMFFMKGGMJKGDLRJJJKNGIJEFRKJILDDIIMEDKOFIG 0
-SL-XBA 1 6 2 1793 2004 0 2 GAACTTGACTATCTCTTCTAATTTTATTGTTTATTTTGTGTTTACTGCCCAGCTACTTCCCACCTTCCACTTGCTT a^S_b_[J]\TVFRa]\H^S]aa`^J\_a_]VLZ___`\aYYV^S[]^I^[WaWR`^\]G]ZaaP`MDL__YW_T\ 0
-SL-XBA 1 6 2 1793 2038 0 2 CCTGTGTCTCAGTGAGCCTTCAGTGCAACATACGGGTAAGAGCAGCCTTCTCTTCACTGAGATGAGACCCCCCCAC a]UQUMQWW^WXMTFT^^UOKSVVMRFDDHJPPQMQPMEQPRRONVTIHTTGTJMNKQIDLKNPHPUQNQFTTUUQ 0
-SL-XBA 1 6 2 1793 829 0 2 TCGCTGTTGTTGCATGTCAGGTTGGAGAGTGTGCCCGTGGCCCCGGTGCGGCCGGTGGCCGCCCCCCCCCCCCGCC `a_aa`\`a^``_HW_\_H]\]\`]R\O]S`R`aa_UJ[][G[FWWIWDYWDYSDTQGWDGTTDS]Q[VZIZQDVD 0
-SL-XBA 1 6 2 1793 1117 0 2 TTCTTCAGCTGTATTGAAGTATAATTTACAATACAGTACAATTCATATATTTTAATTGTATAATTTAATGACTTTG JS_MYa\^[F[^_QJ\RW`SJZ]MRYX`]GV^^`OXGO]GGO\`YYZKZJNGYJIVUXHMMFOX]MDJQLS]LFGV 0
-SL-XBA 1 6 2 1793 1478 0 2 CAGCCATTCAAATCCAGTATTTTTTAAGCCTCATTATTGATAAGACAGAGACATACATCACACCTCAACACCTTTT `YZb^FV[]GOIWa^IYSLSZ`][WJLXaa]^NZZVY[VOQFJYG^NXGXQ[JPQ[KTZEFM]_[^IEDIEDRWUT 0
-SL-XBA 1 6 2 1793 1354 0 2 CTGAACCTCAAGTCTCCACCAATCAGAATCTGGGGGAGGGCGCGCGTGCAGGGAGCCGCCTGCTCTCCACCTTCGC `QSGOUNJMQGQP^SX^YLJGTEWETIIS^PFPRMMOFMFDKKXWEDGUOEMJJPGEJ`KKOMMWMPWGMOEJKKN 0
-SL-XBA 1 6 2 1793 666 0 2 ATTTTTGCTTTCCTTGGCCCCCACCAATTTATACATCTCCATTTTCCGACCTCTGGACTAACTGCTTGCTCAGCAC UZa`b^`a__]_WZ_]_aaaa`Y_aW\^ZP]U_``[aS`aYXS[Z\KOF[_[`WVHVa\VR_ZRHFNUXG[KUVFD 0
-SL-XBA 1 6 2 1793 2031 0 2 TGCCAGTAGTTTTGGGTCAAGCCCTCACCTGATTCCACGCTTCATAGCTTCAGCCGTTCCCATCATACTACTAGCT aaab\]\\a\____aaT_HL\ba`XFNa_\]PU_aaHGWFS\`TSL\aYW_GZ^GXFO^`VFP`MXU]RNFSQRTL 0
-SL-XBA 1 6 2 1793 1812 0 2 TCCAGCATGAAGATAATGGCTAATACCAAAGCAGCCTTTTTGCTGTGGTAGGAAGATAATGGCTAATAAAAATGAG abbbbaX`_JJ_S^VJ^bab`_H\HFFNQHW_H\^GZ^^``\E\a_aaOQ[XMHRHMDOLQ[TENJIPDGYFIKDX 0
-SL-XBA 1 6 2 1793 475 0 2 AACTTTTTTACGCAATGTTAATATTCAACTCTTCCTTCCAATAGAAATTTTCTGCTGCTTTTCTTGCTCGTGCTAG abaVVSRRH_PH_IY]`XJ]SOP]_^YI_U\GUbWINQ_[GQ`WDHU^ZXV_XJXZ[FRNSHLPTYRSJHFWFQLL 0
-SL-XBA 1 6 2 1793 1329 0 2 GAGCCCCGCGTCTGTCTCAGAGAACTTTTGCATTCTTCTTGTTCTCCAGGAGAAACGGCATCATCTTCCATGTCTT `_\Iab_LJYUaWFU_ab_b]KZQHTaaaaa]Zabaab_U__a``bba]aZWHOVI[_\FYb][[X`_GUW_\aTX 0
-SL-XBA 1 6 2 1793 404 0 2 ACATGAATCCTCTCCCACAGGAATTATTCAGCTTACCGCGAGTACGCTTCCGTGTTGGAAAGATTCAACTCACCCC ZFVaUQYQG\NW[]`_X`\WW]U[\\YS^DT`W\Z]_IVRKMDU^[FDDTZJHDDLQFPHEDTGLXRVEOHDDO\a 0
-SL-XBA 1 6 2 1793 1455 0 2 GGAAACCAACCCCTCACATGGTAACCCGCTCCAACCCGCACGCCCTGTTCGGCCCCTGACCCGGCCCCCCGGCGCA ]NKJF[YFFFKTFRGTXFJMVOTKNW_XSGKJFT_ZFDVDDZR]WUMIDOSEFDPVGEMTDDJDK]OUQSIDKIYD 0
-SL-XBA 1 6 2 1793 1793 0 2 GTTTATAACTTCTTCTGTGGGATCAGCGGGCACGCCTCTTCCCACCAGCACACTACACGTCTACCAGCGCGGATGG a^`]MXOHG[_ba^b_aWa`]^\^I[EY_^\DZ`aaYEWTE\J]`\DVEJFM_REXEK\QEWPOUQUaVF[TDL]Y 0
-SL-XBA 1 6 2 1793 310 0 2 CGAAACTTGGGTCAGTAAACTGGTGAAGCTGACCTATTTGGCAAGCAGCATGATTCGGAAGCGCGGCAGGCAGAGT ^GT_aaI]TV_Ua_IRSH^\Ua_GHFPWDF^\_`IY_^S_JGS]`ZW[FN_\RUU`_ZNV_GLFGHVGPGWGQFFF 0
-SL-XBA 1 6 2 1793 1969 0 2 GAGAACTCTCTGTGTAGTTGTGACTTCCATCCTTCCGCAACAGTAGTAAGGACCGCGACTTCTGACCACATTGACC YD\\\GK\a]\YLZV[aN^_W_\YW\\]FMK\WU_a_`KKJOVLGXFRT]^TWNN^ZLFJMWGTOFUPXGFFFJNX 0
-SL-XBA 1 6 2 1794 490 0 2 ATAAACTTGAAAATAATTTTCTATGATACAGCTTTCAGGTAGAAAAATGAATTTTCGTCGTGTTTAACAATGTTGT `aabab``b_ZT__VVaaa^bbaaa^_abaab`a__R[`U]]HXX^O[a_U^]__aaU`X]aT`[_U[DJ]_[[YO 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_2_0003_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_2_0003_qseq.txt
deleted file mode 100644
index 090d345..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_2_0003_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 6 3 1793 1282 0 2 AAGCACACCAAGCTTCCCGCAGCTGCGGCGCCCCCGCTCCAAGGCCAGCAGCTGCCCCCTCTGCCCCCACCCCCTC GITVXMPGMNN]a_LPVJ\MMN_X\I\GMGMZ[MPF]Z[YFFFV\ZFMFY\\YTTPXRWIVMVZYDVYFFZ_ZUOX 0
-SL-XBA 1 6 3 1793 1301 0 2 GCATTGCGTCCATCTCTTTACAGAAGAACTCAGCCCACACCCTAGAATGTACACCTTTGGAAAAAGGAGAAGTGCT \GUZXI``ZIababbb`aa_ba_H^^_]_aaabbb`U_W^bb]X_]\^_LQHX`aZU]]ZTRRS\R\VJULPS^\L 0
-SL-XBA 1 6 3 1793 1311 0 2 CAGCAAAAGTGCCGGCTAGTCCGGTTTGTTGAAAATACAGTAGAAAAGCTGATTCTGGTTATCTCTCTCAGGACAA a[`aa`S\`P^bbaaIaX^Y]F]_H^`_[``VSZ`_^a\]HFUFUP[TWGYNVT`^VGO\\\_\_SIVDRTTN]SO 0
-SL-XBA 1 6 3 1793 1326 0 2 CAAGATCATACTAACACACTCCAGCCTGGGCAACAGAGTGGGACTCTGTATCCAAAAAAAATTCTCTACCAACTAC a`aa\\a`^_ba^^aabbbbaaL_`bOa[Kbbbb`_S[_`ZZ`bJbab`Kab`P\`Y\X[\`Kb^J[^a^R[aK^b 0
-SL-XBA 1 6 3 1793 1389 0 2 ACCACAGGCACCACCAGCCACGGACCCACGCCTGCCACTCCCCACCCCCCCCCCCCCAGCCACGCCACCGTCCCAC V_]I_OYR_Q__Vaa\`aaRa\TDZa]G]ODYZ[`\O_\WFZEGY^`]Q]VD[ZDY`ZR_]JMIDDMJ[ONYH]LH 0
-SL-XBA 1 6 3 1793 1405 0 2 GCCTTGTTTGGCCCTGATCTCTGACTTCTAGAGCCCCAGCTGCTGGCGGCTGCTGGGATATCCTCCCCGCTCGGGT _aaaaa`__Xaaaa`PP\aaaaa`aaaaaX\XaaaaaX`a`aa_I\a__VPXMQ\RRDWQQ_]FFY`TDPJDVVDG 0
-SL-XBA 1 6 3 1793 1507 0 2 CAGAGCGCGTTGGCGTGAGTGACAGAGCGGCCAGTGGCCGCCGCCCACCCGCCCACGCCCCCGAGGGCCCCCCTGC _PPJP^S]SSRSS\TRRKQTQMZPPKL]SMEVMIIKLTJJMKGMVIEKPIDDDMIGDMMMKIDIJKDDJPGEJDKM 0
-SL-XBA 1 6 3 1793 1557 0 2 CGGCTTTTTTTTTATTGAGACCAGCTCCTGCCCTACCCCCGCGGCTGCGGAGCAAGGTCCCCTTCATGCGCCCCCC TEONGVIR]XU\XH[IJDFJTKNDFEVDVJUVTDFDDJOXIGIFQGTDDKEGMEKDDGKUDGEFVEJEKELKJTTS 0
-SL-XBA 1 6 3 1793 1570 0 2 CAGACACCTTTCATATCTTTATGGCAACTTAATTTTTGGCCTTTTATCACTCTGTCATACCAGCATTCTGCCGTCA `_]Za_baTSXFRS\XaZ^]N`_^W__Z\[GXNTJJ[VSaZa[DMMZbLGMW^_G]FX_]][U]GSZ[DIMGMI\Y 0
-SL-XBA 1 6 3 1793 1709 0 2 AGCCACTGTCCCGTGTATAACTTGGCATTAGAGCACCAGGTCTGTTGGATGGTGGTGGCAGGCCCAATTAATTTTT K^_HV_a_UabbbZb^_`ZJ_`Zaaa\Za`_U_aUa_G]aWb``U[a^UXa^Ga\LY_]LV_WTYDMHHREVRLDH 0
-SL-XBA 1 6 3 1793 1738 0 2 TCCCTGACTGGATACAGGCAGCTGACCCCTTCTCCCGACACCTCAAGGAGTAACTGGGCTGTTGGTGACCCCCGAC `aaaa`_aaa`[aVa_`aa`aZGYFZaa`\`_O__IXO_H_a[G]H]]G]GJZ_X_YDZI[GTS_JMDR_G]TGDF 0
-SL-XBA 1 6 3 1793 1779 0 2 CACTGAAATGTTTAGGACCATATTATAAGTAAGTACTTATCAATGTACTTTAGGACCATATTATAAGTAAGTGCTT \Y`a]G]US`\ZQV`_\a_H\US__YTH_X[H\Yaaa_Y\F^FXaIab]HUVa_`b_Z\X]HO_IW^YSOY[ab\[ 0
-SL-XBA 1 6 3 1793 1859 0 2 CGATTTTTAAGGACCCCGTGCCTCTGGGGGCCGATGAACTCCACGATGGGACGCACCTGGAGCTCTACCATCAATA aaTT`X^_]MGV```a^RK`]`\`]`U_^]QXGSRSGMFOa^QY^QUU[QNKXPYaXMPHOUSTPNNEEVW`POKQ 0
-SL-XBA 1 6 3 1793 1898 0 2 CCGGCCAAGCAGGCATGTGTGAATGAACGTGGCCGCTGACTCAGAACAGAGGACATCCCAGGGCCGCAAGCGCGGA aa]`aaR\Z]ETGPDQ\S\TTQLFKRV`\KSP]PGPFKJMRVFPKEXNRRPGNXNFUMJFFOKGDKQEGMPKNNMG 0
-SL-XBA 1 6 3 1793 1143 0 2 CTGCAGAGCAGTTGTGGCACTGGGCTTTGGCCACTCAAACTCAGGCTGGTCCGGAACCTCCCCCACCCCGCCCCAC `\\aTX]]`_WNV\KPXYJYFRSS`MMRUU^`X\S]PUW^PYPPRZSQKDVYRLEPVVETX\ZWEK\QDGWJVDDQ 0
-SL-XBA 1 6 3 1793 141 0 2 CTCTCCCGCGCCTGCTACGGAGCCCGCTCGGGGGGGCCACGCCGCTCCCGAGGACGTAGCACCTCCTCCACTCACG SYLIUXTIYEVGMRRR^XIFG_GUMGGDDKZUQJIMMGMNOG]RNEDPSGKPGGOLUEPTDDMU]GEFDJQOEJRG 0
-SL-XBA 1 6 3 1793 1617 0 2 GTGGTCATAACTGTTTCTGGACCCATTTGAACTTCATCTGAATATAGAAATCTCAGCAGCGCCCGGACGGCTGCGG `[ba`aS]\K_aa_a`b_a\I`_IJ]`aaXSaa_aZ]a^Z]__T`Za\OSUb__GU`XZ`Q`[FXOFGYL^DRYNY 0
-SL-XBA 1 6 3 1793 1031 0 2 CCCATACCAGCACAGAGCATACAGAAACACAGAAAAAATATTCCCAGTAAAACATGTGCAACTGTCCAGGCAGTCG JT``_XQJ]S``aa`U_ZFGLZ[\QQHaW___V]`_[TWRSXW_UQLSTYLW]WZYOOWPIXTULZVMHIDMSHHO 0
-SL-XBA 1 6 3 1793 1793 0 2 GCTCAAATTTGTGCTACCAATGATATCGAGTTTATAGCAAATTTTCTACGGGAAGTCTATGCGGCAATTTTCTCAT ab`\WJR^b\`LW`_Y`ba^K_ZWZ_J_I_ZbRKWHWb^JX\ZQI\J\FQ`^WXWIJODGHHPWHSQY^`Va]^FY 0
-SL-XBA 1 6 3 1793 456 0 2 TCCATCCACTTCCCTGAGCCTCAGAAAAGGGCAAGGCATGGCTCACATACTCTCAGCCACGGCCTGGCCTGCTGCC aaa[`aa_aaaaaa\__`aa^aT_VVV\ZZ`a`X`Za^\][aa_U_``^a]aX]I]``X`TR^]GDWXGMX]Z[YG 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_3_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_3_0001_qseq.txt
deleted file mode 100644
index 8938efe..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_3_0001_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 6 1 1793 1420 0 3 G..... \DDDDD 0
-SL-XBA 1 6 1 1793 1441 0 3 C..... GDDDDD 0
-SL-XBA 1 6 1 1793 1483 0 3 G..... YDDDDD 0
-SL-XBA 1 6 1 1793 1495 0 3 G..... VDDDDD 0
-SL-XBA 1 6 1 1793 1527 0 3 G..... MDDDDD 0
-SL-XBA 1 6 1 1793 1545 0 3 C..... HDDDDD 0
-SL-XBA 1 6 1 1793 1583 0 3 G..... YDDDDD 0
-SL-XBA 1 6 1 1793 1596 0 3 G..... TDDDDD 0
-SL-XBA 1 6 1 1793 1658 0 3 C..... GDDDDD 0
-SL-XBA 1 6 1 1793 1718 0 3 G..... YDDDDD 0
-SL-XBA 1 6 1 1793 1745 0 3 C..... PDDDDD 0
-SL-XBA 1 6 1 1793 1777 0 3 G..... YDDDDD 0
-SL-XBA 1 6 1 1793 1813 0 3 G..... VDDDDD 0
-SL-XBA 1 6 1 1793 1916 0 3 G..... [DDDDD 0
-SL-XBA 1 6 1 1793 1959 0 3 G..... [DDDDD 0
-SL-XBA 1 6 1 1793 808 0 3 T..... YDDDDD 0
-SL-XBA 1 6 1 1793 602 0 3 T..... [DDDDD 0
-SL-XBA 1 6 1 1793 1602 0 3 C..... [DDDDD 0
-SL-XBA 1 6 1 1793 1681 0 3 C..... ^DDDDD 0
-SL-XBA 1 6 1 1793 1011 0 3 A..... GDDDDD 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_3_0002_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_3_0002_qseq.txt
deleted file mode 100644
index 1ffeeea..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_3_0002_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 6 2 1793 1893 0 3 G.TCC.. ODZb[DD 0
-SL-XBA 1 6 2 1793 1909 0 3 G.CCT.. GD[_WDD 0
-SL-XBA 1 6 2 1793 1931 0 3 G.CTA.. [DWMFDD 0
-SL-XBA 1 6 2 1793 2004 0 3 G.GTT.. WDPR[DD 0
-SL-XBA 1 6 2 1793 2038 0 3 G.GCG.. ^DYLZDD 0
-SL-XBA 1 6 2 1793 829 0 3 T.GGC.. ZDZ]IDD 0
-SL-XBA 1 6 2 1793 1117 0 3 G.GGG.. RDZaVDD 0
-SL-XBA 1 6 2 1793 1478 0 3 T.TTT.. \D^b^DD 0
-SL-XBA 1 6 2 1793 1354 0 3 T.GCT.. PDZ`ZDD 0
-SL-XBA 1 6 2 1793 666 0 3 C.GAG.. ^DXGXDD 0
-SL-XBA 1 6 2 1793 2031 0 3 C.CCG.. YDFIYDD 0
-SL-XBA 1 6 2 1793 1812 0 3 C.CTC.. GD^a]DD 0
-SL-XBA 1 6 2 1793 475 0 3 C.GGG.. ^DX^RDD 0
-SL-XBA 1 6 2 1793 1329 0 3 C.TCT.. WDWOTDD 0
-SL-XBA 1 6 2 1793 404 0 3 C.CCC.. YDH^ODD 0
-SL-XBA 1 6 2 1793 1455 0 3 C.TTC.. ^DW\^DD 0
-SL-XBA 1 6 2 1793 1793 0 3 C.CCA.. \D^DHDD 0
-SL-XBA 1 6 2 1793 310 0 3 C.GGA.. GDTZFDD 0
-SL-XBA 1 6 2 1793 1969 0 3 T.CGC.. TDWGGDD 0
-SL-XBA 1 6 2 1794 490 0 3 C.TCC.. ^DWb^DD 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_3_0003_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_3_0003_qseq.txt
deleted file mode 100644
index 32ab1c7..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBarcodeParsingTest/BaseCalls/s_6_3_0003_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 6 3 1793 1282 0 3 G.TAG. [DZGMD 0
-SL-XBA 1 6 3 1793 1301 0 3 G.AGG. ^DIYRD 0
-SL-XBA 1 6 3 1793 1311 0 3 G.TAT. [DGH[D 0
-SL-XBA 1 6 3 1793 1326 0 3 G.CCA. ^D^_VD 0
-SL-XBA 1 6 3 1793 1389 0 3 G.GGG. YD[aZD 0
-SL-XBA 1 6 3 1793 1405 0 3 G.TGG. VDPb\D 0
-SL-XBA 1 6 3 1793 1507 0 3 G.GTG. \D\\WD 0
-SL-XBA 1 6 3 1793 1557 0 3 G.GGA. GDZIGD 0
-SL-XBA 1 6 3 1793 1570 0 3 G.TCT. UDRaUD 0
-SL-XBA 1 6 3 1793 1709 0 3 G.GGG. WD]a[D 0
-SL-XBA 1 6 3 1793 1738 0 3 G.GCC. ^DYb^D 0
-SL-XBA 1 6 3 1793 1779 0 3 G.GCA. \DT`OD 0
-SL-XBA 1 6 3 1793 1859 0 3 G.GAG. [DGGZD 0
-SL-XBA 1 6 3 1793 1898 0 3 G.ACA. YDN\GD 0
-SL-XBA 1 6 3 1793 1143 0 3 T.GGG. YDGaRD 0
-SL-XBA 1 6 3 1793 141 0 3 T.CTC. ZDZXKD 0
-SL-XBA 1 6 3 1793 1617 0 3 C.GAA. YDVTFD 0
-SL-XBA 1 6 3 1793 1031 0 3 C.ACT. ^D[^GD 0
-SL-XBA 1 6 3 1793 1793 0 3 C.TCT. YDP_UD 0
-SL-XBA 1 6 3 1793 456 0 3 C.TAT. ^DU_WD 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGAC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGAC.1.fastq
deleted file mode 100644
index 7c7dde1..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGAC.1.fastq
+++ /dev/null
@@ -1,52 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:358 :N:0:AACTTGAC
-NTCTGTTGTTATTTCCCTGTTACTTTTGGT
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:3:1222 :Y:0:AACTTGAC
-TGGCATCCAGCTTTGTACTCATGAAAATTG
-+
-A?=@CBA@=7A@>@9 at BBA?>B=;<=@?B@
- at machine1:HiMom:abcdeACXX:7:1:3:1450 :N:0:AACTTGAC
-NGATTCGATTAGAATCATCGAATGGACTCG
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:3:162 :Y:0:AACTTGAC
-AATGAAGGCCACAGAGTGGTCCAAATAGCC
-+
-?@@5@@@>>A<0?;=0839:2<AAABA=##
- at machine1:HiMom:abcdeACXX:7:1:3:1677 :Y:0:AACTTGAC
-AGTGCAGTGGCGTGATCTTGGCTCACTGCA
-+
-A?7BBB@?9969A7B7;@;1>9:'=7;7 at B
- at machine1:HiMom:abcdeACXX:7:1:3:1760 :Y:0:AACTTGAC
-ACAAGAGACCCTAACATTAGGTAGGAATAT
-+
-A:@@5A<B<48 at B@=>?A?:;:?5>AB?@@
- at machine1:HiMom:abcdeACXX:7:1:3:985 :Y:0:AACTTGAC
-AGGTTTAATTGGTTCCAGGAGGTCACACTG
-+
-?898 at BBB?@6<;@>;B::>:-79BA at A@:
- at machine1:HiMom:abcdeACXX:7:2:2:1365 :N:0:AACTTGAC
-NATAAAGATTATCCGTGAATGGCGCCTCCA
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:1209 :Y:0:AACTTGAC
-NTTGAGGATGTTACTACATTATTATACAAA
-+
-%/3370/010.55#################
- at machine1:HiMom:abcdeACXX:7:2:3:1326 :N:0:AACTTGAC
-AGGAGGGAATGATGAACCAGTAGGTTAAGG
-+
-B>=<28+<B5%9:/;A78>+/=A#######
- at machine1:HiMom:abcdeACXX:7:2:3:1807 :N:0:AACTTGAC
-NGCATACTTCTTTCTTTCTTATTTTTCTTT
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:1941 :Y:0:AACTTGAC
-TGTACTCGTGTAGCCTTTCACAGGCACAGC
-+
-B<.ACBBB2;9C>@5ABBBCBCBABCCC5B
- at machine1:HiMom:abcdeACXX:7:2:3:2038 :N:0:AACTTGAC
-NANAGATAGATAGATAGATAGATAGATAGA
-+
-##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGAC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGAC.barcode_1.fastq
deleted file mode 100644
index d1921ed..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGAC.barcode_1.fastq
+++ /dev/null
@@ -1,52 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:358 :N:0:AACTTGAC
-AACTTGAC
-+
-A?;65173
- at machine1:HiMom:abcdeACXX:7:1:3:1222 :Y:0:AACTTGAC
-AACTTGAC
-+
- at CC=@@>B
- at machine1:HiMom:abcdeACXX:7:1:3:1450 :N:0:AACTTGAC
-AACTTGAC
-+
-BC1'<7A#
- at machine1:HiMom:abcdeACXX:7:1:3:162 :Y:0:AACTTGAC
-AACTTGAC
-+
-BBBC at 5>?
- at machine1:HiMom:abcdeACXX:7:1:3:1677 :Y:0:AACTTGAC
-AACTTGAC
-+
-BCA>=4=B
- at machine1:HiMom:abcdeACXX:7:1:3:1760 :Y:0:AACTTGAC
-AACTTGAC
-+
-BABBABAA
- at machine1:HiMom:abcdeACXX:7:1:3:985 :Y:0:AACTTGAC
-AACTTGAC
-+
-BBBB@>@B
- at machine1:HiMom:abcdeACXX:7:2:2:1365 :N:0:AACTTGAC
-AACTTGAC
-+
-BCAB>>AB
- at machine1:HiMom:abcdeACXX:7:2:3:1209 :Y:0:AACTTGAC
-AACTTGAC
-+
-3?@?92;B
- at machine1:HiMom:abcdeACXX:7:2:3:1326 :N:0:AACTTGAC
-AACTTGAC
-+
-BCBBB3BB
- at machine1:HiMom:abcdeACXX:7:2:3:1807 :N:0:AACTTGAC
-AACTTGAC
-+
-B?4=B@><
- at machine1:HiMom:abcdeACXX:7:2:3:1941 :Y:0:AACTTGAC
-AACTTGAC
-+
-BCBBBBBB
- at machine1:HiMom:abcdeACXX:7:2:3:2038 :N:0:AACTTGAC
-AACTTGAC
-+
-BA@;(1>B
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.1.fastq
deleted file mode 100644
index c2dcba1..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.1.fastq
+++ /dev/null
@@ -1,52 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:358 :N:0:AACTTGACTTGAGCCT
-NTCTGTTGTTATTTCCCTGTTACTTTTGGT
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:3:1222 :Y:0:AACTTGACTTGAGCCT
-TGGCATCCAGCTTTGTACTCATGAAAATTG
-+
-A?=@CBA@=7A@>@9 at BBA?>B=;<=@?B@
- at machine1:HiMom:abcdeACXX:9:1:3:1450 :N:0:AACTTGACTTGAGCCT
-NGATTCGATTAGAATCATCGAATGGACTCG
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:3:162 :Y:0:AACTTGACTTGAGCCT
-AATGAAGGCCACAGAGTGGTCCAAATAGCC
-+
-?@@5@@@>>A<0?;=0839:2<AAABA=##
- at machine1:HiMom:abcdeACXX:9:1:3:1677 :Y:0:AACTTGACTTGAGCCT
-AGTGCAGTGGCGTGATCTTGGCTCACTGCA
-+
-A?7BBB@?9969A7B7;@;1>9:'=7;7 at B
- at machine1:HiMom:abcdeACXX:9:1:3:1760 :Y:0:AACTTGACTTGAGCCT
-ACAAGAGACCCTAACATTAGGTAGGAATAT
-+
-A:@@5A<B<48 at B@=>?A?:;:?5>AB?@@
- at machine1:HiMom:abcdeACXX:9:1:3:985 :Y:0:AACTTGACTTGAGCCT
-AGGTTTAATTGGTTCCAGGAGGTCACACTG
-+
-?898 at BBB?@6<;@>;B::>:-79BA at A@:
- at machine1:HiMom:abcdeACXX:9:2:2:1365 :N:0:AACTTGACTTGAGCCT
-NATAAAGATTATCCGTGAATGGCGCCTCCA
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:1209 :Y:0:AACTTGACTTGAGCCT
-NTTGAGGATGTTACTACATTATTATACAAA
-+
-%/3370/010.55#################
- at machine1:HiMom:abcdeACXX:9:2:3:1326 :N:0:AACTTGACTTGAGCCT
-AGGAGGGAATGATGAACCAGTAGGTTAAGG
-+
-B>=<28+<B5%9:/;A78>+/=A#######
- at machine1:HiMom:abcdeACXX:9:2:3:1807 :N:0:AACTTGACTTGAGCCT
-NGCATACTTCTTTCTTTCTTATTTTTCTTT
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:1941 :Y:0:AACTTGACTTGAGCCT
-TGTACTCGTGTAGCCTTTCACAGGCACAGC
-+
-B<.ACBBB2;9C>@5ABBBCBCBABCCC5B
- at machine1:HiMom:abcdeACXX:9:2:3:2038 :N:0:AACTTGACTTGAGCCT
-NANAGATAGATAGATAGATAGATAGATAGA
-+
-##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.barcode_1.fastq
deleted file mode 100644
index 34ef16f..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.barcode_1.fastq
+++ /dev/null
@@ -1,52 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:358 :N:0:AACTTGACTTGAGCCT
-AACTTGAC
-+
-A?;65173
- at machine1:HiMom:abcdeACXX:9:1:3:1222 :Y:0:AACTTGACTTGAGCCT
-AACTTGAC
-+
- at CC=@@>B
- at machine1:HiMom:abcdeACXX:9:1:3:1450 :N:0:AACTTGACTTGAGCCT
-AACTTGAC
-+
-BC1'<7A#
- at machine1:HiMom:abcdeACXX:9:1:3:162 :Y:0:AACTTGACTTGAGCCT
-AACTTGAC
-+
-BBBC at 5>?
- at machine1:HiMom:abcdeACXX:9:1:3:1677 :Y:0:AACTTGACTTGAGCCT
-AACTTGAC
-+
-BCA>=4=B
- at machine1:HiMom:abcdeACXX:9:1:3:1760 :Y:0:AACTTGACTTGAGCCT
-AACTTGAC
-+
-BABBABAA
- at machine1:HiMom:abcdeACXX:9:1:3:985 :Y:0:AACTTGACTTGAGCCT
-AACTTGAC
-+
-BBBB@>@B
- at machine1:HiMom:abcdeACXX:9:2:2:1365 :N:0:AACTTGACTTGAGCCT
-AACTTGAC
-+
-BCAB>>AB
- at machine1:HiMom:abcdeACXX:9:2:3:1209 :Y:0:AACTTGACTTGAGCCT
-AACTTGAC
-+
-3?@?92;B
- at machine1:HiMom:abcdeACXX:9:2:3:1326 :N:0:AACTTGACTTGAGCCT
-AACTTGAC
-+
-BCBBB3BB
- at machine1:HiMom:abcdeACXX:9:2:3:1807 :N:0:AACTTGACTTGAGCCT
-AACTTGAC
-+
-B?4=B@><
- at machine1:HiMom:abcdeACXX:9:2:3:1941 :Y:0:AACTTGACTTGAGCCT
-AACTTGAC
-+
-BCBBBBBB
- at machine1:HiMom:abcdeACXX:9:2:3:2038 :N:0:AACTTGACTTGAGCCT
-AACTTGAC
-+
-BA@;(1>B
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.barcode_2.fastq
deleted file mode 100644
index 068fcfd..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AACTTGACTTGAGCCT.barcode_2.fastq
+++ /dev/null
@@ -1,52 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:358 :N:0:AACTTGACTTGAGCCT
-TTGAGCCT
-+
-A?;65173
- at machine1:HiMom:abcdeACXX:9:1:3:1222 :Y:0:AACTTGACTTGAGCCT
-TTGAGCCT
-+
- at CC=@@>B
- at machine1:HiMom:abcdeACXX:9:1:3:1450 :N:0:AACTTGACTTGAGCCT
-TTGAGCCT
-+
-BC1'<7A#
- at machine1:HiMom:abcdeACXX:9:1:3:162 :Y:0:AACTTGACTTGAGCCT
-TTGAGCCT
-+
-BBBC at 5>?
- at machine1:HiMom:abcdeACXX:9:1:3:1677 :Y:0:AACTTGACTTGAGCCT
-TTGAGCCT
-+
-BCA>=4=B
- at machine1:HiMom:abcdeACXX:9:1:3:1760 :Y:0:AACTTGACTTGAGCCT
-TTGAGCCT
-+
-BABBABAA
- at machine1:HiMom:abcdeACXX:9:1:3:985 :Y:0:AACTTGACTTGAGCCT
-TTGAGCCT
-+
-BBBB@>@B
- at machine1:HiMom:abcdeACXX:9:2:2:1365 :N:0:AACTTGACTTGAGCCT
-TTGAGCCT
-+
-BCAB>>AB
- at machine1:HiMom:abcdeACXX:9:2:3:1209 :Y:0:AACTTGACTTGAGCCT
-TTGAGCCT
-+
-3?@?92;B
- at machine1:HiMom:abcdeACXX:9:2:3:1326 :N:0:AACTTGACTTGAGCCT
-TTGAGCCT
-+
-BCBBB3BB
- at machine1:HiMom:abcdeACXX:9:2:3:1807 :N:0:AACTTGACTTGAGCCT
-TTGAGCCT
-+
-B?4=B@><
- at machine1:HiMom:abcdeACXX:9:2:3:1941 :Y:0:AACTTGACTTGAGCCT
-TTGAGCCT
-+
-BCBBBBBB
- at machine1:HiMom:abcdeACXX:9:2:3:2038 :N:0:AACTTGACTTGAGCCT
-TTGAGCCT
-+
-BA@;(1>B
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGT.1.fastq
deleted file mode 100644
index c0696c6..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGT.1.fastq
+++ /dev/null
@@ -1,52 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:1417 :Y:0:AAGGATGT
-NATTCCATTCGATGATTCCATTCGAGTCCA
-+
-%-::567;93-510788014:8538122##
- at machine1:HiMom:abcdeACXX:7:1:2:1889 :Y:0:AAGGATGT
-NGAAATGTATCAAGGTTTGTATAATTGCTG
-+
-%-7<<:::<2:::8:4<<:07547765978
- at machine1:HiMom:abcdeACXX:7:1:3:1764 :N:0:AAGGATGT
-NTCTATGGGGTGTGTATCTGTTTCTGGACT
-+
-%09::845(4586/6666884;8851.314
- at machine1:HiMom:abcdeACXX:7:1:3:2027 :Y:0:AAGGATGT
-AATGTATTATGTTTCATAAGAAAACAAAAG
-+
-BA7/- at 8=@4,*1=>?:A@:>B at BBCB@8#
- at machine1:HiMom:abcdeACXX:7:1:3:273 :N:0:AAGGATGT
-NAATTGACATAAATCAATATTGTTAAAATG
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:3:608 :Y:0:AAGGATGT
-NTGTGCTTCAATGATGCTATCAGGTGTGTT
-+
-%.9675:747:766553::9:7119::8::
- at machine1:HiMom:abcdeACXX:7:2:2:1842 :N:0:AAGGATGT
-NGGTGGATCCCCTGAGGTCAGGAGTTCAAG
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:2:1944 :Y:0:AAGGATGT
-NATTAAATATATATTTTATTCTGAACATAA
-+
-%09::<<<<<;:<<<:99<<9<<;<;<:<<
- at machine1:HiMom:abcdeACXX:7:2:2:1985 :N:0:AAGGATGT
-NGACTATCACTCTAGGGCCTCCACCCTTGC
-+
-%%2266466667186(66############
- at machine1:HiMom:abcdeACXX:7:2:3:1952 :Y:0:AAGGATGT
-NATAGATGATAAAAACATTTGACAGTGAAA
-+
-%.8737868:::<;<;9;9979::9858;;
- at machine1:HiMom:abcdeACXX:7:2:3:470 :Y:0:AAGGATGT
-TGTGGATTCCATTCGAATTCATTCGATTAT
-+
-BBCBBACC at CCCC>)@CBA>@CB?BCCCCC
- at machine1:HiMom:abcdeACXX:7:2:3:490 :N:0:AAGGATGT
-NCTAATTGATGGGTAAGAGGCAAAGCATGA
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:589 :Y:0:AAGGATGT
-TGAATGCAGGTGCCAGGGAGACGTGACTTC
-+
-=8ACBB??>@=?<ACB9<;?A>??;A<>?3
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGT.barcode_1.fastq
deleted file mode 100644
index f4f317f..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGT.barcode_1.fastq
+++ /dev/null
@@ -1,52 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:1417 :Y:0:AAGGATGT
-AAGGATGT
-+
-B?5??BC?
- at machine1:HiMom:abcdeACXX:7:1:2:1889 :Y:0:AAGGATGT
-NAGGATGT
-+
-%.46:;;9
- at machine1:HiMom:abcdeACXX:7:1:3:1764 :N:0:AAGGATGT
-AAGGATGT
-+
-BB?BB@:A
- at machine1:HiMom:abcdeACXX:7:1:3:2027 :Y:0:AAGGATGT
-AAGGATGT
-+
-B>7-<::#
- at machine1:HiMom:abcdeACXX:7:1:3:273 :N:0:AAGGATGT
-AAGGATGT
-+
-38=5+AC7
- at machine1:HiMom:abcdeACXX:7:1:3:608 :Y:0:AAGGATGT
-AAGGATGT
-+
-AA5B?BB@
- at machine1:HiMom:abcdeACXX:7:2:2:1842 :N:0:AAGGATGT
-AAGGATGT
-+
-@:1;39B>
- at machine1:HiMom:abcdeACXX:7:2:2:1944 :Y:0:AAGGATGT
-AAGGATGT
-+
-BB9BBA:#
- at machine1:HiMom:abcdeACXX:7:2:2:1985 :N:0:AAGGATGT
-AAGGATGT
-+
-BC?7>2<8
- at machine1:HiMom:abcdeACXX:7:2:3:1952 :Y:0:AAGGATGT
-AAGGATGT
-+
-BB?BB at B<
- at machine1:HiMom:abcdeACXX:7:2:3:470 :Y:0:AAGGATGT
-AAGGATGT
-+
-B at 6::=B:
- at machine1:HiMom:abcdeACXX:7:2:3:490 :N:0:AAGGATGT
-AAGGATGT
-+
-?#######
- at machine1:HiMom:abcdeACXX:7:2:3:589 :Y:0:AAGGATGT
-AAGGATGT
-+
-?BB9BB at 9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.1.fastq
deleted file mode 100644
index 377ac1f..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.1.fastq
+++ /dev/null
@@ -1,52 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:1417 :Y:0:AAGGATGTTTCGCTGA
-NATTCCATTCGATGATTCCATTCGAGTCCA
-+
-%-::567;93-510788014:8538122##
- at machine1:HiMom:abcdeACXX:9:1:2:1889 :Y:0:AAGGATGTTTCGCTGA
-NGAAATGTATCAAGGTTTGTATAATTGCTG
-+
-%-7<<:::<2:::8:4<<:07547765978
- at machine1:HiMom:abcdeACXX:9:1:3:1764 :N:0:AAGGATGTTTCGCTGA
-NTCTATGGGGTGTGTATCTGTTTCTGGACT
-+
-%09::845(4586/6666884;8851.314
- at machine1:HiMom:abcdeACXX:9:1:3:2027 :Y:0:AAGGATGTTTCGCTGA
-AATGTATTATGTTTCATAAGAAAACAAAAG
-+
-BA7/- at 8=@4,*1=>?:A@:>B at BBCB@8#
- at machine1:HiMom:abcdeACXX:9:1:3:273 :N:0:AAGGATGTTTCGCTGA
-NAATTGACATAAATCAATATTGTTAAAATG
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:3:608 :Y:0:AAGGATGTTTCGCTGA
-NTGTGCTTCAATGATGCTATCAGGTGTGTT
-+
-%.9675:747:766553::9:7119::8::
- at machine1:HiMom:abcdeACXX:9:2:2:1842 :N:0:AAGGATGTTTCGCTGA
-NGGTGGATCCCCTGAGGTCAGGAGTTCAAG
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:2:1944 :Y:0:AAGGATGTTTCGCTGA
-NATTAAATATATATTTTATTCTGAACATAA
-+
-%09::<<<<<;:<<<:99<<9<<;<;<:<<
- at machine1:HiMom:abcdeACXX:9:2:2:1985 :N:0:AAGGATGTTTCGCTGA
-NGACTATCACTCTAGGGCCTCCACCCTTGC
-+
-%%2266466667186(66############
- at machine1:HiMom:abcdeACXX:9:2:3:1952 :Y:0:AAGGATGTTTCGCTGA
-NATAGATGATAAAAACATTTGACAGTGAAA
-+
-%.8737868:::<;<;9;9979::9858;;
- at machine1:HiMom:abcdeACXX:9:2:3:470 :Y:0:AAGGATGTTTCGCTGA
-TGTGGATTCCATTCGAATTCATTCGATTAT
-+
-BBCBBACC at CCCC>)@CBA>@CB?BCCCCC
- at machine1:HiMom:abcdeACXX:9:2:3:490 :N:0:AAGGATGTTTCGCTGA
-NCTAATTGATGGGTAAGAGGCAAAGCATGA
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:589 :Y:0:AAGGATGTTTCGCTGA
-TGAATGCAGGTGCCAGGGAGACGTGACTTC
-+
-=8ACBB??>@=?<ACB9<;?A>??;A<>?3
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.barcode_1.fastq
deleted file mode 100644
index 99ac8f1..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.barcode_1.fastq
+++ /dev/null
@@ -1,52 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:1417 :Y:0:AAGGATGTTTCGCTGA
-AAGGATGT
-+
-B?5??BC?
- at machine1:HiMom:abcdeACXX:9:1:2:1889 :Y:0:AAGGATGTTTCGCTGA
-NAGGATGT
-+
-%.46:;;9
- at machine1:HiMom:abcdeACXX:9:1:3:1764 :N:0:AAGGATGTTTCGCTGA
-AAGGATGT
-+
-BB?BB@:A
- at machine1:HiMom:abcdeACXX:9:1:3:2027 :Y:0:AAGGATGTTTCGCTGA
-AAGGATGT
-+
-B>7-<::#
- at machine1:HiMom:abcdeACXX:9:1:3:273 :N:0:AAGGATGTTTCGCTGA
-AAGGATGT
-+
-38=5+AC7
- at machine1:HiMom:abcdeACXX:9:1:3:608 :Y:0:AAGGATGTTTCGCTGA
-AAGGATGT
-+
-AA5B?BB@
- at machine1:HiMom:abcdeACXX:9:2:2:1842 :N:0:AAGGATGTTTCGCTGA
-AAGGATGT
-+
-@:1;39B>
- at machine1:HiMom:abcdeACXX:9:2:2:1944 :Y:0:AAGGATGTTTCGCTGA
-AAGGATGT
-+
-BB9BBA:#
- at machine1:HiMom:abcdeACXX:9:2:2:1985 :N:0:AAGGATGTTTCGCTGA
-AAGGATGT
-+
-BC?7>2<8
- at machine1:HiMom:abcdeACXX:9:2:3:1952 :Y:0:AAGGATGTTTCGCTGA
-AAGGATGT
-+
-BB?BB at B<
- at machine1:HiMom:abcdeACXX:9:2:3:470 :Y:0:AAGGATGTTTCGCTGA
-AAGGATGT
-+
-B at 6::=B:
- at machine1:HiMom:abcdeACXX:9:2:3:490 :N:0:AAGGATGTTTCGCTGA
-AAGGATGT
-+
-?#######
- at machine1:HiMom:abcdeACXX:9:2:3:589 :Y:0:AAGGATGTTTCGCTGA
-AAGGATGT
-+
-?BB9BB at 9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.barcode_2.fastq
deleted file mode 100644
index b4130ae..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AAGGATGTTTCGCTGA.barcode_2.fastq
+++ /dev/null
@@ -1,52 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:1417 :Y:0:AAGGATGTTTCGCTGA
-TTCGCTGA
-+
-B?5??BC?
- at machine1:HiMom:abcdeACXX:9:1:2:1889 :Y:0:AAGGATGTTTCGCTGA
-TTCGCTGA
-+
-%.46:;;9
- at machine1:HiMom:abcdeACXX:9:1:3:1764 :N:0:AAGGATGTTTCGCTGA
-TTCGCTGA
-+
-BB?BB@:A
- at machine1:HiMom:abcdeACXX:9:1:3:2027 :Y:0:AAGGATGTTTCGCTGA
-TTCGCTGA
-+
-B>7-<::#
- at machine1:HiMom:abcdeACXX:9:1:3:273 :N:0:AAGGATGTTTCGCTGA
-TTCGCTGA
-+
-38=5+AC7
- at machine1:HiMom:abcdeACXX:9:1:3:608 :Y:0:AAGGATGTTTCGCTGA
-TTCGCTGA
-+
-AA5B?BB@
- at machine1:HiMom:abcdeACXX:9:2:2:1842 :N:0:AAGGATGTTTCGCTGA
-TTCGCTGA
-+
-@:1;39B>
- at machine1:HiMom:abcdeACXX:9:2:2:1944 :Y:0:AAGGATGTTTCGCTGA
-TTCGCTGA
-+
-BB9BBA:#
- at machine1:HiMom:abcdeACXX:9:2:2:1985 :N:0:AAGGATGTTTCGCTGA
-TTCGCTGA
-+
-BC?7>2<8
- at machine1:HiMom:abcdeACXX:9:2:3:1952 :Y:0:AAGGATGTTTCGCTGA
-TTCGCTGA
-+
-BB?BB at B<
- at machine1:HiMom:abcdeACXX:9:2:3:470 :Y:0:AAGGATGTTTCGCTGA
-TTCGCTGA
-+
-B at 6::=B:
- at machine1:HiMom:abcdeACXX:9:2:3:490 :N:0:AAGGATGTTTCGCTGA
-TTCGCTGA
-+
-?#######
- at machine1:HiMom:abcdeACXX:9:2:3:589 :Y:0:AAGGATGTTTCGCTGA
-TTCGCTGA
-+
-?BB9BB at 9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTG.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTG.1.fastq
deleted file mode 100644
index 9cc5451..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTG.1.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1219 :Y:0:ACCAACTG
-AGTTACTTATAGTGAATGGTTATTACTCCA
-+
-BA>BBBBBBA@?:?AA;;<8 at B9=97>9>A
- at machine1:HiMom:abcdeACXX:7:1:3:1319 :N:0:ACCAACTG
-TAAATGATTGCCTTCCACAGTATACATGTG
-+
-BAAA<::=B at 7:89)>=>B+)B at B@=####
- at machine1:HiMom:abcdeACXX:7:1:3:795 :N:0:ACCAACTG
-NGTAATGGAAGTCCTAGTACTAAAAATTAG
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:2:1298 :N:0:ACCAACTG
-NGATTCCATTCAATGAATCCATTCGATTCC
-+
-%.235+22976###################
- at machine1:HiMom:abcdeACXX:7:2:2:1745 :Y:0:ACCAACTG
-NGGGAGCTAAGTAACTGGAACAAGTTTTTG
-+
-%-5237789999:8886689:9:9569887
- at machine1:HiMom:abcdeACXX:7:2:2:1874 :Y:0:ACCAACTG
-NGGCATATATCCTTTTACATACCCAACACA
-+
-%,0137:949699;9;88798789717996
- at machine1:HiMom:abcdeACXX:7:2:2:904 :N:0:ACCAACTG
-NTTAGACACCATGAAGGTAACTTCCTACTC
-+
-%0:62667999/&.6058::5978489366
- at machine1:HiMom:abcdeACXX:7:2:3:207 :Y:0:ACCAACTG
-AGTTAGAAACAGAATACGGGTAATAATGTA
-+
-BBCCCA at BA@AAABC at CC@AACBCBBBCBC
- at machine1:HiMom:abcdeACXX:7:2:3:577 :N:0:ACCAACTG
-NTTCAACTCTGGGAGTTGAATGCAAACATC
-+
-##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTG.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTG.barcode_1.fastq
deleted file mode 100644
index a43dd6e..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTG.barcode_1.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1219 :Y:0:ACCAACTG
-ACCAACTG
-+
-B?@@A??9
- at machine1:HiMom:abcdeACXX:7:1:3:1319 :N:0:ACCAACTG
-ACCAACTG
-+
-??8 at A>8:
- at machine1:HiMom:abcdeACXX:7:1:3:795 :N:0:ACCAACTG
-ACCAACTG
-+
->88 at A>##
- at machine1:HiMom:abcdeACXX:7:2:2:1298 :N:0:ACCAACTG
-ACCAACTG
-+
-A7><<%;<
- at machine1:HiMom:abcdeACXX:7:2:2:1745 :Y:0:ACCAACTG
-ACCAACTG
-+
-BA>BBABB
- at machine1:HiMom:abcdeACXX:7:2:2:1874 :Y:0:ACCAACTG
-ACCAACTG
-+
-B>>>?8@=
- at machine1:HiMom:abcdeACXX:7:2:2:904 :N:0:ACCAACTG
-ACCAACTG
-+
-A?ABB?;7
- at machine1:HiMom:abcdeACXX:7:2:3:207 :Y:0:ACCAACTG
-ACCAACTG
-+
-BA;6@??@
- at machine1:HiMom:abcdeACXX:7:2:3:577 :N:0:ACCAACTG
-ACCAACTG
-+
-B?:4<A??
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.1.fastq
deleted file mode 100644
index c9771ab..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.1.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1219 :Y:0:ACCAACTGTGTCGGAT
-AGTTACTTATAGTGAATGGTTATTACTCCA
-+
-BA>BBBBBBA@?:?AA;;<8 at B9=97>9>A
- at machine1:HiMom:abcdeACXX:9:1:3:1319 :N:0:ACCAACTGTGTCGGAT
-TAAATGATTGCCTTCCACAGTATACATGTG
-+
-BAAA<::=B at 7:89)>=>B+)B at B@=####
- at machine1:HiMom:abcdeACXX:9:1:3:795 :N:0:ACCAACTGTGTCGGAT
-NGTAATGGAAGTCCTAGTACTAAAAATTAG
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:2:1298 :N:0:ACCAACTGTGTCGGAT
-NGATTCCATTCAATGAATCCATTCGATTCC
-+
-%.235+22976###################
- at machine1:HiMom:abcdeACXX:9:2:2:1745 :Y:0:ACCAACTGTGTCGGAT
-NGGGAGCTAAGTAACTGGAACAAGTTTTTG
-+
-%-5237789999:8886689:9:9569887
- at machine1:HiMom:abcdeACXX:9:2:2:1874 :Y:0:ACCAACTGTGTCGGAT
-NGGCATATATCCTTTTACATACCCAACACA
-+
-%,0137:949699;9;88798789717996
- at machine1:HiMom:abcdeACXX:9:2:2:904 :N:0:ACCAACTGTGTCGGAT
-NTTAGACACCATGAAGGTAACTTCCTACTC
-+
-%0:62667999/&.6058::5978489366
- at machine1:HiMom:abcdeACXX:9:2:3:207 :Y:0:ACCAACTGTGTCGGAT
-AGTTAGAAACAGAATACGGGTAATAATGTA
-+
-BBCCCA at BA@AAABC at CC@AACBCBBBCBC
- at machine1:HiMom:abcdeACXX:9:2:3:577 :N:0:ACCAACTGTGTCGGAT
-NTTCAACTCTGGGAGTTGAATGCAAACATC
-+
-##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.barcode_1.fastq
deleted file mode 100644
index bdc8147..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.barcode_1.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1219 :Y:0:ACCAACTGTGTCGGAT
-ACCAACTG
-+
-B?@@A??9
- at machine1:HiMom:abcdeACXX:9:1:3:1319 :N:0:ACCAACTGTGTCGGAT
-ACCAACTG
-+
-??8 at A>8:
- at machine1:HiMom:abcdeACXX:9:1:3:795 :N:0:ACCAACTGTGTCGGAT
-ACCAACTG
-+
->88 at A>##
- at machine1:HiMom:abcdeACXX:9:2:2:1298 :N:0:ACCAACTGTGTCGGAT
-ACCAACTG
-+
-A7><<%;<
- at machine1:HiMom:abcdeACXX:9:2:2:1745 :Y:0:ACCAACTGTGTCGGAT
-ACCAACTG
-+
-BA>BBABB
- at machine1:HiMom:abcdeACXX:9:2:2:1874 :Y:0:ACCAACTGTGTCGGAT
-ACCAACTG
-+
-B>>>?8@=
- at machine1:HiMom:abcdeACXX:9:2:2:904 :N:0:ACCAACTGTGTCGGAT
-ACCAACTG
-+
-A?ABB?;7
- at machine1:HiMom:abcdeACXX:9:2:3:207 :Y:0:ACCAACTGTGTCGGAT
-ACCAACTG
-+
-BA;6@??@
- at machine1:HiMom:abcdeACXX:9:2:3:577 :N:0:ACCAACTGTGTCGGAT
-ACCAACTG
-+
-B?:4<A??
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.barcode_2.fastq
deleted file mode 100644
index 95db720..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ACCAACTGTGTCGGAT.barcode_2.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1219 :Y:0:ACCAACTGTGTCGGAT
-TGTCGGAT
-+
-B?@@A??9
- at machine1:HiMom:abcdeACXX:9:1:3:1319 :N:0:ACCAACTGTGTCGGAT
-TGTCGGAT
-+
-??8 at A>8:
- at machine1:HiMom:abcdeACXX:9:1:3:795 :N:0:ACCAACTGTGTCGGAT
-TGTCGGAT
-+
->88 at A>##
- at machine1:HiMom:abcdeACXX:9:2:2:1298 :N:0:ACCAACTGTGTCGGAT
-TGTCGGAT
-+
-A7><<%;<
- at machine1:HiMom:abcdeACXX:9:2:2:1745 :Y:0:ACCAACTGTGTCGGAT
-TGTCGGAT
-+
-BA>BBABB
- at machine1:HiMom:abcdeACXX:9:2:2:1874 :Y:0:ACCAACTGTGTCGGAT
-TGTCGGAT
-+
-B>>>?8@=
- at machine1:HiMom:abcdeACXX:9:2:2:904 :N:0:ACCAACTGTGTCGGAT
-TGTCGGAT
-+
-A?ABB?;7
- at machine1:HiMom:abcdeACXX:9:2:3:207 :Y:0:ACCAACTGTGTCGGAT
-TGTCGGAT
-+
-BA;6@??@
- at machine1:HiMom:abcdeACXX:9:2:3:577 :N:0:ACCAACTGTGTCGGAT
-TGTCGGAT
-+
-B?:4<A??
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTC.1.fastq
deleted file mode 100644
index d967158..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTC.1.fastq
+++ /dev/null
@@ -1,32 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:1507 :Y:0:AGCAATTC
-NGGCTTGGAAAGTGTAGGAGGGAGAGTCAC
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:2:658 :Y:0:AGCAATTC
-NGATGCTTCTGTCCTAAGAAGCTTGAGACA
-+
-%%2632887412107753560555542255
- at machine1:HiMom:abcdeACXX:7:2:2:599 :N:0:AGCAATTC
-NAAACAAAAAAGCTGATGGCCTGGCGGGGT
-+
-%.836844751583,38-)/8638######
- at machine1:HiMom:abcdeACXX:7:2:3:1133 :Y:0:AGCAATTC
-AGAAGCTTTCTATTCTGATCCCCAAGGAGT
-+
-BACBA>BB=1;?BA??5A>:@25<=.43;?
- at machine1:HiMom:abcdeACXX:7:2:3:157 :Y:0:AGCAATTC
-TGGGTGGTTCAAACTAAGCAGTCCAACTGC
-+
-BACC at BBABBBBCBBCBBBBBB?AAB?B?A
- at machine1:HiMom:abcdeACXX:7:2:3:1602 :Y:0:AGCAATTC
-AATTCATGAATACTTTTCAGTCTTTAAAAA
-+
-BCBAAABBBBB?<@BAB?AA=?BBBBBBBB
- at machine1:HiMom:abcdeACXX:7:2:3:808 :N:0:AGCAATTC
-NGAGTGTAATACAATGGTATGGATTTTAAC
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:991 :Y:0:AGCAATTC
-TGGAAGCCAGCCAAAGATACACTCTTGGCA
-+
-BABC>6BBCBBBBCAAA at BACB<<?BABBB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTC.barcode_1.fastq
deleted file mode 100644
index f6603a3..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTC.barcode_1.fastq
+++ /dev/null
@@ -1,32 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:1507 :Y:0:AGCAATTC
-AGCAATTC
-+
-?2=@9A<>
- at machine1:HiMom:abcdeACXX:7:1:2:658 :Y:0:AGCAATTC
-AGCAATTC
-+
- at 7=@@@=;
- at machine1:HiMom:abcdeACXX:7:2:2:599 :N:0:AGCAATTC
-AGCAATTC
-+
-:-8BABB?
- at machine1:HiMom:abcdeACXX:7:2:3:1133 :Y:0:AGCAATTC
-AGCAATTC
-+
-??9 at 5AB;
- at machine1:HiMom:abcdeACXX:7:2:3:157 :Y:0:AGCAATTC
-AGCAATTC
-+
-BBB??CBA
- at machine1:HiMom:abcdeACXX:7:2:3:1602 :Y:0:AGCAATTC
-AGCAATTC
-+
-?6<A at B>8
- at machine1:HiMom:abcdeACXX:7:2:3:808 :N:0:AGCAATTC
-AGCAATTC
-+
->25:9?##
- at machine1:HiMom:abcdeACXX:7:2:3:991 :Y:0:AGCAATTC
-AGCAATTC
-+
-BBAB at BB<
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.1.fastq
deleted file mode 100644
index f3139dd..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.1.fastq
+++ /dev/null
@@ -1,32 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:1507 :Y:0:AGCAATTCTGCTCGAC
-NGGCTTGGAAAGTGTAGGAGGGAGAGTCAC
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:2:658 :Y:0:AGCAATTCTGCTCGAC
-NGATGCTTCTGTCCTAAGAAGCTTGAGACA
-+
-%%2632887412107753560555542255
- at machine1:HiMom:abcdeACXX:9:2:2:599 :N:0:AGCAATTCTGCTCGAC
-NAAACAAAAAAGCTGATGGCCTGGCGGGGT
-+
-%.836844751583,38-)/8638######
- at machine1:HiMom:abcdeACXX:9:2:3:1133 :Y:0:AGCAATTCTGCTCGAC
-AGAAGCTTTCTATTCTGATCCCCAAGGAGT
-+
-BACBA>BB=1;?BA??5A>:@25<=.43;?
- at machine1:HiMom:abcdeACXX:9:2:3:157 :Y:0:AGCAATTCTGCTCGAC
-TGGGTGGTTCAAACTAAGCAGTCCAACTGC
-+
-BACC at BBABBBBCBBCBBBBBB?AAB?B?A
- at machine1:HiMom:abcdeACXX:9:2:3:1602 :Y:0:AGCAATTCTGCTCGAC
-AATTCATGAATACTTTTCAGTCTTTAAAAA
-+
-BCBAAABBBBB?<@BAB?AA=?BBBBBBBB
- at machine1:HiMom:abcdeACXX:9:2:3:808 :N:0:AGCAATTCTGCTCGAC
-NGAGTGTAATACAATGGTATGGATTTTAAC
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:991 :Y:0:AGCAATTCTGCTCGAC
-TGGAAGCCAGCCAAAGATACACTCTTGGCA
-+
-BABC>6BBCBBBBCAAA at BACB<<?BABBB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.barcode_1.fastq
deleted file mode 100644
index 8d51016..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.barcode_1.fastq
+++ /dev/null
@@ -1,32 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:1507 :Y:0:AGCAATTCTGCTCGAC
-AGCAATTC
-+
-?2=@9A<>
- at machine1:HiMom:abcdeACXX:9:1:2:658 :Y:0:AGCAATTCTGCTCGAC
-AGCAATTC
-+
- at 7=@@@=;
- at machine1:HiMom:abcdeACXX:9:2:2:599 :N:0:AGCAATTCTGCTCGAC
-AGCAATTC
-+
-:-8BABB?
- at machine1:HiMom:abcdeACXX:9:2:3:1133 :Y:0:AGCAATTCTGCTCGAC
-AGCAATTC
-+
-??9 at 5AB;
- at machine1:HiMom:abcdeACXX:9:2:3:157 :Y:0:AGCAATTCTGCTCGAC
-AGCAATTC
-+
-BBB??CBA
- at machine1:HiMom:abcdeACXX:9:2:3:1602 :Y:0:AGCAATTCTGCTCGAC
-AGCAATTC
-+
-?6<A at B>8
- at machine1:HiMom:abcdeACXX:9:2:3:808 :N:0:AGCAATTCTGCTCGAC
-AGCAATTC
-+
->25:9?##
- at machine1:HiMom:abcdeACXX:9:2:3:991 :Y:0:AGCAATTCTGCTCGAC
-AGCAATTC
-+
-BBAB at BB<
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.barcode_2.fastq
deleted file mode 100644
index 93196d5..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGCAATTCTGCTCGAC.barcode_2.fastq
+++ /dev/null
@@ -1,32 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:1507 :Y:0:AGCAATTCTGCTCGAC
-TGCTCGAC
-+
-?2=@9A<>
- at machine1:HiMom:abcdeACXX:9:1:2:658 :Y:0:AGCAATTCTGCTCGAC
-TGCTCGAC
-+
- at 7=@@@=;
- at machine1:HiMom:abcdeACXX:9:2:2:599 :N:0:AGCAATTCTGCTCGAC
-TGCTCGAC
-+
-:-8BABB?
- at machine1:HiMom:abcdeACXX:9:2:3:1133 :Y:0:AGCAATTCTGCTCGAC
-TGCTCGAC
-+
-??9 at 5AB;
- at machine1:HiMom:abcdeACXX:9:2:3:157 :Y:0:AGCAATTCTGCTCGAC
-TGCTCGAC
-+
-BBB??CBA
- at machine1:HiMom:abcdeACXX:9:2:3:1602 :Y:0:AGCAATTCTGCTCGAC
-TGCTCGAC
-+
-?6<A at B>8
- at machine1:HiMom:abcdeACXX:9:2:3:808 :N:0:AGCAATTCTGCTCGAC
-TGCTCGAC
-+
->25:9?##
- at machine1:HiMom:abcdeACXX:9:2:3:991 :Y:0:AGCAATTCTGCTCGAC
-TGCTCGAC
-+
-BBAB at BB<
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTT.1.fastq
deleted file mode 100644
index efd45c4..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTT.1.fastq
+++ /dev/null
@@ -1,32 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1341 :Y:0:AGTTGCTT
-TGAAGAGTTTCTGGCACATAGGCACTCAAC
-+
-B7AACB;>C7A??4AB<B>B:':@CAAAAB
- at machine1:HiMom:abcdeACXX:7:1:3:1861 :Y:0:AGTTGCTT
-NGATTAATGAATAGAGTGAATAGTGTCTGA
-+
-%-07:::5.3<<7788529:<<530:9646
- at machine1:HiMom:abcdeACXX:7:1:3:699 :N:0:AGTTGCTT
-NTGTCTTCTTACACTATTTTTTTTAAAATC
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:1962 :Y:0:AGTTGCTT
-ACTAAATCCAAGAGCACATCAAAATGTTAA
-+
-B5;BBB@@8 at BAB9>BBBABACB@@B;@BB
- at machine1:HiMom:abcdeACXX:7:2:3:274 :Y:0:AGTTGCTT
-AGTGAAGTGCTTAGCACCTGGGCCAGCAGC
-+
-:57.:@@>96=@97>@=;=>;@;@=@9=9;
- at machine1:HiMom:abcdeACXX:7:2:3:640 :Y:0:AGTTGCTT
-AGATTAAAAAAAAATGACGTGACAAATTAA
-+
-=6CBC at CABCBBCBC@>@=@ABBCCBBBCC
- at machine1:HiMom:abcdeACXX:7:2:3:691 :Y:0:AGTTGCTT
-ATTTTCAAATCATAAATATGGATTGCTGTG
-+
-BBBABACBBA at ABBBBBBB727AB8+;B55
- at machine1:HiMom:abcdeACXX:7:2:3:72 :Y:0:AGTTGCTT
-CTAGTCTTTGACTTATATCAATTCAGTATT
-+
-BBC?ACCCCCB at CCCCCCCBCCCCCA@BCC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTT.barcode_1.fastq
deleted file mode 100644
index d3c3fdc..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTT.barcode_1.fastq
+++ /dev/null
@@ -1,32 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1341 :Y:0:AGTTGCTT
-AGATGCTT
-+
-B#######
- at machine1:HiMom:abcdeACXX:7:1:3:1861 :Y:0:AGTTGCTT
-AGTTGCTT
-+
-B9@><A<C
- at machine1:HiMom:abcdeACXX:7:1:3:699 :N:0:AGTTGCTT
-AGTTGCTT
-+
-98?>8>##
- at machine1:HiMom:abcdeACXX:7:2:3:1962 :Y:0:AGTTGCTT
-AGTTGCTT
-+
-A76 at 8=0=
- at machine1:HiMom:abcdeACXX:7:2:3:274 :Y:0:AGTTGCTT
-AGTTGCTT
-+
-@@??<?BC
- at machine1:HiMom:abcdeACXX:7:2:3:640 :Y:0:AGTTGCTT
-AGTTGCTT
-+
-A=BBB;<A
- at machine1:HiMom:abcdeACXX:7:2:3:691 :Y:0:AGTTGCTT
-AGTTGCTT
-+
-@=8@>@?A
- at machine1:HiMom:abcdeACXX:7:2:3:72 :Y:0:AGTTGCTT
-AGTTGCTT
-+
-BCBCA>BB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.1.fastq
deleted file mode 100644
index 0e8e846..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.1.fastq
+++ /dev/null
@@ -1,32 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1341 :Y:0:AGTTGCTTTCTGGCGA
-TGAAGAGTTTCTGGCACATAGGCACTCAAC
-+
-B7AACB;>C7A??4AB<B>B:':@CAAAAB
- at machine1:HiMom:abcdeACXX:9:1:3:1861 :Y:0:AGTTGCTTTCTGGCGA
-NGATTAATGAATAGAGTGAATAGTGTCTGA
-+
-%-07:::5.3<<7788529:<<530:9646
- at machine1:HiMom:abcdeACXX:9:1:3:699 :N:0:AGTTGCTTTCTGGCGA
-NTGTCTTCTTACACTATTTTTTTTAAAATC
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:1962 :Y:0:AGTTGCTTTCTGGCGA
-ACTAAATCCAAGAGCACATCAAAATGTTAA
-+
-B5;BBB@@8 at BAB9>BBBABACB@@B;@BB
- at machine1:HiMom:abcdeACXX:9:2:3:274 :Y:0:AGTTGCTTTCTGGCGA
-AGTGAAGTGCTTAGCACCTGGGCCAGCAGC
-+
-:57.:@@>96=@97>@=;=>;@;@=@9=9;
- at machine1:HiMom:abcdeACXX:9:2:3:640 :Y:0:AGTTGCTTTCTGGCGA
-AGATTAAAAAAAAATGACGTGACAAATTAA
-+
-=6CBC at CABCBBCBC@>@=@ABBCCBBBCC
- at machine1:HiMom:abcdeACXX:9:2:3:691 :Y:0:AGTTGCTTTCTGGCGA
-ATTTTCAAATCATAAATATGGATTGCTGTG
-+
-BBBABACBBA at ABBBBBBB727AB8+;B55
- at machine1:HiMom:abcdeACXX:9:2:3:72 :Y:0:AGTTGCTTTCTGGCGA
-CTAGTCTTTGACTTATATCAATTCAGTATT
-+
-BBC?ACCCCCB at CCCCCCCBCCCCCA@BCC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.barcode_1.fastq
deleted file mode 100644
index de4d00e..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.barcode_1.fastq
+++ /dev/null
@@ -1,32 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1341 :Y:0:AGTTGCTTTCTGGCGA
-AGATGCTT
-+
-B#######
- at machine1:HiMom:abcdeACXX:9:1:3:1861 :Y:0:AGTTGCTTTCTGGCGA
-AGTTGCTT
-+
-B9@><A<C
- at machine1:HiMom:abcdeACXX:9:1:3:699 :N:0:AGTTGCTTTCTGGCGA
-AGTTGCTT
-+
-98?>8>##
- at machine1:HiMom:abcdeACXX:9:2:3:1962 :Y:0:AGTTGCTTTCTGGCGA
-AGTTGCTT
-+
-A76 at 8=0=
- at machine1:HiMom:abcdeACXX:9:2:3:274 :Y:0:AGTTGCTTTCTGGCGA
-AGTTGCTT
-+
-@@??<?BC
- at machine1:HiMom:abcdeACXX:9:2:3:640 :Y:0:AGTTGCTTTCTGGCGA
-AGTTGCTT
-+
-A=BBB;<A
- at machine1:HiMom:abcdeACXX:9:2:3:691 :Y:0:AGTTGCTTTCTGGCGA
-AGTTGCTT
-+
-@=8@>@?A
- at machine1:HiMom:abcdeACXX:9:2:3:72 :Y:0:AGTTGCTTTCTGGCGA
-AGTTGCTT
-+
-BCBCA>BB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.barcode_2.fastq
deleted file mode 100644
index 17ca9ad..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/AGTTGCTTTCTGGCGA.barcode_2.fastq
+++ /dev/null
@@ -1,32 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1341 :Y:0:AGTTGCTTTCTGGCGA
-TCTGGCGA
-+
-B#######
- at machine1:HiMom:abcdeACXX:9:1:3:1861 :Y:0:AGTTGCTTTCTGGCGA
-TCTGGCGA
-+
-B9@><A<C
- at machine1:HiMom:abcdeACXX:9:1:3:699 :N:0:AGTTGCTTTCTGGCGA
-TCTGGCGA
-+
-98?>8>##
- at machine1:HiMom:abcdeACXX:9:2:3:1962 :Y:0:AGTTGCTTTCTGGCGA
-TCTGGCGA
-+
-A76 at 8=0=
- at machine1:HiMom:abcdeACXX:9:2:3:274 :Y:0:AGTTGCTTTCTGGCGA
-TCTGGCGA
-+
-@@??<?BC
- at machine1:HiMom:abcdeACXX:9:2:3:640 :Y:0:AGTTGCTTTCTGGCGA
-TCTGGCGA
-+
-A=BBB;<A
- at machine1:HiMom:abcdeACXX:9:2:3:691 :Y:0:AGTTGCTTTCTGGCGA
-TCTGGCGA
-+
-@=8@>@?A
- at machine1:HiMom:abcdeACXX:9:2:3:72 :Y:0:AGTTGCTTTCTGGCGA
-TCTGGCGA
-+
-BCBCA>BB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTT.1.fastq
deleted file mode 100644
index 2ae8e10..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTT.1.fastq
+++ /dev/null
@@ -1,12 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1867 :Y:0:ATTATGTT
-AGAAGCATTCTCAGAAACTTATTTGTGATG
-+
-BB>81>BB?->?;07>4;B at BABB?:<@=:
- at machine1:HiMom:abcdeACXX:7:1:3:347 :N:0:ATTATGTT
-NGTGGTGTGAGGTGTATCTGGGTCAGCAGG
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:889 :N:0:ATTATGTT
-NTTTTTATAACACCTCAGGCATCGTCAAAC
-+
-##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTT.barcode_1.fastq
deleted file mode 100644
index 7086d40..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTT.barcode_1.fastq
+++ /dev/null
@@ -1,12 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1867 :Y:0:ATTATGTT
-ATTATGTT
-+
-BBA at 79>B
- at machine1:HiMom:abcdeACXX:7:1:3:347 :N:0:ATTATGTT
-ATTATGTT
-+
-4A>?@)6<
- at machine1:HiMom:abcdeACXX:7:2:3:889 :N:0:ATTATGTT
-ATTATGTT
-+
-0A6=A<+A
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.1.fastq
deleted file mode 100644
index c01ab5c..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.1.fastq
+++ /dev/null
@@ -1,12 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1867 :Y:0:ATTATGTTTCGGAATG
-AGAAGCATTCTCAGAAACTTATTTGTGATG
-+
-BB>81>BB?->?;07>4;B at BABB?:<@=:
- at machine1:HiMom:abcdeACXX:9:1:3:347 :N:0:ATTATGTTTCGGAATG
-NGTGGTGTGAGGTGTATCTGGGTCAGCAGG
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:889 :N:0:ATTATGTTTCGGAATG
-NTTTTTATAACACCTCAGGCATCGTCAAAC
-+
-##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.barcode_1.fastq
deleted file mode 100644
index 5d34be5..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.barcode_1.fastq
+++ /dev/null
@@ -1,12 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1867 :Y:0:ATTATGTTTCGGAATG
-ATTATGTT
-+
-BBA at 79>B
- at machine1:HiMom:abcdeACXX:9:1:3:347 :N:0:ATTATGTTTCGGAATG
-ATTATGTT
-+
-4A>?@)6<
- at machine1:HiMom:abcdeACXX:9:2:3:889 :N:0:ATTATGTTTCGGAATG
-ATTATGTT
-+
-0A6=A<+A
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.barcode_2.fastq
deleted file mode 100644
index 84ebff8..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/ATTATGTTTCGGAATG.barcode_2.fastq
+++ /dev/null
@@ -1,12 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1867 :Y:0:ATTATGTTTCGGAATG
-TCGGAATG
-+
-BBA at 79>B
- at machine1:HiMom:abcdeACXX:9:1:3:347 :N:0:ATTATGTTTCGGAATG
-TCGGAATG
-+
-4A>?@)6<
- at machine1:HiMom:abcdeACXX:9:2:3:889 :N:0:ATTATGTTTCGGAATG
-TCGGAATG
-+
-0A6=A<+A
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCT.1.fastq
deleted file mode 100644
index 739eb58..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCT.1.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:1465 :N:0:CACATCCT
-NTTGTATTTCTGAAACCCCGAAGGGCATGG
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:3:683 :Y:0:CACATCCT
-NAAGTTTTTATTTATACGTAGAATTTATAC
-+
-%.611<<:;<98;<<<93993789<;<;9:
- at machine1:HiMom:abcdeACXX:7:1:3:751 :Y:0:CACATCCT
-CACTTTTATTCTTAAGTACCACCTTCTGGA
-+
-6A=CCCCBCCCAAA??@CC8@@CCBC:>)@
- at machine1:HiMom:abcdeACXX:7:2:2:1012 :Y:0:CACATCCT
-NAGAAATACCATTTGACCCACCAATCCCAT
-+
-%066:::9636963567778::88895-58
- at machine1:HiMom:abcdeACXX:7:2:2:1402 :N:0:CACATCCT
-NGGATGGCTTCCAGTATGGGAACCTTTTCA
-+
-%.5484-/858865/78/(/62'/886555
- at machine1:HiMom:abcdeACXX:7:2:3:1094 :Y:0:CACATCCT
-CATATGGTATCACCACTCAGATACATAAAG
-+
-AABB<:=1CBBCBC@?AA@)>CCBBCCB?=
- at machine1:HiMom:abcdeACXX:7:2:3:16 :Y:0:CACATCCT
-AGCTGGGCATGGTGATGCGCCCCTGTAATC
-+
-A;?;<<?@9?@@@@4=3)1 at 59??9<5.<2
- at machine1:HiMom:abcdeACXX:7:2:3:1712 :Y:0:CACATCCT
-AGTGCTGTGGCCTGGATGGATGTCAGGATT
-+
->91:?5:=5:77>305>/;=>1:<B9694;
- at machine1:HiMom:abcdeACXX:7:2:3:328 :N:0:CACATCCT
-AGCTTAATATAGCATAGCAGATAAGATTTG
-+
-(:*8>=,3:))<)?A<(8>###########
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCT.barcode_1.fastq
deleted file mode 100644
index 209867c..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCT.barcode_1.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:1465 :N:0:CACATCCT
-CACATCCT
-+
-<:@=BB@@
- at machine1:HiMom:abcdeACXX:7:1:3:683 :Y:0:CACATCCT
-CACATCCT
-+
-B at 8@B?CB
- at machine1:HiMom:abcdeACXX:7:1:3:751 :Y:0:CACATCCT
-CACATCCT
-+
-9 at CACCCC
- at machine1:HiMom:abcdeACXX:7:2:2:1012 :Y:0:CACATCCT
-CACATCCT
-+
-BB?BABBB
- at machine1:HiMom:abcdeACXX:7:2:2:1402 :N:0:CACATCCT
-CACATCCT
-+
-=@@BABCB
- at machine1:HiMom:abcdeACXX:7:2:3:1094 :Y:0:CACATCCT
-CACATCCT
-+
-ABCBC>:B
- at machine1:HiMom:abcdeACXX:7:2:3:16 :Y:0:CACATCCT
-CACATCCT
-+
-<<4@@='@
- at machine1:HiMom:abcdeACXX:7:2:3:1712 :Y:0:CACATCCT
-CACATCCT
-+
-BB>@@?=>
- at machine1:HiMom:abcdeACXX:7:2:3:328 :N:0:CACATCCT
-CAAATCCT
-+
-3<)):<(<
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.1.fastq
deleted file mode 100644
index ba8f8d3..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.1.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:1465 :N:0:CACATCCTTACTTAGC
-NTTGTATTTCTGAAACCCCGAAGGGCATGG
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:3:683 :Y:0:CACATCCTTACTTAGC
-NAAGTTTTTATTTATACGTAGAATTTATAC
-+
-%.611<<:;<98;<<<93993789<;<;9:
- at machine1:HiMom:abcdeACXX:9:1:3:751 :Y:0:CACATCCTTACTTAGC
-CACTTTTATTCTTAAGTACCACCTTCTGGA
-+
-6A=CCCCBCCCAAA??@CC8@@CCBC:>)@
- at machine1:HiMom:abcdeACXX:9:2:2:1012 :Y:0:CACATCCTTACTTAGC
-NAGAAATACCATTTGACCCACCAATCCCAT
-+
-%066:::9636963567778::88895-58
- at machine1:HiMom:abcdeACXX:9:2:2:1402 :N:0:CACATCCTTACTTAGC
-NGGATGGCTTCCAGTATGGGAACCTTTTCA
-+
-%.5484-/858865/78/(/62'/886555
- at machine1:HiMom:abcdeACXX:9:2:3:1094 :Y:0:CACATCCTTACTTAGC
-CATATGGTATCACCACTCAGATACATAAAG
-+
-AABB<:=1CBBCBC@?AA@)>CCBBCCB?=
- at machine1:HiMom:abcdeACXX:9:2:3:16 :Y:0:CACATCCTTACTTAGC
-AGCTGGGCATGGTGATGCGCCCCTGTAATC
-+
-A;?;<<?@9?@@@@4=3)1 at 59??9<5.<2
- at machine1:HiMom:abcdeACXX:9:2:3:1712 :Y:0:CACATCCTTACTTAGC
-AGTGCTGTGGCCTGGATGGATGTCAGGATT
-+
->91:?5:=5:77>305>/;=>1:<B9694;
- at machine1:HiMom:abcdeACXX:9:2:3:328 :N:0:CACATCCTTACTTAGC
-AGCTTAATATAGCATAGCAGATAAGATTTG
-+
-(:*8>=,3:))<)?A<(8>###########
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.barcode_1.fastq
deleted file mode 100644
index 1f3c848..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.barcode_1.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:1465 :N:0:CACATCCTTACTTAGC
-CACATCCT
-+
-<:@=BB@@
- at machine1:HiMom:abcdeACXX:9:1:3:683 :Y:0:CACATCCTTACTTAGC
-CACATCCT
-+
-B at 8@B?CB
- at machine1:HiMom:abcdeACXX:9:1:3:751 :Y:0:CACATCCTTACTTAGC
-CACATCCT
-+
-9 at CACCCC
- at machine1:HiMom:abcdeACXX:9:2:2:1012 :Y:0:CACATCCTTACTTAGC
-CACATCCT
-+
-BB?BABBB
- at machine1:HiMom:abcdeACXX:9:2:2:1402 :N:0:CACATCCTTACTTAGC
-CACATCCT
-+
-=@@BABCB
- at machine1:HiMom:abcdeACXX:9:2:3:1094 :Y:0:CACATCCTTACTTAGC
-CACATCCT
-+
-ABCBC>:B
- at machine1:HiMom:abcdeACXX:9:2:3:16 :Y:0:CACATCCTTACTTAGC
-CACATCCT
-+
-<<4@@='@
- at machine1:HiMom:abcdeACXX:9:2:3:1712 :Y:0:CACATCCTTACTTAGC
-CACATCCT
-+
-BB>@@?=>
- at machine1:HiMom:abcdeACXX:9:2:3:328 :N:0:CACATCCTTACTTAGC
-CAAATCCT
-+
-3<)):<(<
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.barcode_2.fastq
deleted file mode 100644
index 7d7b0f8..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CACATCCTTACTTAGC.barcode_2.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:1465 :N:0:CACATCCTTACTTAGC
-TACTTAGC
-+
-<:@=BB@@
- at machine1:HiMom:abcdeACXX:9:1:3:683 :Y:0:CACATCCTTACTTAGC
-TACTTAGC
-+
-B at 8@B?CB
- at machine1:HiMom:abcdeACXX:9:1:3:751 :Y:0:CACATCCTTACTTAGC
-TACTTAGC
-+
-9 at CACCCC
- at machine1:HiMom:abcdeACXX:9:2:2:1012 :Y:0:CACATCCTTACTTAGC
-TACTTAGC
-+
-BB?BABBB
- at machine1:HiMom:abcdeACXX:9:2:2:1402 :N:0:CACATCCTTACTTAGC
-TACTTAGC
-+
-=@@BABCB
- at machine1:HiMom:abcdeACXX:9:2:3:1094 :Y:0:CACATCCTTACTTAGC
-TACTTAGC
-+
-ABCBC>:B
- at machine1:HiMom:abcdeACXX:9:2:3:16 :Y:0:CACATCCTTACTTAGC
-TACTTAGC
-+
-<<4@@='@
- at machine1:HiMom:abcdeACXX:9:2:3:1712 :Y:0:CACATCCTTACTTAGC
-TACTTAGC
-+
-BB>@@?=>
- at machine1:HiMom:abcdeACXX:9:2:3:328 :N:0:CACATCCTTACTTAGC
-TACTTAGC
-+
-3<)):<(<
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCC.1.fastq
deleted file mode 100644
index e13284a..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCC.1.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:1336 :Y:0:CAGGAGCC
-NAAGTCTAAAATTATCTTGAAGTAAAAAGT
-+
-%.75795:89<<<<4-7::58579<<<8.7
- at machine1:HiMom:abcdeACXX:7:1:2:1878 :Y:0:CAGGAGCC
-NAATACTGAGATGTATTTAAGGCTGACACT
-+
-%.9:957/3767079:::7:5/57::9999
- at machine1:HiMom:abcdeACXX:7:1:2:425 :Y:0:CAGGAGCC
-NAATATATGCAAGACTCCTGTTATTAGAAA
-+
-%099:99055:726<<9<9977::9:::<<
- at machine1:HiMom:abcdeACXX:7:1:2:802 :Y:0:CAGGAGCC
-NAAGTTAATTGTGTATTATTAACATCATTC
-+
-%/627<<<<444358<<::::989957972
- at machine1:HiMom:abcdeACXX:7:1:3:1927 :N:0:CAGGAGCC
-CACATCACCTTCTACTACATTTGAAATTCT
-+
-BCACA8B>C=BA?C8BC:'8=-5@)@=0=B
- at machine1:HiMom:abcdeACXX:7:2:2:303 :N:0:CAGGAGCC
-NAGATCTTGTCTTTCAATCTTTTTAAATTC
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:2:953 :N:0:CAGGAGCC
-NGTTTAGTACATACTAGGTTTCACCAAATT
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:151 :Y:0:CAGGAGCC
-AGAGAACAGATAGGTCTGTCAGGGCTGACC
-+
-?>=99B>BA?B>)?;5AB;89;=6??<73>
- at machine1:HiMom:abcdeACXX:7:2:3:99 :N:0:CAGGAGCC
-CATATCTGTGTTATTTTAGCATAAATTTGA
-+
-1 at +@31?('4(A;73>)?73))@))@C?##
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCC.barcode_1.fastq
deleted file mode 100644
index 4779a34..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCC.barcode_1.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:1336 :Y:0:CAGGAGCC
-CAGGAGCC
-+
-7 at 9=B=7@
- at machine1:HiMom:abcdeACXX:7:1:2:1878 :Y:0:CAGGAGCC
-CAGGAGCC
-+
-B<81<=7;
- at machine1:HiMom:abcdeACXX:7:1:2:425 :Y:0:CAGGAGCC
-CAGGAGCC
-+
-AA@@=9;<
- at machine1:HiMom:abcdeACXX:7:1:2:802 :Y:0:CAGGAGCC
-CAGGAGCC
-+
-=>0>?7>#
- at machine1:HiMom:abcdeACXX:7:1:3:1927 :N:0:CAGGAGCC
-CAGGAGCC
-+
-B@<@@=@?
- at machine1:HiMom:abcdeACXX:7:2:2:303 :N:0:CAGGAGCC
-CAGGAGCC
-+
-A>*@@9##
- at machine1:HiMom:abcdeACXX:7:2:2:953 :N:0:CAGGAGCC
-CAGGAACC
-+
-5(:9;';;
- at machine1:HiMom:abcdeACXX:7:2:3:151 :Y:0:CAGGAGCC
-CAGGAGCC
-+
- at A8/;A==
- at machine1:HiMom:abcdeACXX:7:2:3:99 :N:0:CAGGAGCC
-CAGGAGCG
-+
-(1;A;###
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.1.fastq
deleted file mode 100644
index ec27872..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.1.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:1336 :Y:0:CAGGAGCCGTATAACA
-NAAGTCTAAAATTATCTTGAAGTAAAAAGT
-+
-%.75795:89<<<<4-7::58579<<<8.7
- at machine1:HiMom:abcdeACXX:9:1:2:1878 :Y:0:CAGGAGCCGTATAACA
-NAATACTGAGATGTATTTAAGGCTGACACT
-+
-%.9:957/3767079:::7:5/57::9999
- at machine1:HiMom:abcdeACXX:9:1:2:425 :Y:0:CAGGAGCCGTATAACA
-NAATATATGCAAGACTCCTGTTATTAGAAA
-+
-%099:99055:726<<9<9977::9:::<<
- at machine1:HiMom:abcdeACXX:9:1:2:802 :Y:0:CAGGAGCCGTATAACA
-NAAGTTAATTGTGTATTATTAACATCATTC
-+
-%/627<<<<444358<<::::989957972
- at machine1:HiMom:abcdeACXX:9:1:3:1927 :N:0:CAGGAGCCGTATAACA
-CACATCACCTTCTACTACATTTGAAATTCT
-+
-BCACA8B>C=BA?C8BC:'8=-5@)@=0=B
- at machine1:HiMom:abcdeACXX:9:2:2:303 :N:0:CAGGAGCCGTATAACA
-NAGATCTTGTCTTTCAATCTTTTTAAATTC
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:2:953 :N:0:CAGGAGCCGTATAACA
-NGTTTAGTACATACTAGGTTTCACCAAATT
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:151 :Y:0:CAGGAGCCGTATAACA
-AGAGAACAGATAGGTCTGTCAGGGCTGACC
-+
-?>=99B>BA?B>)?;5AB;89;=6??<73>
- at machine1:HiMom:abcdeACXX:9:2:3:99 :N:0:CAGGAGCCGTATAACA
-CATATCTGTGTTATTTTAGCATAAATTTGA
-+
-1 at +@31?('4(A;73>)?73))@))@C?##
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.barcode_1.fastq
deleted file mode 100644
index 5ad708c..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.barcode_1.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:1336 :Y:0:CAGGAGCCGTATAACA
-CAGGAGCC
-+
-7 at 9=B=7@
- at machine1:HiMom:abcdeACXX:9:1:2:1878 :Y:0:CAGGAGCCGTATAACA
-CAGGAGCC
-+
-B<81<=7;
- at machine1:HiMom:abcdeACXX:9:1:2:425 :Y:0:CAGGAGCCGTATAACA
-CAGGAGCC
-+
-AA@@=9;<
- at machine1:HiMom:abcdeACXX:9:1:2:802 :Y:0:CAGGAGCCGTATAACA
-CAGGAGCC
-+
-=>0>?7>#
- at machine1:HiMom:abcdeACXX:9:1:3:1927 :N:0:CAGGAGCCGTATAACA
-CAGGAGCC
-+
-B@<@@=@?
- at machine1:HiMom:abcdeACXX:9:2:2:303 :N:0:CAGGAGCCGTATAACA
-CAGGAGCC
-+
-A>*@@9##
- at machine1:HiMom:abcdeACXX:9:2:2:953 :N:0:CAGGAGCCGTATAACA
-CAGGAACC
-+
-5(:9;';;
- at machine1:HiMom:abcdeACXX:9:2:3:151 :Y:0:CAGGAGCCGTATAACA
-CAGGAGCC
-+
- at A8/;A==
- at machine1:HiMom:abcdeACXX:9:2:3:99 :N:0:CAGGAGCCGTATAACA
-CAGGAGCG
-+
-(1;A;###
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.barcode_2.fastq
deleted file mode 100644
index f2361f4..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CAGGAGCCGTATAACA.barcode_2.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:1336 :Y:0:CAGGAGCCGTATAACA
-GTATAACA
-+
-7 at 9=B=7@
- at machine1:HiMom:abcdeACXX:9:1:2:1878 :Y:0:CAGGAGCCGTATAACA
-GTATAACA
-+
-B<81<=7;
- at machine1:HiMom:abcdeACXX:9:1:2:425 :Y:0:CAGGAGCCGTATAACA
-GTATAACA
-+
-AA@@=9;<
- at machine1:HiMom:abcdeACXX:9:1:2:802 :Y:0:CAGGAGCCGTATAACA
-GTATAACA
-+
-=>0>?7>#
- at machine1:HiMom:abcdeACXX:9:1:3:1927 :N:0:CAGGAGCCGTATAACA
-GTATAACA
-+
-B@<@@=@?
- at machine1:HiMom:abcdeACXX:9:2:2:303 :N:0:CAGGAGCCGTATAACA
-GTATAACA
-+
-A>*@@9##
- at machine1:HiMom:abcdeACXX:9:2:2:953 :N:0:CAGGAGCCGTATAACA
-GTATAACA
-+
-5(:9;';;
- at machine1:HiMom:abcdeACXX:9:2:3:151 :Y:0:CAGGAGCCGTATAACA
-GTATAACA
-+
- at A8/;A==
- at machine1:HiMom:abcdeACXX:9:2:3:99 :N:0:CAGGAGCCGTATAACA
-GTATAACA
-+
-(1;A;###
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGA.1.fastq
deleted file mode 100644
index 27cd699..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGA.1.fastq
+++ /dev/null
@@ -1,48 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:119 :Y:0:CATAGCGA
-NGATTGGAATCAACCCGAGTGGAATGGAAT
-+
-%06:75577786742-6-66///288517#
- at machine1:HiMom:abcdeACXX:7:1:2:1895 :Y:0:CATAGCGA
-NAAAACTTCTAAGTAATCATGAAGCTCTGC
-+
-%.7;9:::::<84:99989:<678<:6776
- at machine1:HiMom:abcdeACXX:7:1:2:190 :Y:0:CATAGCGA
-NATAAGTGTATATTTATTTGTACCATGACA
-+
-%-;8694777:8;;9<:<<<<99998:996
- at machine1:HiMom:abcdeACXX:7:1:3:1513 :Y:0:CATAGCGA
-CACGCCACTGCGCCTGCAGCCTGGGCAATA
-+
-B=55 at AA6@=;>;>/;@@9@<>52<?@ABA
- at machine1:HiMom:abcdeACXX:7:1:3:277 :N:0:CATAGCGA
-NGATGGGAAGGCCCCGGCCTGGGGAGGTGG
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:2:463 :N:0:CATAGCGA
-NGTGCTTGGGGGCGTCTGTGTTGATGCGTG
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:2:611 :N:0:CATAGCGA
-NGGAACCAGGCAGGGCCACACACAGGTAGC
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:1016 :Y:0:CATAGCGA
-TGGCTCTGTCCTAATATCTTATTCTTACAA
-+
-<3=@BBA?@<=BBCC@>6>BBBBB at B?@AC
- at machine1:HiMom:abcdeACXX:7:2:3:1898 :N:0:CATAGCGA
-NTTGAATTGCTGGACTTCAATGTGTGTGGG
-+
-%08868:64680+0-5:8765255647522
- at machine1:HiMom:abcdeACXX:7:2:3:2013 :N:0:CATAGCGA
-AGCAGAAGCCTGCTGTGGGAACACTCAGTC
-+
-B?B###########################
- at machine1:HiMom:abcdeACXX:7:2:3:399 :Y:0:CATAGCGA
-AGGGTATGTAAACCGAGTTTTGCGGGGGAT
-+
-A@@@>BBBBBAA>@;?B?BBAA>@:@:?AB
- at machine1:HiMom:abcdeACXX:7:2:3:983 :Y:0:CATAGCGA
-TGTTTTTTATTTTAACAGATGAAGTACCAA
-+
-B=BCCCCCCCCCCCA>AACCBCC at AC@>BC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGA.barcode_1.fastq
deleted file mode 100644
index 6ccf796..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGA.barcode_1.fastq
+++ /dev/null
@@ -1,48 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:119 :Y:0:CATAGCGA
-CATAGCGA
-+
-?@>=;<CB
- at machine1:HiMom:abcdeACXX:7:1:2:1895 :Y:0:CATAGCGA
-CATAGCGA
-+
-?@CC@>BC
- at machine1:HiMom:abcdeACXX:7:1:2:190 :Y:0:CATAGCGA
-CATAGCGA
-+
-AACC==@B
- at machine1:HiMom:abcdeACXX:7:1:3:1513 :Y:0:CATAGCGA
-CATAGCGA
-+
-5 at B=37 at B
- at machine1:HiMom:abcdeACXX:7:1:3:277 :N:0:CATAGCGA
-CATAGCGA
-+
-BA?;3>B=
- at machine1:HiMom:abcdeACXX:7:2:2:463 :N:0:CATAGCGA
-CNTAGCGA
-+
-:%98.(>9
- at machine1:HiMom:abcdeACXX:7:2:2:611 :N:0:CATAGCGA
-CATAGCGA
-+
-8 at CCB=;@
- at machine1:HiMom:abcdeACXX:7:2:3:1016 :Y:0:CATAGCGA
-CATAGCGA
-+
->@C@@1 at C
- at machine1:HiMom:abcdeACXX:7:2:3:1898 :N:0:CATAGCGA
-CATAGCGA
-+
-BBCB@=B@
- at machine1:HiMom:abcdeACXX:7:2:3:2013 :N:0:CATAGCGA
-CATAGCGA
-+
-7BCB<@?<
- at machine1:HiMom:abcdeACXX:7:2:3:399 :Y:0:CATAGCGA
-CATAGCGA
-+
-=BB@==A@
- at machine1:HiMom:abcdeACXX:7:2:3:983 :Y:0:CATAGCGA
-CATAGCGA
-+
-ACCC@?A?
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.1.fastq
deleted file mode 100644
index 7b2474a..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.1.fastq
+++ /dev/null
@@ -1,48 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:119 :Y:0:CATAGCGAGGTCCAGA
-NGATTGGAATCAACCCGAGTGGAATGGAAT
-+
-%06:75577786742-6-66///288517#
- at machine1:HiMom:abcdeACXX:9:1:2:1895 :Y:0:CATAGCGAGGTCCAGA
-NAAAACTTCTAAGTAATCATGAAGCTCTGC
-+
-%.7;9:::::<84:99989:<678<:6776
- at machine1:HiMom:abcdeACXX:9:1:2:190 :Y:0:CATAGCGAGGTCCAGA
-NATAAGTGTATATTTATTTGTACCATGACA
-+
-%-;8694777:8;;9<:<<<<99998:996
- at machine1:HiMom:abcdeACXX:9:1:3:1513 :Y:0:CATAGCGAGGTCCAGA
-CACGCCACTGCGCCTGCAGCCTGGGCAATA
-+
-B=55 at AA6@=;>;>/;@@9@<>52<?@ABA
- at machine1:HiMom:abcdeACXX:9:1:3:277 :N:0:CATAGCGAGGTCCAGA
-NGATGGGAAGGCCCCGGCCTGGGGAGGTGG
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:2:463 :N:0:CATAGCGAGGTCCAGA
-NGTGCTTGGGGGCGTCTGTGTTGATGCGTG
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:2:611 :N:0:CATAGCGAGGTCCAGA
-NGGAACCAGGCAGGGCCACACACAGGTAGC
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:1016 :Y:0:CATAGCGAGGTCCAGA
-TGGCTCTGTCCTAATATCTTATTCTTACAA
-+
-<3=@BBA?@<=BBCC@>6>BBBBB at B?@AC
- at machine1:HiMom:abcdeACXX:9:2:3:1898 :N:0:CATAGCGAGGTCCAGA
-NTTGAATTGCTGGACTTCAATGTGTGTGGG
-+
-%08868:64680+0-5:8765255647522
- at machine1:HiMom:abcdeACXX:9:2:3:2013 :N:0:CATAGCGAGGTCCAGA
-AGCAGAAGCCTGCTGTGGGAACACTCAGTC
-+
-B?B###########################
- at machine1:HiMom:abcdeACXX:9:2:3:399 :Y:0:CATAGCGAGGTCCAGA
-AGGGTATGTAAACCGAGTTTTGCGGGGGAT
-+
-A@@@>BBBBBAA>@;?B?BBAA>@:@:?AB
- at machine1:HiMom:abcdeACXX:9:2:3:983 :Y:0:CATAGCGAGGTCCAGA
-TGTTTTTTATTTTAACAGATGAAGTACCAA
-+
-B=BCCCCCCCCCCCA>AACCBCC at AC@>BC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.barcode_1.fastq
deleted file mode 100644
index a18a3f0..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.barcode_1.fastq
+++ /dev/null
@@ -1,48 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:119 :Y:0:CATAGCGAGGTCCAGA
-CATAGCGA
-+
-?@>=;<CB
- at machine1:HiMom:abcdeACXX:9:1:2:1895 :Y:0:CATAGCGAGGTCCAGA
-CATAGCGA
-+
-?@CC@>BC
- at machine1:HiMom:abcdeACXX:9:1:2:190 :Y:0:CATAGCGAGGTCCAGA
-CATAGCGA
-+
-AACC==@B
- at machine1:HiMom:abcdeACXX:9:1:3:1513 :Y:0:CATAGCGAGGTCCAGA
-CATAGCGA
-+
-5 at B=37 at B
- at machine1:HiMom:abcdeACXX:9:1:3:277 :N:0:CATAGCGAGGTCCAGA
-CATAGCGA
-+
-BA?;3>B=
- at machine1:HiMom:abcdeACXX:9:2:2:463 :N:0:CATAGCGAGGTCCAGA
-CNTAGCGA
-+
-:%98.(>9
- at machine1:HiMom:abcdeACXX:9:2:2:611 :N:0:CATAGCGAGGTCCAGA
-CATAGCGA
-+
-8 at CCB=;@
- at machine1:HiMom:abcdeACXX:9:2:3:1016 :Y:0:CATAGCGAGGTCCAGA
-CATAGCGA
-+
->@C@@1 at C
- at machine1:HiMom:abcdeACXX:9:2:3:1898 :N:0:CATAGCGAGGTCCAGA
-CATAGCGA
-+
-BBCB@=B@
- at machine1:HiMom:abcdeACXX:9:2:3:2013 :N:0:CATAGCGAGGTCCAGA
-CATAGCGA
-+
-7BCB<@?<
- at machine1:HiMom:abcdeACXX:9:2:3:399 :Y:0:CATAGCGAGGTCCAGA
-CATAGCGA
-+
-=BB@==A@
- at machine1:HiMom:abcdeACXX:9:2:3:983 :Y:0:CATAGCGAGGTCCAGA
-CATAGCGA
-+
-ACCC@?A?
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.barcode_2.fastq
deleted file mode 100644
index 4c51eff..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATAGCGAGGTCCAGA.barcode_2.fastq
+++ /dev/null
@@ -1,48 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:119 :Y:0:CATAGCGAGGTCCAGA
-GGTCCAGA
-+
-?@>=;<CB
- at machine1:HiMom:abcdeACXX:9:1:2:1895 :Y:0:CATAGCGAGGTCCAGA
-GGTCCAGA
-+
-?@CC@>BC
- at machine1:HiMom:abcdeACXX:9:1:2:190 :Y:0:CATAGCGAGGTCCAGA
-GGTCCAGA
-+
-AACC==@B
- at machine1:HiMom:abcdeACXX:9:1:3:1513 :Y:0:CATAGCGAGGTCCAGA
-GGTCCAGA
-+
-5 at B=37 at B
- at machine1:HiMom:abcdeACXX:9:1:3:277 :N:0:CATAGCGAGGTCCAGA
-GGTCCAGA
-+
-BA?;3>B=
- at machine1:HiMom:abcdeACXX:9:2:2:463 :N:0:CATAGCGAGGTCCAGA
-GGTCCAGA
-+
-:%98.(>9
- at machine1:HiMom:abcdeACXX:9:2:2:611 :N:0:CATAGCGAGGTCCAGA
-GGTCCAGA
-+
-8 at CCB=;@
- at machine1:HiMom:abcdeACXX:9:2:3:1016 :Y:0:CATAGCGAGGTCCAGA
-GGTCCAGA
-+
->@C@@1 at C
- at machine1:HiMom:abcdeACXX:9:2:3:1898 :N:0:CATAGCGAGGTCCAGA
-GGTCCAGA
-+
-BBCB@=B@
- at machine1:HiMom:abcdeACXX:9:2:3:2013 :N:0:CATAGCGAGGTCCAGA
-GGTCCAGA
-+
-7BCB<@?<
- at machine1:HiMom:abcdeACXX:9:2:3:399 :Y:0:CATAGCGAGGTCCAGA
-GGTCCAGA
-+
-=BB@==A@
- at machine1:HiMom:abcdeACXX:9:2:3:983 :Y:0:CATAGCGAGGTCCAGA
-GGTCCAGA
-+
-ACCC@?A?
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTA.1.fastq
deleted file mode 100644
index fae42f1..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTA.1.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1525 :Y:0:CATGCTTA
-AGAAAATATCTGCATAGATGTGTTGAAGTC
-+
-BBBBBBAA@@?<3<:B=?B@@A at BAAA@=A
- at machine1:HiMom:abcdeACXX:7:2:2:679 :N:0:CATGCTTA
-NCTCTGTCTCAAAAAATAAAAATAAAAATA
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:1775 :Y:0:CATGCTTA
-NAATCCGACAATTATGTGTCTTGGAGTTGC
-+
-%.22301499988866456250*.424955
- at machine1:HiMom:abcdeACXX:7:2:3:584 :Y:0:CATGCTTA
-AAAGTCCTGGGATTACAGGCATGAGCCACT
-+
-ABC2<@=>8;6=>?>3>-3<>B9@/=9A;<
- at machine1:HiMom:abcdeACXX:7:2:3:932 :Y:0:CATGCTTA
-AGAAAGACAGACAGACAAACTGACTCTCAG
-+
-@>@C at 4A=?2 at B@.>ABABBBB>=A:;>@#
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTA.barcode_1.fastq
deleted file mode 100644
index ebfad4f..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTA.barcode_1.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1525 :Y:0:CATGCTTA
-CATGCTTA
-+
-BBB;BBBB
- at machine1:HiMom:abcdeACXX:7:2:2:679 :N:0:CATGCTTA
-CATGCTTA
-+
-5?@??8<@
- at machine1:HiMom:abcdeACXX:7:2:3:1775 :Y:0:CATGCTTA
-CATGCTTA
-+
-;<39<;@@
- at machine1:HiMom:abcdeACXX:7:2:3:584 :Y:0:CATGCTTA
-CATGCTTA
-+
->A??<CCC
- at machine1:HiMom:abcdeACXX:7:2:3:932 :Y:0:CATGCTTA
-CATGCTTA
-+
-=C at AACCB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.1.fastq
deleted file mode 100644
index eea26aa..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.1.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1525 :Y:0:CATGCTTAGCACATCT
-AGAAAATATCTGCATAGATGTGTTGAAGTC
-+
-BBBBBBAA@@?<3<:B=?B@@A at BAAA@=A
- at machine1:HiMom:abcdeACXX:9:2:2:679 :N:0:CATGCTTAGCACATCT
-NCTCTGTCTCAAAAAATAAAAATAAAAATA
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:1775 :Y:0:CATGCTTAGCACATCT
-NAATCCGACAATTATGTGTCTTGGAGTTGC
-+
-%.22301499988866456250*.424955
- at machine1:HiMom:abcdeACXX:9:2:3:584 :Y:0:CATGCTTAGCACATCT
-AAAGTCCTGGGATTACAGGCATGAGCCACT
-+
-ABC2<@=>8;6=>?>3>-3<>B9@/=9A;<
- at machine1:HiMom:abcdeACXX:9:2:3:932 :Y:0:CATGCTTAGCACATCT
-AGAAAGACAGACAGACAAACTGACTCTCAG
-+
-@>@C at 4A=?2 at B@.>ABABBBB>=A:;>@#
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.barcode_1.fastq
deleted file mode 100644
index c325e36..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.barcode_1.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1525 :Y:0:CATGCTTAGCACATCT
-CATGCTTA
-+
-BBB;BBBB
- at machine1:HiMom:abcdeACXX:9:2:2:679 :N:0:CATGCTTAGCACATCT
-CATGCTTA
-+
-5?@??8<@
- at machine1:HiMom:abcdeACXX:9:2:3:1775 :Y:0:CATGCTTAGCACATCT
-CATGCTTA
-+
-;<39<;@@
- at machine1:HiMom:abcdeACXX:9:2:3:584 :Y:0:CATGCTTAGCACATCT
-CATGCTTA
-+
->A??<CCC
- at machine1:HiMom:abcdeACXX:9:2:3:932 :Y:0:CATGCTTAGCACATCT
-CATGCTTA
-+
-=C at AACCB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.barcode_2.fastq
deleted file mode 100644
index b7db855..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CATGCTTAGCACATCT.barcode_2.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1525 :Y:0:CATGCTTAGCACATCT
-GCACATCT
-+
-BBB;BBBB
- at machine1:HiMom:abcdeACXX:9:2:2:679 :N:0:CATGCTTAGCACATCT
-GCACATCT
-+
-5?@??8<@
- at machine1:HiMom:abcdeACXX:9:2:3:1775 :Y:0:CATGCTTAGCACATCT
-GCACATCT
-+
-;<39<;@@
- at machine1:HiMom:abcdeACXX:9:2:3:584 :Y:0:CATGCTTAGCACATCT
-GCACATCT
-+
->A??<CCC
- at machine1:HiMom:abcdeACXX:9:2:3:932 :Y:0:CATGCTTAGCACATCT
-GCACATCT
-+
-=C at AACCB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAG.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAG.1.fastq
deleted file mode 100644
index 36ae850..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAG.1.fastq
+++ /dev/null
@@ -1,44 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1688 :Y:0:CCAGTTAG
-NCCTTCTTTACACACTGAGGAACTTAACCT
-+
-%..99999:9:7753564-357708:9777
- at machine1:HiMom:abcdeACXX:7:1:3:583 :Y:0:CCAGTTAG
-GGCTTACACAGTCAAACTGGAGAGAAGTAG
-+
-(56=CCCC=B8BABBBC@:=BBAAA?, at A<
- at machine1:HiMom:abcdeACXX:7:1:3:996 :Y:0:CCAGTTAG
-AAGGGAATTCTTGGACTTGATTAAATTGGT
-+
-=C9?6?BBB?6;6>;>A?BA?@2<@BB:##
- at machine1:HiMom:abcdeACXX:7:2:2:1671 :N:0:CCAGTTAG
-NGGGAATTACATGGAAAATGATCAAAGGAA
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:2:1723 :N:0:CCAGTTAG
-NGAAGCTGACATTACAGGTTTCAGACACCA
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:2:255 :Y:0:CCAGTTAG
-NGGGTCCAAATAAGAGAAGGAGAAAAACAG
-+
-%00412036893057554167465;98977
- at machine1:HiMom:abcdeACXX:7:2:3:112 :Y:0:CCAGTTAG
-NATGGAGTCTTGCTCTATTGCCCAGGCTGG
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:1179 :N:0:CCAGTTAG
-ATTTAATAAATAAAGCAACCTGACAACTGA
-+
- at 15;'88?A at 1/3='106/9A7.*:/08##
- at machine1:HiMom:abcdeACXX:7:2:3:1387 :N:0:CCAGTTAG
-NCGATTATGACTCTGAGAGAAAGTAGGGCA
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:1484 :Y:0:CCAGTTAG
-CATCAACCTGTCACAAAATGACAAAACCTA
-+
-=A at 5@CB?B5@?B@@BBBB?ABCCBC at ABB
- at machine1:HiMom:abcdeACXX:7:2:3:1576 :N:0:CCAGTTAG
-NGAAACCACGTGCCCATTTTCAGTTCTGGT
-+
-%*/%.55663117868788787/765####
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAG.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAG.barcode_1.fastq
deleted file mode 100644
index 9de336b..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAG.barcode_1.fastq
+++ /dev/null
@@ -1,44 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1688 :Y:0:CCAGTTAG
-CCAGTTAG
-+
->@==;CA=
- at machine1:HiMom:abcdeACXX:7:1:3:583 :Y:0:CCAGTTAG
-CCAGTTAG
-+
-=>93;CA>
- at machine1:HiMom:abcdeACXX:7:1:3:996 :Y:0:CCAGTTAG
-CCAGTTAG
-+
-A at 5=>C<#
- at machine1:HiMom:abcdeACXX:7:2:2:1671 :N:0:CCAGTTAG
-CCAGTTAG
-+
-@>>B;BA9
- at machine1:HiMom:abcdeACXX:7:2:2:1723 :N:0:CCAGTTAG
-CCAATTAG
-+
- at A######
- at machine1:HiMom:abcdeACXX:7:2:2:255 :Y:0:CCAGTTAG
-CCAGTTAG
-+
-A<?CAA@;
- at machine1:HiMom:abcdeACXX:7:2:3:112 :Y:0:CCAGTTAG
-CCAGTTAG
-+
-B@<CAC at 6
- at machine1:HiMom:abcdeACXX:7:2:3:1179 :N:0:CCAGTTAG
-CCAGTTAG
-+
-);;9@@;#
- at machine1:HiMom:abcdeACXX:7:2:3:1387 :N:0:CCAGTTAG
-CCAGTTAG
-+
-;+B,232A
- at machine1:HiMom:abcdeACXX:7:2:3:1484 :Y:0:CCAGTTAG
-CCAGTTAG
-+
->BAAAC@<
- at machine1:HiMom:abcdeACXX:7:2:3:1576 :N:0:CCAGTTAG
-CCAGTTAG
-+
-:B?=CACA
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.1.fastq
deleted file mode 100644
index 8bb1096..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.1.fastq
+++ /dev/null
@@ -1,44 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1688 :Y:0:CCAGTTAGGCACACGA
-NCCTTCTTTACACACTGAGGAACTTAACCT
-+
-%..99999:9:7753564-357708:9777
- at machine1:HiMom:abcdeACXX:9:1:3:583 :Y:0:CCAGTTAGGCACACGA
-GGCTTACACAGTCAAACTGGAGAGAAGTAG
-+
-(56=CCCC=B8BABBBC@:=BBAAA?, at A<
- at machine1:HiMom:abcdeACXX:9:1:3:996 :Y:0:CCAGTTAGGCACACGA
-AAGGGAATTCTTGGACTTGATTAAATTGGT
-+
-=C9?6?BBB?6;6>;>A?BA?@2<@BB:##
- at machine1:HiMom:abcdeACXX:9:2:2:1671 :N:0:CCAGTTAGGCACACGA
-NGGGAATTACATGGAAAATGATCAAAGGAA
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:2:1723 :N:0:CCAGTTAGGCACACGA
-NGAAGCTGACATTACAGGTTTCAGACACCA
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:2:255 :Y:0:CCAGTTAGGCACACGA
-NGGGTCCAAATAAGAGAAGGAGAAAAACAG
-+
-%00412036893057554167465;98977
- at machine1:HiMom:abcdeACXX:9:2:3:112 :Y:0:CCAGTTAGGCACACGA
-NATGGAGTCTTGCTCTATTGCCCAGGCTGG
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:1179 :N:0:CCAGTTAGGCACACGA
-ATTTAATAAATAAAGCAACCTGACAACTGA
-+
- at 15;'88?A at 1/3='106/9A7.*:/08##
- at machine1:HiMom:abcdeACXX:9:2:3:1387 :N:0:CCAGTTAGGCACACGA
-NCGATTATGACTCTGAGAGAAAGTAGGGCA
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:1484 :Y:0:CCAGTTAGGCACACGA
-CATCAACCTGTCACAAAATGACAAAACCTA
-+
-=A at 5@CB?B5@?B@@BBBB?ABCCBC at ABB
- at machine1:HiMom:abcdeACXX:9:2:3:1576 :N:0:CCAGTTAGGCACACGA
-NGAAACCACGTGCCCATTTTCAGTTCTGGT
-+
-%*/%.55663117868788787/765####
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.barcode_1.fastq
deleted file mode 100644
index 9891cd6..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.barcode_1.fastq
+++ /dev/null
@@ -1,44 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1688 :Y:0:CCAGTTAGGCACACGA
-CCAGTTAG
-+
->@==;CA=
- at machine1:HiMom:abcdeACXX:9:1:3:583 :Y:0:CCAGTTAGGCACACGA
-CCAGTTAG
-+
-=>93;CA>
- at machine1:HiMom:abcdeACXX:9:1:3:996 :Y:0:CCAGTTAGGCACACGA
-CCAGTTAG
-+
-A at 5=>C<#
- at machine1:HiMom:abcdeACXX:9:2:2:1671 :N:0:CCAGTTAGGCACACGA
-CCAGTTAG
-+
-@>>B;BA9
- at machine1:HiMom:abcdeACXX:9:2:2:1723 :N:0:CCAGTTAGGCACACGA
-CCAATTAG
-+
- at A######
- at machine1:HiMom:abcdeACXX:9:2:2:255 :Y:0:CCAGTTAGGCACACGA
-CCAGTTAG
-+
-A<?CAA@;
- at machine1:HiMom:abcdeACXX:9:2:3:112 :Y:0:CCAGTTAGGCACACGA
-CCAGTTAG
-+
-B@<CAC at 6
- at machine1:HiMom:abcdeACXX:9:2:3:1179 :N:0:CCAGTTAGGCACACGA
-CCAGTTAG
-+
-);;9@@;#
- at machine1:HiMom:abcdeACXX:9:2:3:1387 :N:0:CCAGTTAGGCACACGA
-CCAGTTAG
-+
-;+B,232A
- at machine1:HiMom:abcdeACXX:9:2:3:1484 :Y:0:CCAGTTAGGCACACGA
-CCAGTTAG
-+
->BAAAC@<
- at machine1:HiMom:abcdeACXX:9:2:3:1576 :N:0:CCAGTTAGGCACACGA
-CCAGTTAG
-+
-:B?=CACA
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.barcode_2.fastq
deleted file mode 100644
index 62a5fcb..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCAGTTAGGCACACGA.barcode_2.fastq
+++ /dev/null
@@ -1,44 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1688 :Y:0:CCAGTTAGGCACACGA
-GCACACGA
-+
->@==;CA=
- at machine1:HiMom:abcdeACXX:9:1:3:583 :Y:0:CCAGTTAGGCACACGA
-GCACACGA
-+
-=>93;CA>
- at machine1:HiMom:abcdeACXX:9:1:3:996 :Y:0:CCAGTTAGGCACACGA
-GCACACGA
-+
-A at 5=>C<#
- at machine1:HiMom:abcdeACXX:9:2:2:1671 :N:0:CCAGTTAGGCACACGA
-GCACACGA
-+
-@>>B;BA9
- at machine1:HiMom:abcdeACXX:9:2:2:1723 :N:0:CCAGTTAGGCACACGA
-GCACACGA
-+
- at A######
- at machine1:HiMom:abcdeACXX:9:2:2:255 :Y:0:CCAGTTAGGCACACGA
-GCACACGA
-+
-A<?CAA@;
- at machine1:HiMom:abcdeACXX:9:2:3:112 :Y:0:CCAGTTAGGCACACGA
-GCACACGA
-+
-B@<CAC at 6
- at machine1:HiMom:abcdeACXX:9:2:3:1179 :N:0:CCAGTTAGGCACACGA
-GCACACGA
-+
-);;9@@;#
- at machine1:HiMom:abcdeACXX:9:2:3:1387 :N:0:CCAGTTAGGCACACGA
-GCACACGA
-+
-;+B,232A
- at machine1:HiMom:abcdeACXX:9:2:3:1484 :Y:0:CCAGTTAGGCACACGA
-GCACACGA
-+
->BAAAC@<
- at machine1:HiMom:abcdeACXX:9:2:3:1576 :N:0:CCAGTTAGGCACACGA
-GCACACGA
-+
-:B?=CACA
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCAT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCAT.1.fastq
deleted file mode 100644
index b2a2949..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCAT.1.fastq
+++ /dev/null
@@ -1,8 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:636 :N:0:CCTACCAT
-NGATCATTTACTGTTGTCAACTACCAAAAT
-+
-%/72'+769621513-1-563202356557
- at machine1:HiMom:abcdeACXX:7:2:3:875 :N:0:CCTACCAT
-AGGCAGTAGTCTAATCCCGAGGATCCCAAG
-+
-:,73=@?<.=@;??@::3?8)5<=9%:?>7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCAT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCAT.barcode_1.fastq
deleted file mode 100644
index 194905a..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCAT.barcode_1.fastq
+++ /dev/null
@@ -1,8 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:636 :N:0:CCTACCAT
-CCTACCAT
-+
-63<@A?B=
- at machine1:HiMom:abcdeACXX:7:2:3:875 :N:0:CCTACCAT
-CCTACCAT
-+
-;=@@@8 at B
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.1.fastq
deleted file mode 100644
index 96084b9..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.1.fastq
+++ /dev/null
@@ -1,8 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:636 :N:0:CCTACCATCTACCAGG
-NGATCATTTACTGTTGTCAACTACCAAAAT
-+
-%/72'+769621513-1-563202356557
- at machine1:HiMom:abcdeACXX:9:2:3:875 :N:0:CCTACCATCTACCAGG
-AGGCAGTAGTCTAATCCCGAGGATCCCAAG
-+
-:,73=@?<.=@;??@::3?8)5<=9%:?>7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.barcode_1.fastq
deleted file mode 100644
index b2ac984..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.barcode_1.fastq
+++ /dev/null
@@ -1,8 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:636 :N:0:CCTACCATCTACCAGG
-CCTACCAT
-+
-63<@A?B=
- at machine1:HiMom:abcdeACXX:9:2:3:875 :N:0:CCTACCATCTACCAGG
-CCTACCAT
-+
-;=@@@8 at B
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.barcode_2.fastq
deleted file mode 100644
index 626028b..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CCTACCATCTACCAGG.barcode_2.fastq
+++ /dev/null
@@ -1,8 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:636 :N:0:CCTACCATCTACCAGG
-CTACCAGG
-+
-63<@A?B=
- at machine1:HiMom:abcdeACXX:9:2:3:875 :N:0:CCTACCATCTACCAGG
-CTACCAGG
-+
-;=@@@8 at B
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGG.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGG.1.fastq
deleted file mode 100644
index b45415d..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGG.1.fastq
+++ /dev/null
@@ -1,24 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:1995 :Y:0:CTACCAGG
-NATTTCCTGAACACAGCACAGGGAAGAGGA
-+
-%/78777738777:8877786776858225
- at machine1:HiMom:abcdeACXX:7:1:3:1358 :N:0:CTACCAGG
-NTCCTTCCTCAAGGGGACCCCGCCTCCCCT
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:3:176 :Y:0:CTACCAGG
-ATATTTCATGAAAGACATAAATTTACAGTT
-+
-BBBCCB at BBBABBBB?ABBBBBBBBABB at B
- at machine1:HiMom:abcdeACXX:7:1:3:198 :Y:0:CTACCAGG
-TATAATTTAATGGTTTTTATATATTCAGAG
-+
-BBC=BBCCA=@=8<BCBCBBABBCB=BB<9
- at machine1:HiMom:abcdeACXX:7:1:3:900 :N:0:CTACCAGG
-TGAATCTTTGTTCAACACAGATTATTCCAG
-+
-)>@+5*<B1':(5,23A>5)@:)(/>:=##
- at machine1:HiMom:abcdeACXX:7:2:3:1970 :Y:0:CTACCAGG
-NTAATACTCTTTGAGAAAGGACTGAGGGAA
-+
-%.:77558:68862.3;8455:0057535;
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGG.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGG.barcode_1.fastq
deleted file mode 100644
index 95d94ae..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGG.barcode_1.fastq
+++ /dev/null
@@ -1,24 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:1995 :Y:0:CTACCAGG
-CTACCAGG
-+
-B=AA?BBA
- at machine1:HiMom:abcdeACXX:7:1:3:1358 :N:0:CTACCAGG
-CTACAAGG
-+
-62BB####
- at machine1:HiMom:abcdeACXX:7:1:3:176 :Y:0:CTACCAGG
-CTACCAGG
-+
-ABBB?ABB
- at machine1:HiMom:abcdeACXX:7:1:3:198 :Y:0:CTACCAGG
-CTACCAGG
-+
-ABBBAA?@
- at machine1:HiMom:abcdeACXX:7:1:3:900 :N:0:CTACCAGG
-CTCCCAGG
-+
-(((.A at 85
- at machine1:HiMom:abcdeACXX:7:2:3:1970 :Y:0:CTACCAGG
-CTACCAGG
-+
-BABBBAB@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.1.fastq
deleted file mode 100644
index 23d3451..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.1.fastq
+++ /dev/null
@@ -1,24 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:1995 :Y:0:CTACCAGGCCTACCAT
-NATTTCCTGAACACAGCACAGGGAAGAGGA
-+
-%/78777738777:8877786776858225
- at machine1:HiMom:abcdeACXX:9:1:3:1358 :N:0:CTACCAGGCCTACCAT
-NTCCTTCCTCAAGGGGACCCCGCCTCCCCT
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:3:176 :Y:0:CTACCAGGCCTACCAT
-ATATTTCATGAAAGACATAAATTTACAGTT
-+
-BBBCCB at BBBABBBB?ABBBBBBBBABB at B
- at machine1:HiMom:abcdeACXX:9:1:3:198 :Y:0:CTACCAGGCCTACCAT
-TATAATTTAATGGTTTTTATATATTCAGAG
-+
-BBC=BBCCA=@=8<BCBCBBABBCB=BB<9
- at machine1:HiMom:abcdeACXX:9:1:3:900 :N:0:CTACCAGGCCTACCAT
-TGAATCTTTGTTCAACACAGATTATTCCAG
-+
-)>@+5*<B1':(5,23A>5)@:)(/>:=##
- at machine1:HiMom:abcdeACXX:9:2:3:1970 :Y:0:CTACCAGGCCTACCAT
-NTAATACTCTTTGAGAAAGGACTGAGGGAA
-+
-%.:77558:68862.3;8455:0057535;
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.barcode_1.fastq
deleted file mode 100644
index fc9c0d0..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.barcode_1.fastq
+++ /dev/null
@@ -1,24 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:1995 :Y:0:CTACCAGGCCTACCAT
-CTACCAGG
-+
-B=AA?BBA
- at machine1:HiMom:abcdeACXX:9:1:3:1358 :N:0:CTACCAGGCCTACCAT
-CTACAAGG
-+
-62BB####
- at machine1:HiMom:abcdeACXX:9:1:3:176 :Y:0:CTACCAGGCCTACCAT
-CTACCAGG
-+
-ABBB?ABB
- at machine1:HiMom:abcdeACXX:9:1:3:198 :Y:0:CTACCAGGCCTACCAT
-CTACCAGG
-+
-ABBBAA?@
- at machine1:HiMom:abcdeACXX:9:1:3:900 :N:0:CTACCAGGCCTACCAT
-CTCCCAGG
-+
-(((.A at 85
- at machine1:HiMom:abcdeACXX:9:2:3:1970 :Y:0:CTACCAGGCCTACCAT
-CTACCAGG
-+
-BABBBAB@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.barcode_2.fastq
deleted file mode 100644
index 20a2a23..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/CTACCAGGCCTACCAT.barcode_2.fastq
+++ /dev/null
@@ -1,24 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:1995 :Y:0:CTACCAGGCCTACCAT
-CCTACCAT
-+
-B=AA?BBA
- at machine1:HiMom:abcdeACXX:9:1:3:1358 :N:0:CTACCAGGCCTACCAT
-CCTACCAT
-+
-62BB####
- at machine1:HiMom:abcdeACXX:9:1:3:176 :Y:0:CTACCAGGCCTACCAT
-CCTACCAT
-+
-ABBB?ABB
- at machine1:HiMom:abcdeACXX:9:1:3:198 :Y:0:CTACCAGGCCTACCAT
-CCTACCAT
-+
-ABBBAA?@
- at machine1:HiMom:abcdeACXX:9:1:3:900 :N:0:CTACCAGGCCTACCAT
-CCTACCAT
-+
-(((.A at 85
- at machine1:HiMom:abcdeACXX:9:2:3:1970 :Y:0:CTACCAGGCCTACCAT
-CCTACCAT
-+
-BABBBAB@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGA.1.fastq
deleted file mode 100644
index 591d507..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGA.1.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1311 :Y:0:GCACACGA
-AGACATAAAACCAGAGAGAAGATAGTGGGT
-+
-@@@BBBBCBA;>B>ABBBBBBBBA?;9:3>
- at machine1:HiMom:abcdeACXX:7:1:3:1544 :N:0:GCACACGA
-CGTGGATGGTTTTGATGAGTCCCACTGCAC
-+
-=@=<)*@22375A9@?36(768@:'897<#
- at machine1:HiMom:abcdeACXX:7:1:3:301 :N:0:GCACACGA
-NTACGTGTGTGGCTGGATAGTCTGGACCAT
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:3:959 :Y:0:GCACACGA
-NAAAGTTTCCTGTGAGAAGGCGCATGGCAT
-+
-%.52-487848866757#############
- at machine1:HiMom:abcdeACXX:7:2:2:184 :N:0:GCACACGA
-NGAAACGTTTTTCGGTTGAGGAAACTTTTT
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:1025 :Y:0:GCACACGA
-NAATGGAAAGGAGTCCAATGGAAGGGAATC
-+
-%/4626885-+3-3777:532570313837
- at machine1:HiMom:abcdeACXX:7:2:3:1290 :N:0:GCACACGA
-NTCACCTGAATCCACGTTAGCTGGGGAAGA
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:1917 :N:0:GCACACGA
-NTCCACAAAAAAAAAAAAAATTAGTTGGGT
-+
-%*6<737<4756##################
- at machine1:HiMom:abcdeACXX:7:2:3:495 :N:0:GCACACGA
-NTCCGTTTTTATAACTGTAAATTTATCACT
-+
-##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGA.barcode_1.fastq
deleted file mode 100644
index 97f5863..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGA.barcode_1.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1311 :Y:0:GCACACGA
-GCACACGA
-+
-<?BAA at AB
- at machine1:HiMom:abcdeACXX:7:1:3:1544 :N:0:GCACACGA
-GCACACGA
-+
-((<.;;1;
- at machine1:HiMom:abcdeACXX:7:1:3:301 :N:0:GCACACGA
-GCACACGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:3:959 :Y:0:GCACACGA
-GCACACGA
-+
-3?;AB?=<
- at machine1:HiMom:abcdeACXX:7:2:2:184 :N:0:GCACACGA
-GCACACGA
-+
->;<@A@@3
- at machine1:HiMom:abcdeACXX:7:2:3:1025 :Y:0:GCACACGA
-GCACACGA
-+
-@=ABA@@@
- at machine1:HiMom:abcdeACXX:7:2:3:1290 :N:0:GCACACGA
-GCACACGA
-+
-)5;=@<(;
- at machine1:HiMom:abcdeACXX:7:2:3:1917 :N:0:GCACACGA
-GCACACGA
-+
-/5;@=;B9
- at machine1:HiMom:abcdeACXX:7:2:3:495 :N:0:GCACACGA
-GCACACGA
-+
-5;5<A@=;
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.1.fastq
deleted file mode 100644
index 967a3bb..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.1.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1311 :Y:0:GCACACGACCAGTTAG
-AGACATAAAACCAGAGAGAAGATAGTGGGT
-+
-@@@BBBBCBA;>B>ABBBBBBBBA?;9:3>
- at machine1:HiMom:abcdeACXX:9:1:3:1544 :N:0:GCACACGACCAGTTAG
-CGTGGATGGTTTTGATGAGTCCCACTGCAC
-+
-=@=<)*@22375A9@?36(768@:'897<#
- at machine1:HiMom:abcdeACXX:9:1:3:301 :N:0:GCACACGACCAGTTAG
-NTACGTGTGTGGCTGGATAGTCTGGACCAT
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:3:959 :Y:0:GCACACGACCAGTTAG
-NAAAGTTTCCTGTGAGAAGGCGCATGGCAT
-+
-%.52-487848866757#############
- at machine1:HiMom:abcdeACXX:9:2:2:184 :N:0:GCACACGACCAGTTAG
-NGAAACGTTTTTCGGTTGAGGAAACTTTTT
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:1025 :Y:0:GCACACGACCAGTTAG
-NAATGGAAAGGAGTCCAATGGAAGGGAATC
-+
-%/4626885-+3-3777:532570313837
- at machine1:HiMom:abcdeACXX:9:2:3:1290 :N:0:GCACACGACCAGTTAG
-NTCACCTGAATCCACGTTAGCTGGGGAAGA
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:1917 :N:0:GCACACGACCAGTTAG
-NTCCACAAAAAAAAAAAAAATTAGTTGGGT
-+
-%*6<737<4756##################
- at machine1:HiMom:abcdeACXX:9:2:3:495 :N:0:GCACACGACCAGTTAG
-NTCCGTTTTTATAACTGTAAATTTATCACT
-+
-##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.barcode_1.fastq
deleted file mode 100644
index 6c2aa56..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.barcode_1.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1311 :Y:0:GCACACGACCAGTTAG
-GCACACGA
-+
-<?BAA at AB
- at machine1:HiMom:abcdeACXX:9:1:3:1544 :N:0:GCACACGACCAGTTAG
-GCACACGA
-+
-((<.;;1;
- at machine1:HiMom:abcdeACXX:9:1:3:301 :N:0:GCACACGACCAGTTAG
-GCACACGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:3:959 :Y:0:GCACACGACCAGTTAG
-GCACACGA
-+
-3?;AB?=<
- at machine1:HiMom:abcdeACXX:9:2:2:184 :N:0:GCACACGACCAGTTAG
-GCACACGA
-+
->;<@A@@3
- at machine1:HiMom:abcdeACXX:9:2:3:1025 :Y:0:GCACACGACCAGTTAG
-GCACACGA
-+
-@=ABA@@@
- at machine1:HiMom:abcdeACXX:9:2:3:1290 :N:0:GCACACGACCAGTTAG
-GCACACGA
-+
-)5;=@<(;
- at machine1:HiMom:abcdeACXX:9:2:3:1917 :N:0:GCACACGACCAGTTAG
-GCACACGA
-+
-/5;@=;B9
- at machine1:HiMom:abcdeACXX:9:2:3:495 :N:0:GCACACGACCAGTTAG
-GCACACGA
-+
-5;5<A@=;
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.barcode_2.fastq
deleted file mode 100644
index c77a493..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACACGACCAGTTAG.barcode_2.fastq
+++ /dev/null
@@ -1,36 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1311 :Y:0:GCACACGACCAGTTAG
-CCAGTTAG
-+
-<?BAA at AB
- at machine1:HiMom:abcdeACXX:9:1:3:1544 :N:0:GCACACGACCAGTTAG
-CCAGTTAG
-+
-((<.;;1;
- at machine1:HiMom:abcdeACXX:9:1:3:301 :N:0:GCACACGACCAGTTAG
-CCAGTTAG
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:3:959 :Y:0:GCACACGACCAGTTAG
-CCAGTTAG
-+
-3?;AB?=<
- at machine1:HiMom:abcdeACXX:9:2:2:184 :N:0:GCACACGACCAGTTAG
-CCAGTTAG
-+
->;<@A@@3
- at machine1:HiMom:abcdeACXX:9:2:3:1025 :Y:0:GCACACGACCAGTTAG
-CCAGTTAG
-+
-@=ABA@@@
- at machine1:HiMom:abcdeACXX:9:2:3:1290 :N:0:GCACACGACCAGTTAG
-CCAGTTAG
-+
-)5;=@<(;
- at machine1:HiMom:abcdeACXX:9:2:3:1917 :N:0:GCACACGACCAGTTAG
-CCAGTTAG
-+
-/5;@=;B9
- at machine1:HiMom:abcdeACXX:9:2:3:495 :N:0:GCACACGACCAGTTAG
-CCAGTTAG
-+
-5;5<A@=;
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCT.1.fastq
deleted file mode 100644
index 3b95cbd..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCT.1.fastq
+++ /dev/null
@@ -1,12 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:389 :N:0:GCACATCT
-NGATGTTCAAACATGCATAACTCTAAGTAT
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:2:1567 :Y:0:GCACATCT
-NAGACAGCAGTAACCTCTGCAGACTTAAAC
-+
-%,67:720544;4667:62-5667::6877
- at machine1:HiMom:abcdeACXX:7:2:3:1053 :N:0:GCACATCT
-NTTTGATCATGATTCCATTCGAGACCATTC
-+
-%.;;##########################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCT.barcode_1.fastq
deleted file mode 100644
index ac9d40b..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCT.barcode_1.fastq
+++ /dev/null
@@ -1,12 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:389 :N:0:GCACATCT
-GCACATCT
-+
-<:@@@56;
- at machine1:HiMom:abcdeACXX:7:2:2:1567 :Y:0:GCACATCT
-GCACATCT
-+
- at B=;@B?@
- at machine1:HiMom:abcdeACXX:7:2:3:1053 :N:0:GCACATCT
-GCACATCT
-+
-6<?B?C at 4
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.1.fastq
deleted file mode 100644
index 1c0c245..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.1.fastq
+++ /dev/null
@@ -1,12 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:389 :N:0:GCACATCTCATGCTTA
-NGATGTTCAAACATGCATAACTCTAAGTAT
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:2:1567 :Y:0:GCACATCTCATGCTTA
-NAGACAGCAGTAACCTCTGCAGACTTAAAC
-+
-%,67:720544;4667:62-5667::6877
- at machine1:HiMom:abcdeACXX:9:2:3:1053 :N:0:GCACATCTCATGCTTA
-NTTTGATCATGATTCCATTCGAGACCATTC
-+
-%.;;##########################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.barcode_1.fastq
deleted file mode 100644
index 8d9ec57..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.barcode_1.fastq
+++ /dev/null
@@ -1,12 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:389 :N:0:GCACATCTCATGCTTA
-GCACATCT
-+
-<:@@@56;
- at machine1:HiMom:abcdeACXX:9:2:2:1567 :Y:0:GCACATCTCATGCTTA
-GCACATCT
-+
- at B=;@B?@
- at machine1:HiMom:abcdeACXX:9:2:3:1053 :N:0:GCACATCTCATGCTTA
-GCACATCT
-+
-6<?B?C at 4
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.barcode_2.fastq
deleted file mode 100644
index cb34b4b..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GCACATCTCATGCTTA.barcode_2.fastq
+++ /dev/null
@@ -1,12 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:389 :N:0:GCACATCTCATGCTTA
-CATGCTTA
-+
-<:@@@56;
- at machine1:HiMom:abcdeACXX:9:2:2:1567 :Y:0:GCACATCTCATGCTTA
-CATGCTTA
-+
- at B=;@B?@
- at machine1:HiMom:abcdeACXX:9:2:3:1053 :N:0:GCACATCTCATGCTTA
-CATGCTTA
-+
-6<?B?C at 4
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGA.1.fastq
deleted file mode 100644
index edba24c..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGA.1.fastq
+++ /dev/null
@@ -1,28 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:33 :N:0:GGTCCAGA
-CGGGCGCGGTGGATTCCGCCTTTAATCCTA
-+
-71@=>3?BA#####################
- at machine1:HiMom:abcdeACXX:7:1:3:471 :Y:0:GGTCCAGA
-AGAAAAAGACAAGCAGGCCTCTCACAGAGC
-+
-@=B>CB@?8BBBA<B<@ABBAAA=<@>>3<
- at machine1:HiMom:abcdeACXX:7:1:3:676 :N:0:GGTCCAGA
-ATAAGAAAATGCCAACCCATTTACAGTTTT
-+
-?':7%68>?<(.9A7(=:68>A=2>(9@??
- at machine1:HiMom:abcdeACXX:7:2:2:1038 :N:0:GGTCCAGA
-NATGGAATCAACCTGAGTGGAATGAAATGG
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:1352 :Y:0:GGTCCAGA
-AAAGTGGCCCTTTCTGCATAATTCTTCTTG
-+
- at B@>2:@@:>B at AAA:AA>?B?>:=<1=<#
- at machine1:HiMom:abcdeACXX:7:2:3:1733 :Y:0:GGTCCAGA
-NTTAAATGAGTGTAAATATTCAATTATGCA
-+
-%,:6::2/5;393<<9:<;919<97#####
- at machine1:HiMom:abcdeACXX:7:2:3:386 :N:0:GGTCCAGA
-NTGAATAAATAAATATCTGTATTATTCCTA
-+
-%156;99:999:5773,4-57973851.48
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGA.barcode_1.fastq
deleted file mode 100644
index 55d0c05..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGA.barcode_1.fastq
+++ /dev/null
@@ -1,28 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:33 :N:0:GGTCCAGA
-GGTCCAGA
-+
-17=;,'@@
- at machine1:HiMom:abcdeACXX:7:1:3:471 :Y:0:GGTCCAGA
-GGTCCAGA
-+
-<A=@B=?@
- at machine1:HiMom:abcdeACXX:7:1:3:676 :N:0:GGTCCAGA
-GATCCAGA
-+
-:(.<((:@
- at machine1:HiMom:abcdeACXX:7:2:2:1038 :N:0:GGTCCAGA
-GGTCCAGA
-+
-=7=??B@@
- at machine1:HiMom:abcdeACXX:7:2:3:1352 :Y:0:GGTCCAGA
-GGTCCAGA
-+
-0)<0;@@@
- at machine1:HiMom:abcdeACXX:7:2:3:1733 :Y:0:GGTCCAGA
-GGTCCAGA
-+
-/>BBBAA=
- at machine1:HiMom:abcdeACXX:7:2:3:386 :N:0:GGTCCAGA
-GGTCCAGA
-+
-9@@99@@9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.1.fastq
deleted file mode 100644
index 6223ca0..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.1.fastq
+++ /dev/null
@@ -1,28 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:33 :N:0:GGTCCAGACATAGCGA
-CGGGCGCGGTGGATTCCGCCTTTAATCCTA
-+
-71@=>3?BA#####################
- at machine1:HiMom:abcdeACXX:9:1:3:471 :Y:0:GGTCCAGACATAGCGA
-AGAAAAAGACAAGCAGGCCTCTCACAGAGC
-+
-@=B>CB@?8BBBA<B<@ABBAAA=<@>>3<
- at machine1:HiMom:abcdeACXX:9:1:3:676 :N:0:GGTCCAGACATAGCGA
-ATAAGAAAATGCCAACCCATTTACAGTTTT
-+
-?':7%68>?<(.9A7(=:68>A=2>(9@??
- at machine1:HiMom:abcdeACXX:9:2:2:1038 :N:0:GGTCCAGACATAGCGA
-NATGGAATCAACCTGAGTGGAATGAAATGG
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:1352 :Y:0:GGTCCAGACATAGCGA
-AAAGTGGCCCTTTCTGCATAATTCTTCTTG
-+
- at B@>2:@@:>B at AAA:AA>?B?>:=<1=<#
- at machine1:HiMom:abcdeACXX:9:2:3:1733 :Y:0:GGTCCAGACATAGCGA
-NTTAAATGAGTGTAAATATTCAATTATGCA
-+
-%,:6::2/5;393<<9:<;919<97#####
- at machine1:HiMom:abcdeACXX:9:2:3:386 :N:0:GGTCCAGACATAGCGA
-NTGAATAAATAAATATCTGTATTATTCCTA
-+
-%156;99:999:5773,4-57973851.48
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.barcode_1.fastq
deleted file mode 100644
index 4a21eb6..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.barcode_1.fastq
+++ /dev/null
@@ -1,28 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:33 :N:0:GGTCCAGACATAGCGA
-GGTCCAGA
-+
-17=;,'@@
- at machine1:HiMom:abcdeACXX:9:1:3:471 :Y:0:GGTCCAGACATAGCGA
-GGTCCAGA
-+
-<A=@B=?@
- at machine1:HiMom:abcdeACXX:9:1:3:676 :N:0:GGTCCAGACATAGCGA
-GATCCAGA
-+
-:(.<((:@
- at machine1:HiMom:abcdeACXX:9:2:2:1038 :N:0:GGTCCAGACATAGCGA
-GGTCCAGA
-+
-=7=??B@@
- at machine1:HiMom:abcdeACXX:9:2:3:1352 :Y:0:GGTCCAGACATAGCGA
-GGTCCAGA
-+
-0)<0;@@@
- at machine1:HiMom:abcdeACXX:9:2:3:1733 :Y:0:GGTCCAGACATAGCGA
-GGTCCAGA
-+
-/>BBBAA=
- at machine1:HiMom:abcdeACXX:9:2:3:386 :N:0:GGTCCAGACATAGCGA
-GGTCCAGA
-+
-9@@99@@9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.barcode_2.fastq
deleted file mode 100644
index c6b3f2d..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GGTCCAGACATAGCGA.barcode_2.fastq
+++ /dev/null
@@ -1,28 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:33 :N:0:GGTCCAGACATAGCGA
-CATAGCGA
-+
-17=;,'@@
- at machine1:HiMom:abcdeACXX:9:1:3:471 :Y:0:GGTCCAGACATAGCGA
-CATAGCGA
-+
-<A=@B=?@
- at machine1:HiMom:abcdeACXX:9:1:3:676 :N:0:GGTCCAGACATAGCGA
-CATAGCGA
-+
-:(.<((:@
- at machine1:HiMom:abcdeACXX:9:2:2:1038 :N:0:GGTCCAGACATAGCGA
-CATAGCGA
-+
-=7=??B@@
- at machine1:HiMom:abcdeACXX:9:2:3:1352 :Y:0:GGTCCAGACATAGCGA
-CATAGCGA
-+
-0)<0;@@@
- at machine1:HiMom:abcdeACXX:9:2:3:1733 :Y:0:GGTCCAGACATAGCGA
-CATAGCGA
-+
-/>BBBAA=
- at machine1:HiMom:abcdeACXX:9:2:3:386 :N:0:GGTCCAGACATAGCGA
-CATAGCGA
-+
-9@@99@@9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACA.1.fastq
deleted file mode 100644
index c1ae9f8..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACA.1.fastq
+++ /dev/null
@@ -1,40 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:11 :N:0:GTATAACA
-NAAATGAAAAAAGAAATGCATTGTCAGGTG
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:2:455 :N:0:GTATAACA
-NGCTTGAACTCAGGATTCACAATTTCAACC
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:3:1188 :Y:0:GTATAACA
-GCGAATGCCATTATTTCATTCCTTTTCATG
-+
-=@CACA?AABCCCCCCCCAB??CBCBCCBB
- at machine1:HiMom:abcdeACXX:7:1:3:131 :Y:0:GTATAACA
-TAAAATAAAGTAAAAAGAAAGCAAGGTCCT
-+
-BBBBCCCBBA<CCCCA<<CBC>BBC=AC=C
- at machine1:HiMom:abcdeACXX:7:1:3:1488 :Y:0:GTATAACA
-NATTCTGAGTAGCATGCTGGATCCCACCCC
-+
-%-445014,42/1666423###########
- at machine1:HiMom:abcdeACXX:7:1:3:1973 :Y:0:GTATAACA
-NCTTTTATTGAATTAGCTTCTGTGGAAACC
-+
-%.<774<<145;105<<:6<7<:88;####
- at machine1:HiMom:abcdeACXX:7:1:3:289 :Y:0:GTATAACA
-ATAGTGCTACAATAAACATGGGAGTGCAGA
-+
-BB=;>AABB at BBBBBB@ACBA>>BA;9@?A
- at machine1:HiMom:abcdeACXX:7:2:2:1662 :N:0:GTATAACA
-NACTAAAGACCTTATTCATGTAGCCAAATA
-+
-%.2556331)%079799::9:71855<88:
- at machine1:HiMom:abcdeACXX:7:2:2:61 :Y:0:GTATAACA
-NTTTCGATGGTGTTTCCATTTGATTCATTC
-+
-%0;:9:;799:8:97779:<679<977;::
- at machine1:HiMom:abcdeACXX:7:2:3:1581 :N:0:GTATAACA
-NATAGGCAGGGAGCAAACCTCAATAAAAAG
-+
-##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACA.barcode_1.fastq
deleted file mode 100644
index 250d81c..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACA.barcode_1.fastq
+++ /dev/null
@@ -1,40 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:11 :N:0:GTATAACA
-GTATAAGA
-+
- at 7==@7##
- at machine1:HiMom:abcdeACXX:7:1:2:455 :N:0:GTATAACA
-GTATAACT
-+
-,@######
- at machine1:HiMom:abcdeACXX:7:1:3:1188 :Y:0:GTATAACA
-GTATAACA
-+
-BBBCBCCB
- at machine1:HiMom:abcdeACXX:7:1:3:131 :Y:0:GTATAACA
-GTATAACA
-+
-48CCACAC
- at machine1:HiMom:abcdeACXX:7:1:3:1488 :Y:0:GTATAACA
-GTATAACA
-+
-)7<9BBBB
- at machine1:HiMom:abcdeACXX:7:1:3:1973 :Y:0:GTATAACA
-GTATAACA
-+
-7;CACCBC
- at machine1:HiMom:abcdeACXX:7:1:3:289 :Y:0:GTATAACA
-GTATAACA
-+
->BCCCCB>
- at machine1:HiMom:abcdeACXX:7:2:2:1662 :N:0:GTATAACA
-GTATAACA
-+
-82BA at AAB
- at machine1:HiMom:abcdeACXX:7:2:2:61 :Y:0:GTATAACA
-GTATAACA
-+
-<ABCBB9B
- at machine1:HiMom:abcdeACXX:7:2:3:1581 :N:0:GTATAACA
-GTATAACA
-+
-:4<BAAAC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.1.fastq
deleted file mode 100644
index c3a3023..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.1.fastq
+++ /dev/null
@@ -1,40 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:11 :N:0:GTATAACACAGGAGCC
-NAAATGAAAAAAGAAATGCATTGTCAGGTG
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:2:455 :N:0:GTATAACACAGGAGCC
-NGCTTGAACTCAGGATTCACAATTTCAACC
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:3:1188 :Y:0:GTATAACACAGGAGCC
-GCGAATGCCATTATTTCATTCCTTTTCATG
-+
-=@CACA?AABCCCCCCCCAB??CBCBCCBB
- at machine1:HiMom:abcdeACXX:9:1:3:131 :Y:0:GTATAACACAGGAGCC
-TAAAATAAAGTAAAAAGAAAGCAAGGTCCT
-+
-BBBBCCCBBA<CCCCA<<CBC>BBC=AC=C
- at machine1:HiMom:abcdeACXX:9:1:3:1488 :Y:0:GTATAACACAGGAGCC
-NATTCTGAGTAGCATGCTGGATCCCACCCC
-+
-%-445014,42/1666423###########
- at machine1:HiMom:abcdeACXX:9:1:3:1973 :Y:0:GTATAACACAGGAGCC
-NCTTTTATTGAATTAGCTTCTGTGGAAACC
-+
-%.<774<<145;105<<:6<7<:88;####
- at machine1:HiMom:abcdeACXX:9:1:3:289 :Y:0:GTATAACACAGGAGCC
-ATAGTGCTACAATAAACATGGGAGTGCAGA
-+
-BB=;>AABB at BBBBBB@ACBA>>BA;9@?A
- at machine1:HiMom:abcdeACXX:9:2:2:1662 :N:0:GTATAACACAGGAGCC
-NACTAAAGACCTTATTCATGTAGCCAAATA
-+
-%.2556331)%079799::9:71855<88:
- at machine1:HiMom:abcdeACXX:9:2:2:61 :Y:0:GTATAACACAGGAGCC
-NTTTCGATGGTGTTTCCATTTGATTCATTC
-+
-%0;:9:;799:8:97779:<679<977;::
- at machine1:HiMom:abcdeACXX:9:2:3:1581 :N:0:GTATAACACAGGAGCC
-NATAGGCAGGGAGCAAACCTCAATAAAAAG
-+
-##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.barcode_1.fastq
deleted file mode 100644
index 9ab10a3..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.barcode_1.fastq
+++ /dev/null
@@ -1,40 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:11 :N:0:GTATAACACAGGAGCC
-GTATAAGA
-+
- at 7==@7##
- at machine1:HiMom:abcdeACXX:9:1:2:455 :N:0:GTATAACACAGGAGCC
-GTATAACT
-+
-,@######
- at machine1:HiMom:abcdeACXX:9:1:3:1188 :Y:0:GTATAACACAGGAGCC
-GTATAACA
-+
-BBBCBCCB
- at machine1:HiMom:abcdeACXX:9:1:3:131 :Y:0:GTATAACACAGGAGCC
-GTATAACA
-+
-48CCACAC
- at machine1:HiMom:abcdeACXX:9:1:3:1488 :Y:0:GTATAACACAGGAGCC
-GTATAACA
-+
-)7<9BBBB
- at machine1:HiMom:abcdeACXX:9:1:3:1973 :Y:0:GTATAACACAGGAGCC
-GTATAACA
-+
-7;CACCBC
- at machine1:HiMom:abcdeACXX:9:1:3:289 :Y:0:GTATAACACAGGAGCC
-GTATAACA
-+
->BCCCCB>
- at machine1:HiMom:abcdeACXX:9:2:2:1662 :N:0:GTATAACACAGGAGCC
-GTATAACA
-+
-82BA at AAB
- at machine1:HiMom:abcdeACXX:9:2:2:61 :Y:0:GTATAACACAGGAGCC
-GTATAACA
-+
-<ABCBB9B
- at machine1:HiMom:abcdeACXX:9:2:3:1581 :N:0:GTATAACACAGGAGCC
-GTATAACA
-+
-:4<BAAAC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.barcode_2.fastq
deleted file mode 100644
index ade5931..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/GTATAACACAGGAGCC.barcode_2.fastq
+++ /dev/null
@@ -1,40 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:11 :N:0:GTATAACACAGGAGCC
-CAGGAGCC
-+
- at 7==@7##
- at machine1:HiMom:abcdeACXX:9:1:2:455 :N:0:GTATAACACAGGAGCC
-CAGGAGCC
-+
-,@######
- at machine1:HiMom:abcdeACXX:9:1:3:1188 :Y:0:GTATAACACAGGAGCC
-CAGGAGCC
-+
-BBBCBCCB
- at machine1:HiMom:abcdeACXX:9:1:3:131 :Y:0:GTATAACACAGGAGCC
-CAGGAGCC
-+
-48CCACAC
- at machine1:HiMom:abcdeACXX:9:1:3:1488 :Y:0:GTATAACACAGGAGCC
-CAGGAGCC
-+
-)7<9BBBB
- at machine1:HiMom:abcdeACXX:9:1:3:1973 :Y:0:GTATAACACAGGAGCC
-CAGGAGCC
-+
-7;CACCBC
- at machine1:HiMom:abcdeACXX:9:1:3:289 :Y:0:GTATAACACAGGAGCC
-CAGGAGCC
-+
->BCCCCB>
- at machine1:HiMom:abcdeACXX:9:2:2:1662 :N:0:GTATAACACAGGAGCC
-CAGGAGCC
-+
-82BA at AAB
- at machine1:HiMom:abcdeACXX:9:2:2:61 :Y:0:GTATAACACAGGAGCC
-CAGGAGCC
-+
-<ABCBB9B
- at machine1:HiMom:abcdeACXX:9:2:3:1581 :N:0:GTATAACACAGGAGCC
-CAGGAGCC
-+
-:4<BAAAC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/N.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/N.1.fastq
deleted file mode 100644
index 0d031e7..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/N.1.fastq
+++ /dev/null
@@ -1,892 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:0:1038 :N:0:
-NNNNNCNNCANNNCNNNCNCCNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:1093 :N:0:
-NNNNNCNNGTNNNANNNGNAANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:113 :N:0:
-NNNNNNNNGNNNNNNNNNNNANNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:1193 :N:0:
-NNNNNNNNTNNNNTNNNTNNTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:1291 :N:0:
-NNNNNNNNANNNNNNNNANNTNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:1307 :N:0:
-NNNNNNNNCNNNNANNNTNNTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:1434 :N:0:
-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:1475 :N:0:
-NNNNNGNNANNNNANNNANNANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:1690 :N:0:
-NNNNNNNNANNNNNNNNGNNCNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:1703 :N:0:
-NNNNNNNNANNNNNNNNNNNANNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:1940 :N:0:
-NNNNNNNNCNNNNNNNNTNNTNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:2001 :N:0:
-NNNNNANNTGNNNGNNNANGCNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:205 :N:0:
-NNNNNNNNANNNNNNNNANNTNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:275 :N:0:
-NNNNNANNCANNNTNNNGNCCNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:324 :N:0:
-NNNNNNNNTNNNNNNNNTNNANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:37 :N:0:
-NNNNNNNNANNNNNNNNCNNTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:464 :N:0:
-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:586 :N:0:
-NNNNNNNNCNNNNNNNNCNNCNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:841 :N:0:
-NNNNNNNNCNNNNNNNNNNNTNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:0:879 :N:0:
-NNNNNNNNTNNNNNNNNNNNTNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1013 :N:0:
-NNCNNTNCAGNNNCNNNANGTNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:111 :N:0:
-NNCNNTNGCGNNNTNNNANCTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1153 :N:0:
-NNTNNTNTGGNNNTNNNCNTCNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1184 :N:0:
-NNANNGNTCGNNNANNNTNCANNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1241 :N:0:
-NNANNGNTGGNNNTNNNCNTGNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1243 :N:0:
-NNANNANGGANNNANNNCNTANNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1247 :N:0:
-NCCAGCNTTTNNNTNNNTNCTNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1282 :N:0:
-NNANNANGGGNNNTNNNGNAGNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:132 :N:0:
-NNANNGNGGGNNNGNNNGNGGNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1320 :N:0:
-NNANNTNAGTNNNGNNNGNTANNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1372 :N:0:
-NACATTTTTTAGNTNANTTGTTNACNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1379 :N:0:
-NAATATAATTNNNTNNNTTAGANTTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1391 :N:0:
-NNGNNTNTAANNNANNNTNATNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:140 :N:0:
-NNANNTNTAANNNGNNNCNTTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1513 :N:0:
-NNNNNANNTTNNNANNNANAANNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1521 :N:0:
-NAACAANATTNNNTNNNANTANNTANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:155 :N:0:
-NNGNNCNAGTNNNCNNNANTTNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1555 :N:0:
-NNTNNGNAGANNNANNNCNTANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:164 :N:0:
-NNANNANTAANNNTNNNTNATNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1684 :N:0:
-NNGNNANGGTNNNGNNNTNTCNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1696 :N:0:
-NNANNGNNGCNNNGNNNANACNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:170 :N:0:
-NNTNNCNCACNNNGNNNGNTCNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:173 :N:0:
-NNNNNANNATNNNTNNNCNTTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1733 :N:0:
-NNANNGNGTCNNNTNNNTNAGNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1770 :N:0:
-NNCNNTNCTGNNNGNNNGNCANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:18 :N:0:
-NATCAGNCTGNNNANNNTNGTNNAANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1815 :N:0:
-NATGAAAATANNNTNNNTAAATNATNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1836 :N:0:
-NNNNNGNNTANNNGNNNTNCTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:184 :N:0:
-NNCNNTNTAANNNANNNTNATNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1886 :Y:0:
-NACATATGCATACATATATAATAGATANNN
-+
-%.9:;<217;:999;<;;<<<;;#######
- at machine1:HiMom:abcdeACXX:7:1:1:1906 :N:0:
-NNTNNCNATANNNCNNNTNCTNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1917 :N:0:
-NNNNNTNNGANNNCNNNANAANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:195 :N:0:
-NNANNGNGTGNNNGNNNCNATNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:1954 :N:0:
-NAGANTNCTTNNNGNNNGNAGNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:2 :N:0:
-NNANNGNGAANNNCNNNNNNNNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:2011 :N:0:
-NACAGCTGGCANNTNNNAGAGCNAGNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:240 :N:0:
-NNGNNANGTANNNTNNNTNCCNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:262 :N:0:
-NNCNNGNCATNNNANNNCNTGNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:264 :N:0:
-NAACTGNAATNNNCNNNANCANNCTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:299 :N:0:
-NNCNNTNGCANNNANNNCNAANNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:30 :N:0:
-NNANNANTTTNNNTNNNGNTCNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:353 :N:0:
-NNANNTNTAGNNNANNNTNATNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:367 :N:0:
-NNANNTNAGCNNNGNNNANGTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:41 :N:0:
-NNANNCNAAANNNGNNNTNCANNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:416 :N:0:
-NNANNCNAATNNNGNNNGNACNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:483 :N:0:
-NNGNNGNGGGNNNGNNNGNTTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:486 :N:0:
-NNANNANTTTNNNANNNANAGNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:495 :N:0:
-NNCNNANCGTNNNTNNNTNAANNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:508 :N:0:
-NNGNNCNCAGNNNTNNNCNCTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:517 :N:0:
-NTCATAAAACATCANTATTGGAAAGGANNN
-+
-%.75:<999578##################
- at machine1:HiMom:abcdeACXX:7:1:1:535 :N:0:
-NGCCCAAGTATTGANTATGTGCTCTAANNN
-+
-%.599:7187:940%0::52599#######
- at machine1:HiMom:abcdeACXX:7:1:1:55 :N:0:
-NTTTATGTCCTTNANAACTTAGNAGTTNNN
-+
-%/9<<83599####################
- at machine1:HiMom:abcdeACXX:7:1:1:554 :N:0:
-NNANNGNAGANNNGNNNTNTCNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:567 :N:0:
-NNCNNCNGTTNNNCNNNGNACNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:59 :N:0:
-NNANNGNTGCNNNTNNNTNACNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:613 :N:0:
-NNGNNANTATNNNCNNNGNATNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:622 :N:0:
-NNTNNCNAGTNNNCNNNANCTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:627 :N:0:
-NNANNTNGACNNNTNNNANGCNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:684 :N:0:
-NNTNNTNAGANNNCNNNANAGNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:72 :N:0:
-NACACACATATCACNCACATCATACACNNN
-+
-%..48696;5:6;.%)49;;;9########
- at machine1:HiMom:abcdeACXX:7:1:1:812 :N:0:
-NNANNCNAAGNNNTNNNANTCNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:874 :N:0:
-NNANNANGCCNNNGNNNTNTANNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:931 :N:0:
-NNTNNGNGATNNNGNNNCNTTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:965 :N:0:
-NACTAATCTTCCGCNCATATCCCCAAANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:1:994 :N:0:
-NNANNTNGATNNNTNNNGNTTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:2:1158 :Y:0:
-NGGGTCCTTCATAGTTTTTTTCTACTTTCC
-+
-%0777646;099:::95;;;688::99###
- at machine1:HiMom:abcdeACXX:7:1:2:1238 :N:0:
-NTCCTTATATTCAATTATTAATATTTTTAC
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:2:1275 :Y:0:
-NAGTGAAATAAGCCAGACACAGAAAGACAN
-+
-%/5204:99971773,44755-39717###
- at machine1:HiMom:abcdeACXX:7:1:2:1301 :N:0:
-NAGTAGACTGCATTAATTAATTGGAAGAGN
-+
-%0370)024263144:48;;##########
- at machine1:HiMom:abcdeACXX:7:1:2:1453 :Y:0:
-NATATCTTATTTTCTTTTCTTTCAGGCTCT
-+
-%.:7,,395255##################
- at machine1:HiMom:abcdeACXX:7:1:2:150 :N:0:
-NAAGACTTGATTATATCCCTTGTATGANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:2:1592 :Y:0:
-NGAAAACTGGCACAAGACAAGGATGCCCTC
-+
-%,67786861,3466(8485868648583#
- at machine1:HiMom:abcdeACXX:7:1:2:1706 :Y:0:
-NGATATGTGGATACAGCTCACAAAGAGNNN
-+
-%,99:6/566999/7###############
- at machine1:HiMom:abcdeACXX:7:1:2:1722 :N:0:
-NAAAGAAAATTAAAGAAAAATATACACGTN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:2:1727 :N:0:
-NTATTGAAGGACTTTTGTATCCTCCTTATN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:2:1753 :N:0:
-NGTTCACACAAGGATAATATTTTTGATTAT
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:2:1782 :Y:0:
-NACCAAGTGTTTGGAGTATGCTGCCTANNN
-+
-%0:::668885-5335/85###########
- at machine1:HiMom:abcdeACXX:7:1:2:1827 :Y:0:
-NAACCGAGGATGTACACTGTCCCTGTGAAA
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:2:1932 :Y:0:
-NAGCGATCCTCCCGCCTCTGCCTCCCANNN
-+
-%,1545541455##################
- at machine1:HiMom:abcdeACXX:7:1:2:1946 :N:0:
-NATCTTCTGGAATTTCTAACAGCTTGGAAN
-+
-%0515.,.35<997################
- at machine1:HiMom:abcdeACXX:7:1:2:209 :N:0:
-NGACTCAACTCCTGGGCTCCCTACGACCAT
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:2:246 :N:0:
-NGGAGGTTTCATTTAGCCGATATTGTGNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:2:25 :N:0:
-NGCTTTGGCAAGACAAATCTCCCGTCTGGN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:2:307 :N:0:
-NGGATGAACAGAAACTAAAATAACACANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:2:363 :N:0:
-NATATTCTTTTTTTTTATTTATCAGATNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:2:449 :N:0:
-NATTCTAATTCTAGGAAATTAACAATCNNN
-+
-%.9315<936970%0###############
- at machine1:HiMom:abcdeACXX:7:1:2:546 :N:0:
-NGGTTGTGTCTCTCTCAGCCTTTGGGATCN
-+
-%,46888444685-35##############
- at machine1:HiMom:abcdeACXX:7:1:2:605 :Y:0:
-NGCATTGAGCAGACGTGGCATCCAGATNNN
-+
-%)085222/55453################
- at machine1:HiMom:abcdeACXX:7:1:2:69 :N:0:
-NTCAGTCTGCTGTTTTAAAAAAATACTGTG
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:2:747 :N:0:
-NAACAACAGCGGAAAATAATAAAAAAAAAN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:2:786 :Y:0:
-NTAAACAATAATCTGATGATTTATAATCCN
-+
-%09<<<<;<;<8<9;<9<;<::<<::####
- at machine1:HiMom:abcdeACXX:7:1:2:858 :Y:0:
-NAAACGTTGCTGATCTTCTGTTTTAAACTA
-+
-%/;7-222265366-6977035:::;626;
- at machine1:HiMom:abcdeACXX:7:1:2:943 :Y:0:
-NAATACCAATAAACCTAGAATGTCTCATAC
-+
-%08<9646<6378744774:1005799<4#
- at machine1:HiMom:abcdeACXX:7:1:2:974 :Y:0:
-NGATCAATGATCACATCTTTGGATATGTAT
-+
-%/9979<99:999::9;;:7511<<<77<<
- at machine1:HiMom:abcdeACXX:7:1:2:988 :Y:0:
-NAAAGGAATGTTCAGCTCTGTGAGTTGAAC
-+
-%/92/04:2-2785-3875/404362-162
- at machine1:HiMom:abcdeACXX:7:1:3:1233 :N:0:
-NAACCAATTTCTTTACATACCAAATACGCC
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:3:1294 :N:0:
-TGTAACTTTACTTTAGTTGCTTATTTGTAG
-+
-BA############################
- at machine1:HiMom:abcdeACXX:7:1:3:405 :N:0:
-AAAAAACATAGAACGGGGTCAATATTTTAT
-+
-(?A>8(7B?<(:')?@)8(:(*:<8:0>'>
- at machine1:HiMom:abcdeACXX:7:1:3:579 :N:0:
-NGAAAAATGACCACACTTGCCTCCTGAGAA
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:3:673 :N:0:
-TCCTCAAAAACAAGATAAAACGGTTGAAAT
-+
->()>)''85BBC?#################
- at machine1:HiMom:abcdeACXX:7:1:3:890 :N:0:
-TGCTTCTGTTTCCGTTAGCTAGATAAAGTT
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:3:905 :N:0:
-TGTTATGTTTAATTTTCTTTAGCACCCTTC
-+
->7>?A:-<BA at 0>@:@8=A;5%7;9?=:9@
- at machine1:HiMom:abcdeACXX:7:1:3:918 :N:0:
-TTTTCATTCCTAGTCATCCACCCCATCAGA
-+
-0()@A=:2>3:>(/((<22A>:0(20:@)@
- at machine1:HiMom:abcdeACXX:7:2:0:1073 :N:0:
-NNNNNANCACNNNCNNNCNCANNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:1135 :N:0:
-NNNNNGNNGTNNNANNNTNTANNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:1198 :N:0:
-NNNNNTNCTANNNTNNNCNCANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:1278 :N:0:
-NNNNNNNNTANNNTNNNCNNANNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:135 :N:0:
-NNNNNNNNANNNNNNNNNNNGNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:1547 :N:0:
-NNNNNNNNCNNNNNNNNNNNGNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:1598 :N:0:
-NNNNNNNNATNNNTNNNANNGNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:1620 :N:0:
-NNNNNNNNCANNNNNNNANNCNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:1668 :N:0:
-NNNNNANATANNNANNNGNTGNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:186 :N:0:
-NNNNNNNNCCNNNANNNTNNTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:205 :N:0:
-NNNNNNNNANNNNNNNNTNNCNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:287 :N:0:
-NNNNNNNNCCNNNCNNNTNNANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:382 :N:0:
-NNNNNNNNCANNNTNNNTNNANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:441 :N:0:
-NNNNNNNNTTNNNANNNANNTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:50 :N:0:
-NNNNNNNNTNNNNNNNNTNNGNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:501 :N:0:
-NNNNNGNNAGNNNANNNCNCTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:73 :N:0:
-NNNNNANCATNNNGNNNANACNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:740 :N:0:
-NNNNNNNNTTNNNANNNTNNANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:766 :N:0:
-NNNNNNNNTGNNNANNNANNTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:0:87 :N:0:
-NNNNNNNNGNNNNNNNNANNTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1004 :N:0:
-NATTTATCACTANANATCCGCAAACCCTCC
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1034 :N:0:
-NATCATTTTCATNCNTTTCACTGATACATT
-+
-%.737:887471%-%1:8555545;696::
- at machine1:HiMom:abcdeACXX:7:2:1:1159 :N:0:
-NNACTTNTAGNNNGNNNAAATNNCCNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1168 :N:0:
-NNTCTANCTTNNNTNNNATTGNNTTNTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1180 :N:0:
-NNATGGNCTTNNNCNNNAGAANNTCNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1214 :N:0:
-NAAAAAAAAAAANANTATAAGAAAGAATCA
-+
-%035:#########################
- at machine1:HiMom:abcdeACXX:7:2:1:1221 :N:0:
-NGGTCACACTCACATAGTGTTCAGAGCACT
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1306 :N:0:
-NNACATNAAANNNTNNNAACANNGTNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1351 :N:0:
-NNNNNCNATANNNTNNNANAANNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1424 :N:0:
-NNTCATNTAGNNNCNNNATGGNNGTNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1452 :N:0:
-NGAAATTTGTAAAANCACCTGCAGAATACT
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1515 :N:0:
-NATTAAATATNANANNGTAATAATAATANN
-+
-%/9###########################
- at machine1:HiMom:abcdeACXX:7:2:1:1521 :N:0:
-NNACACNAAANNNGNNNATCTNNTTNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1536 :N:0:
-NAGCAAAGACTTNGNACCAACCCAAATGTT
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1543 :N:0:
-NNTTGANATCNNNANNNAATANNTANCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1617 :N:0:
-NNCCATNATCNNNGNNNCCAGNNGTNTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1627 :N:0:
-NNTGGTNAGANNNCNNNAAAANNCANTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1646 :N:0:
-NTTAATTATANNNANNTAAACATTCTAANN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1653 :N:0:
-NNAATTNAAANNNTNNNATCTNNAGNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1682 :N:0:
-NNTCTTNTTTNNNGNNNAAAANNAANTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:170 :Y:0:
-NAGAAGAAATGGGATCCTGCTGTGGCCAGT
-+
-%/888865284168866767663(6874/5
- at machine1:HiMom:abcdeACXX:7:2:1:1731 :N:0:
-NNTATANGAANNNTNNNTGCTNNAGNTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1755 :N:0:
-NNGTNANTCTNNNCNNNCNTGNNNGNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1812 :N:0:
-NNTTGCNCACNNNCNNNCCATNNAANGNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1853 :N:0:
-NNATCTNTTCNNNANNNAGTGNNATNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1919 :N:0:
-NNAATTNAAANNNANNNAGAANNAGNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1924 :N:0:
-NATATTCTGAAGNANNCCAATGAACCAAAN
-+
-%116<9579<7###################
- at machine1:HiMom:abcdeACXX:7:2:1:1933 :N:0:
-NAGGGTACATNTNCNNAATGTGCGGGTTNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1938 :Y:0:
-NAGTCCAGTGTCTCTGCTTCCGCAGGGACA
-+
-%/818865/058858644866457646668
- at machine1:HiMom:abcdeACXX:7:2:1:1950 :N:0:
-NNTTNANAAANNNCNNNTNCANNNTNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:1959 :N:0:
-NGACACATTCCTACNACAGAGAAAAATTTA
-+
-%*77;;<;<<:<;,%.::;:6:9::<4488
- at machine1:HiMom:abcdeACXX:7:2:1:1987 :N:0:
-NNATNGNACANNNCNNNTNGTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:2006 :N:0:
-NNGTATNTGANNNGNNNCCTTNNAGNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:211 :N:0:
-NNCTGANACANNNGNNNTGCANNACNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:234 :N:0:
-NAAGCCTGTGGGNANNCCCAGTGGGAGCGN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:242 :N:0:
-NNGCTCNAGCNNNANNNATATNNTTNGNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:262 :N:0:
-NNATTGNAATNNNCNNNTTCCNNATNTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:298 :N:0:
-NNTCAANTTGNNNTNNNCTGCNNTTNTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:312 :N:0:
-NNTTGCNAGANNNANNNAACTNNTGNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:363 :Y:0:
-NGAAAGGTTTTGCAGCATGTGCAAACTCAC
-+
-%-5565678:8177656503512/377856
- at machine1:HiMom:abcdeACXX:7:2:1:37 :N:0:
-NTGTAAACGANNNCNNTTCCTGTTCAGCNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:370 :N:0:
-NNCTGGNAGCNNNTNNNCATANNAANCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:377 :N:0:
-NNAGAANGTGNNNTNNNAAATNNAANANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:414 :N:0:
-NNTAGANAGCNNNANNNTCAGNNACNGNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:421 :N:0:
-NNGTTANTTCNNNANNNCGTGNNATNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:428 :N:0:
-NATGTGAATANTNANNTAGTTGGGATTCAN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:44 :N:0:
-NACTACCTCANGNANNAAGCAGGTTCTAAN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:466 :N:0:
-NACACTCACANCNANNTGTTTGGAATGANN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:555 :N:0:
-NNCAATNTCTNNNGNNNTACANNCTNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:558 :N:0:
-NAAAATATCANTNANNAATAAATAATCANN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:56 :N:0:
-NNGCCANGGTNNNANNNTCACNNGGNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:569 :N:0:
-NNAGGCNAGTNNNGNNNGTCCNNGTNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:604 :N:0:
-NATGATGAAACTCTNTCTCTACTAAAAATA
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:628 :N:0:
-NAGTATGCCCNCNCNNACCACTCCTATTNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:64 :N:0:
-NATTAATCTTNNNTNNGCACAATTCATTNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:684 :N:0:
-NAAAAATCAAATGANCATAATTTTATAAAA
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:699 :N:0:
-NNAATTNTTGNNNTNNNATTTNNGANTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:714 :N:0:
-NATTAACTTANANTNNACCACAACCTAANN
-+
-%.:###########################
- at machine1:HiMom:abcdeACXX:7:2:1:722 :N:0:
-NNCCTCNCTGNNNCNNNCTGTNNTGNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:749 :N:0:
-NNAGTGNTACNNNTNNNCTTGNNCTNTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:760 :N:0:
-NGTCTGTTTTATGTNAAATATTTTGTTTAA
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:8 :N:0:
-NNTGCGNTGGNNNCNNNAGGCNNTTNTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:833 :N:0:
-NNGAGCNCCTNNNANNNCTCCNNGANGNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:848 :N:0:
-NNTACTNAGTNNNGNNNTGTTNNGCNTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:893 :N:0:
-NGAGACAGAGTCTCNCTCTGTTCCCTAGCC
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:1:998 :N:0:
-NNATGTNTGCNNNANNNTATANNGGNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:2:0 :N:0:
-NATTCCTTNANNNNNNNNNNNNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:2:131 :Y:0:
-NATATATTGACAGCAGTCATGTTGTTGAAG
-+
-%0<<<:<959874492:96999969:7784
- at machine1:HiMom:abcdeACXX:7:2:2:1636 :N:0:
-NGTGTAAAAGTAGGGAAATACTATAGCAAG
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:2:1974 :N:0:
-NACGCCAATACAAAAATGTTGAAGCTAGCT
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:2:351 :N:0:
-NGGGGTTGAGGTGTAAATAGAACATTTGTA
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:2:646 :N:0:
-NGAATCTAAGAAGACACAAAACTAAGGAAA
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:2:828 :N:0:
-NTCAAGTCAATTTGGGACTTGAAACAGCTC
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:1529 :N:0:
-NTTATATGAATAGATAAATAAATAATCAAT
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:179 :N:0:
-CATTATTGTTAGACTGATTTTTTATAATCT
-+
-B@)104..*0-A(@@(<A9A<(+9)-=6(B
- at machine1:HiMom:abcdeACXX:7:2:3:198 :N:0:
-TGTCATTTTCTTTGCCTTAATTGTTCTTCT
-+
-5 at CBB7-*<=####################
- at machine1:HiMom:abcdeACXX:7:2:3:2030 :N:0:
-CGAGATAATTTTTTAAAAAAAGTCCAAAAA
-+
-((@;()@==*7<(5A@<C>###########
- at machine1:HiMom:abcdeACXX:7:2:3:247 :N:0:
-TGTACATGACCAGGTAATTTGGTTATGTGA
-+
-<@596353;)>@A7=:,A0'6>########
- at machine1:HiMom:abcdeACXX:7:2:3:4 :N:0:
-AGAGGCAATAAGTTTTAANNNNNNNNNNNN
-+
-A>BA at 9BAB3AA##################
- at machine1:HiMom:abcdeACXX:7:2:3:862 :N:0:
-NCTTTAAGAAATCATTCATTCTGCAAACAC
-+
-##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/N.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/N.barcode_1.fastq
deleted file mode 100644
index 37130a3..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/N.barcode_1.fastq
+++ /dev/null
@@ -1,892 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:0:1038 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:1093 :N:0:
-NNNNNTGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:113 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:1193 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:1291 :N:0:
-NNNNNGNN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:1307 :N:0:
-NNNNNTAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:1434 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:1475 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:1690 :N:0:
-NNNNNANN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:1703 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:1940 :N:0:
-NNNNNCNN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:2001 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:205 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:275 :N:0:
-NNNNNATN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:324 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:37 :N:0:
-NNNNNGNN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:464 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:586 :N:0:
-NNNNNCNN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:841 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:0:879 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1013 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:111 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1153 :N:0:
-NNNNNCTN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1184 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1241 :N:0:
-NNNNNCTN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1243 :N:0:
-NNNNNTGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1247 :N:0:
-NNNNNACN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1282 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:132 :N:0:
-NNNNNTGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1320 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1372 :N:0:
-NNNGNTTA
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1379 :N:0:
-NNNCNGAT
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1391 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:140 :N:0:
-NNNNNCAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1513 :N:0:
-NNNNNCTN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1521 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:155 :N:0:
-NNNNNCAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1555 :N:0:
-NNNNNCAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:164 :N:0:
-NNNNNTTN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1684 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1696 :N:0:
-NNNNNCTN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:170 :N:0:
-NNNNNACN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:173 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1733 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1770 :N:0:
-NNNNNTCN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:18 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1815 :N:0:
-NNNTNGAC
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1836 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:184 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1886 :Y:0:
-NNNGNGCC
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1906 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1917 :N:0:
-NNNNNACN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:195 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:1954 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:2 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:2011 :N:0:
-NNNGNTAG
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:240 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:262 :N:0:
-NNNNNCAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:264 :N:0:
-NNNNNCGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:299 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:30 :N:0:
-NNNNNACN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:353 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:367 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:41 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:416 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:483 :N:0:
-NNNNNTAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:486 :N:0:
-NNNNNTGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:495 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:508 :N:0:
-NNNNNCTN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:517 :N:0:
-NNNCNAGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:535 :N:0:
-NNNCNCGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:55 :N:0:
-NNNGNTTA
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:554 :N:0:
-NNNNNTAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:567 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:59 :N:0:
-NNNNNACN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:613 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:622 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:627 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:684 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:72 :N:0:
-NNNTNGAC
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:812 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:874 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:931 :N:0:
-NNNNNCAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:965 :N:0:
-NNNTNTAA
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:1:994 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:1158 :Y:0:
-NNCTTAGC
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:1238 :N:0:
-NNCTAAGC
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:1275 :Y:0:
-NNNANCTG
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:1301 :N:0:
-NNNTAACA
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:1453 :Y:0:
-NNACCAGG
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:150 :N:0:
-NNNANCCT
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:1592 :Y:0:
-NNNGAGCC
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:1706 :Y:0:
-NNNCNGAT
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:1722 :N:0:
-NNNTCGAC
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:1727 :N:0:
-NNNTNCTT
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:1753 :N:0:
-NNTGCTTA
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:1782 :Y:0:
-NNNTNAGC
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:1827 :Y:0:
-NNCAACTG
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:1932 :Y:0:
-NNNCNAGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:1946 :N:0:
-NNNTNGAC
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:209 :N:0:
-NNCATTTC
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:246 :N:0:
-NNNANTTC
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:25 :N:0:
-NNNGATGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:307 :N:0:
-NNNTNGAC
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:363 :N:0:
-NNNTNCTT
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:449 :N:0:
-NNNGNTGT
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:546 :N:0:
-NNNANGTT
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:605 :Y:0:
-NNNTNGAC
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:69 :N:0:
-NNGGAGCC
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:747 :N:0:
-NNNCCAGG
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:786 :Y:0:
-NNNGATGT
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:858 :Y:0:
-NNACATCT
-+
-%%/57799
- at machine1:HiMom:abcdeACXX:7:1:2:943 :Y:0:
-NNACCAGG
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:974 :Y:0:
-NNTATGTT
-+
-%%0::::<
- at machine1:HiMom:abcdeACXX:7:1:2:988 :Y:0:
-NNTGGCGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:3:1233 :N:0:
-CCAACAGG
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:3:1294 :N:0:
-TCACAATG
-+
-*37<<@5<
- at machine1:HiMom:abcdeACXX:7:1:3:405 :N:0:
-ACACAAGA
-+
-0(><=###
- at machine1:HiMom:abcdeACXX:7:1:3:579 :N:0:
-AATCATGT
-+
-73######
- at machine1:HiMom:abcdeACXX:7:1:3:673 :N:0:
-TGCCCAAA
-+
-(<######
- at machine1:HiMom:abcdeACXX:7:1:3:890 :N:0:
-GTCACCAT
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:3:905 :N:0:
-ACATCCTA
-+
-AA78/<:#
- at machine1:HiMom:abcdeACXX:7:1:3:918 :N:0:
-ACTACCTT
-+
-)?4B>###
- at machine1:HiMom:abcdeACXX:7:2:0:1073 :N:0:
-NNNNNCAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:1135 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:1198 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:1278 :N:0:
-NNNNNTAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:135 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:1547 :N:0:
-NNNNNCAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:1598 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:1620 :N:0:
-NNNNNTGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:1668 :N:0:
-NNNNNCTN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:186 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:205 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:287 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:382 :N:0:
-NNNNNTAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:441 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:50 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:501 :N:0:
-NNNNNTAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:73 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:740 :N:0:
-NNNNNGGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:766 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:0:87 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1004 :N:0:
-NNNGCCGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1034 :N:0:
-NNNAGCCT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1159 :N:0:
-NNNTNGAC
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1168 :N:0:
-NNNGNTAG
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1180 :N:0:
-NNNTNAGC
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1214 :N:0:
-NNNCATGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1221 :N:0:
-NNGGATGT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1306 :N:0:
-NNNANCTG
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1351 :N:0:
-NNNNNTTN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1424 :N:0:
-NNNCNTCT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1452 :N:0:
-NNAGATCC
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1515 :N:0:
-NNNGNATG
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1521 :N:0:
-NNNCNAGG
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1536 :N:0:
-NNACATCT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1543 :N:0:
-NNNANTTC
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1617 :N:0:
-NNNCNAGG
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1627 :N:0:
-NNNANCTG
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1646 :N:0:
-NNNTNGAC
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1653 :N:0:
-NNNGNTGT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1682 :N:0:
-NNNGNGCC
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:170 :Y:0:
-NNGAGCCT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1731 :N:0:
-NNNTNAGC
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1755 :N:0:
-NNNNNCAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1812 :N:0:
-NNNCNTAT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1853 :N:0:
-NNNCNCGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1919 :N:0:
-NNNANCTG
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1924 :N:0:
-NNNAACTG
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1933 :N:0:
-NNNTTAGC
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1938 :Y:0:
-NNCTCGAC
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1950 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1959 :N:0:
-NNTGCTTA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:1987 :N:0:
-NNNNNTAN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:2006 :N:0:
-NNNGNGCC
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:211 :N:0:
-NNNGNTGT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:234 :N:0:
-NNNGCTTA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:242 :N:0:
-NNNCNCGC
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:262 :N:0:
-NNNCNAGG
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:298 :N:0:
-NNNGNTAG
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:312 :N:0:
-NNNANGTT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:363 :Y:0:
-NNTATGTT
-+
-%%.99999
- at machine1:HiMom:abcdeACXX:7:2:1:37 :N:0:
-NNNGNCGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:370 :N:0:
-NNNANCAT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:377 :N:0:
-NNNCNTCT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:414 :N:0:
-NNNGNTTA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:421 :N:0:
-NNNANCCT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:428 :N:0:
-NNNATGTT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:44 :N:0:
-NNNAGCGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:466 :N:0:
-NNNTNACA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:555 :N:0:
-NNNCNGAT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:558 :N:0:
-NNNANCGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:56 :N:0:
-NNNTNAGC
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:569 :N:0:
-NNNANCTG
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:604 :N:0:
-NNCAACTG
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:628 :N:0:
-NNNTAACA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:64 :N:0:
-NNNANGTT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:684 :N:0:
-NNAAACGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:699 :N:0:
-NNNCNCGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:714 :N:0:
-NNNAGCGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:722 :N:0:
-NNNCNAGG
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:749 :N:0:
-NNNTNGAC
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:760 :N:0:
-NNACAACA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:8 :N:0:
-NNNANNNN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:833 :N:0:
-NNNANCCT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:848 :N:0:
-NNNANCGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:893 :N:0:
-NNCAATTC
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:1:998 :N:0:
-NNNANGTT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:2:0 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:2:131 :Y:0:
-CACAATCC
-+
-AACCBCA@
- at machine1:HiMom:abcdeACXX:7:2:2:1636 :N:0:
-ATCAACCC
-+
-368?####
- at machine1:HiMom:abcdeACXX:7:2:2:1974 :N:0:
-AGCAATCT
-+
->#######
- at machine1:HiMom:abcdeACXX:7:2:2:351 :N:0:
-TGATAGAA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:2:646 :N:0:
-ATCAATTA
-+
-((>4/406
- at machine1:HiMom:abcdeACXX:7:2:2:828 :N:0:
-TATATCGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:3:1529 :N:0:
-TAGAACCT
-+
-9)@73?B=
- at machine1:HiMom:abcdeACXX:7:2:3:179 :N:0:
-GTTTATTA
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:3:198 :N:0:
-CAGGATCT
-+
-5)0*@782
- at machine1:HiMom:abcdeACXX:7:2:3:2030 :N:0:
-GATCAAGA
-+
-(((>(<@<
- at machine1:HiMom:abcdeACXX:7:2:3:247 :N:0:
-CGGTAGCT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:3:4 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:3:862 :N:0:
-TAACAAGA
-+
-4)=69)=@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.1.fastq
deleted file mode 100644
index 9603643..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.1.fastq
+++ /dev/null
@@ -1,892 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:0:1038 :N:0:
-NNNNNCNNCANNNCNNNCNCCNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:1093 :N:0:
-NNNNNCNNGTNNNANNNGNAANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:113 :N:0:
-NNNNNNNNGNNNNNNNNNNNANNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:1193 :N:0:
-NNNNNNNNTNNNNTNNNTNNTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:1291 :N:0:
-NNNNNNNNANNNNNNNNANNTNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:1307 :N:0:
-NNNNNNNNCNNNNANNNTNNTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:1434 :N:0:
-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:1475 :N:0:
-NNNNNGNNANNNNANNNANNANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:1690 :N:0:
-NNNNNNNNANNNNNNNNGNNCNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:1703 :N:0:
-NNNNNNNNANNNNNNNNNNNANNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:1940 :N:0:
-NNNNNNNNCNNNNNNNNTNNTNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:2001 :N:0:
-NNNNNANNTGNNNGNNNANGCNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:205 :N:0:
-NNNNNNNNANNNNNNNNANNTNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:275 :N:0:
-NNNNNANNCANNNTNNNGNCCNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:324 :N:0:
-NNNNNNNNTNNNNNNNNTNNANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:37 :N:0:
-NNNNNNNNANNNNNNNNCNNTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:464 :N:0:
-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:586 :N:0:
-NNNNNNNNCNNNNNNNNCNNCNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:841 :N:0:
-NNNNNNNNCNNNNNNNNNNNTNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:0:879 :N:0:
-NNNNNNNNTNNNNNNNNNNNTNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1013 :N:0:
-NNCNNTNCAGNNNCNNNANGTNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:111 :N:0:
-NNCNNTNGCGNNNTNNNANCTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1153 :N:0:
-NNTNNTNTGGNNNTNNNCNTCNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1184 :N:0:
-NNANNGNTCGNNNANNNTNCANNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1241 :N:0:
-NNANNGNTGGNNNTNNNCNTGNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1243 :N:0:
-NNANNANGGANNNANNNCNTANNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1247 :N:0:
-NCCAGCNTTTNNNTNNNTNCTNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1282 :N:0:
-NNANNANGGGNNNTNNNGNAGNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:132 :N:0:
-NNANNGNGGGNNNGNNNGNGGNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1320 :N:0:
-NNANNTNAGTNNNGNNNGNTANNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1372 :N:0:
-NACATTTTTTAGNTNANTTGTTNACNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1379 :N:0:
-NAATATAATTNNNTNNNTTAGANTTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1391 :N:0:
-NNGNNTNTAANNNANNNTNATNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:140 :N:0:
-NNANNTNTAANNNGNNNCNTTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1513 :N:0:
-NNNNNANNTTNNNANNNANAANNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1521 :N:0:
-NAACAANATTNNNTNNNANTANNTANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:155 :N:0:
-NNGNNCNAGTNNNCNNNANTTNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1555 :N:0:
-NNTNNGNAGANNNANNNCNTANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:164 :N:0:
-NNANNANTAANNNTNNNTNATNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1684 :N:0:
-NNGNNANGGTNNNGNNNTNTCNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1696 :N:0:
-NNANNGNNGCNNNGNNNANACNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:170 :N:0:
-NNTNNCNCACNNNGNNNGNTCNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:173 :N:0:
-NNNNNANNATNNNTNNNCNTTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1733 :N:0:
-NNANNGNGTCNNNTNNNTNAGNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1770 :N:0:
-NNCNNTNCTGNNNGNNNGNCANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:18 :N:0:
-NATCAGNCTGNNNANNNTNGTNNAANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1815 :N:0:
-NATGAAAATANNNTNNNTAAATNATNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1836 :N:0:
-NNNNNGNNTANNNGNNNTNCTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:184 :N:0:
-NNCNNTNTAANNNANNNTNATNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1886 :Y:0:
-NACATATGCATACATATATAATAGATANNN
-+
-%.9:;<217;:999;<;;<<<;;#######
- at machine1:HiMom:abcdeACXX:9:1:1:1906 :N:0:
-NNTNNCNATANNNCNNNTNCTNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1917 :N:0:
-NNNNNTNNGANNNCNNNANAANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:195 :N:0:
-NNANNGNGTGNNNGNNNCNATNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:1954 :N:0:
-NAGANTNCTTNNNGNNNGNAGNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:2 :N:0:
-NNANNGNGAANNNCNNNNNNNNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:2011 :N:0:
-NACAGCTGGCANNTNNNAGAGCNAGNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:240 :N:0:
-NNGNNANGTANNNTNNNTNCCNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:262 :N:0:
-NNCNNGNCATNNNANNNCNTGNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:264 :N:0:
-NAACTGNAATNNNCNNNANCANNCTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:299 :N:0:
-NNCNNTNGCANNNANNNCNAANNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:30 :N:0:
-NNANNANTTTNNNTNNNGNTCNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:353 :N:0:
-NNANNTNTAGNNNANNNTNATNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:367 :N:0:
-NNANNTNAGCNNNGNNNANGTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:41 :N:0:
-NNANNCNAAANNNGNNNTNCANNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:416 :N:0:
-NNANNCNAATNNNGNNNGNACNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:483 :N:0:
-NNGNNGNGGGNNNGNNNGNTTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:486 :N:0:
-NNANNANTTTNNNANNNANAGNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:495 :N:0:
-NNCNNANCGTNNNTNNNTNAANNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:508 :N:0:
-NNGNNCNCAGNNNTNNNCNCTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:517 :N:0:
-NTCATAAAACATCANTATTGGAAAGGANNN
-+
-%.75:<999578##################
- at machine1:HiMom:abcdeACXX:9:1:1:535 :N:0:
-NGCCCAAGTATTGANTATGTGCTCTAANNN
-+
-%.599:7187:940%0::52599#######
- at machine1:HiMom:abcdeACXX:9:1:1:55 :N:0:
-NTTTATGTCCTTNANAACTTAGNAGTTNNN
-+
-%/9<<83599####################
- at machine1:HiMom:abcdeACXX:9:1:1:554 :N:0:
-NNANNGNAGANNNGNNNTNTCNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:567 :N:0:
-NNCNNCNGTTNNNCNNNGNACNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:59 :N:0:
-NNANNGNTGCNNNTNNNTNACNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:613 :N:0:
-NNGNNANTATNNNCNNNGNATNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:622 :N:0:
-NNTNNCNAGTNNNCNNNANCTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:627 :N:0:
-NNANNTNGACNNNTNNNANGCNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:684 :N:0:
-NNTNNTNAGANNNCNNNANAGNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:72 :N:0:
-NACACACATATCACNCACATCATACACNNN
-+
-%..48696;5:6;.%)49;;;9########
- at machine1:HiMom:abcdeACXX:9:1:1:812 :N:0:
-NNANNCNAAGNNNTNNNANTCNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:874 :N:0:
-NNANNANGCCNNNGNNNTNTANNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:931 :N:0:
-NNTNNGNGATNNNGNNNCNTTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:965 :N:0:
-NACTAATCTTCCGCNCATATCCCCAAANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:1:994 :N:0:
-NNANNTNGATNNNTNNNGNTTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:2:1158 :Y:0:
-NGGGTCCTTCATAGTTTTTTTCTACTTTCC
-+
-%0777646;099:::95;;;688::99###
- at machine1:HiMom:abcdeACXX:9:1:2:1238 :N:0:
-NTCCTTATATTCAATTATTAATATTTTTAC
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:2:1275 :Y:0:
-NAGTGAAATAAGCCAGACACAGAAAGACAN
-+
-%/5204:99971773,44755-39717###
- at machine1:HiMom:abcdeACXX:9:1:2:1301 :N:0:
-NAGTAGACTGCATTAATTAATTGGAAGAGN
-+
-%0370)024263144:48;;##########
- at machine1:HiMom:abcdeACXX:9:1:2:1453 :Y:0:
-NATATCTTATTTTCTTTTCTTTCAGGCTCT
-+
-%.:7,,395255##################
- at machine1:HiMom:abcdeACXX:9:1:2:150 :N:0:
-NAAGACTTGATTATATCCCTTGTATGANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:2:1592 :Y:0:
-NGAAAACTGGCACAAGACAAGGATGCCCTC
-+
-%,67786861,3466(8485868648583#
- at machine1:HiMom:abcdeACXX:9:1:2:1706 :Y:0:
-NGATATGTGGATACAGCTCACAAAGAGNNN
-+
-%,99:6/566999/7###############
- at machine1:HiMom:abcdeACXX:9:1:2:1722 :N:0:
-NAAAGAAAATTAAAGAAAAATATACACGTN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:2:1727 :N:0:
-NTATTGAAGGACTTTTGTATCCTCCTTATN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:2:1753 :N:0:
-NGTTCACACAAGGATAATATTTTTGATTAT
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:2:1782 :Y:0:
-NACCAAGTGTTTGGAGTATGCTGCCTANNN
-+
-%0:::668885-5335/85###########
- at machine1:HiMom:abcdeACXX:9:1:2:1827 :Y:0:
-NAACCGAGGATGTACACTGTCCCTGTGAAA
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:2:1932 :Y:0:
-NAGCGATCCTCCCGCCTCTGCCTCCCANNN
-+
-%,1545541455##################
- at machine1:HiMom:abcdeACXX:9:1:2:1946 :N:0:
-NATCTTCTGGAATTTCTAACAGCTTGGAAN
-+
-%0515.,.35<997################
- at machine1:HiMom:abcdeACXX:9:1:2:209 :N:0:
-NGACTCAACTCCTGGGCTCCCTACGACCAT
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:2:246 :N:0:
-NGGAGGTTTCATTTAGCCGATATTGTGNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:2:25 :N:0:
-NGCTTTGGCAAGACAAATCTCCCGTCTGGN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:2:307 :N:0:
-NGGATGAACAGAAACTAAAATAACACANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:2:363 :N:0:
-NATATTCTTTTTTTTTATTTATCAGATNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:2:449 :N:0:
-NATTCTAATTCTAGGAAATTAACAATCNNN
-+
-%.9315<936970%0###############
- at machine1:HiMom:abcdeACXX:9:1:2:546 :N:0:
-NGGTTGTGTCTCTCTCAGCCTTTGGGATCN
-+
-%,46888444685-35##############
- at machine1:HiMom:abcdeACXX:9:1:2:605 :Y:0:
-NGCATTGAGCAGACGTGGCATCCAGATNNN
-+
-%)085222/55453################
- at machine1:HiMom:abcdeACXX:9:1:2:69 :N:0:
-NTCAGTCTGCTGTTTTAAAAAAATACTGTG
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:2:747 :N:0:
-NAACAACAGCGGAAAATAATAAAAAAAAAN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:2:786 :Y:0:
-NTAAACAATAATCTGATGATTTATAATCCN
-+
-%09<<<<;<;<8<9;<9<;<::<<::####
- at machine1:HiMom:abcdeACXX:9:1:2:858 :Y:0:
-NAAACGTTGCTGATCTTCTGTTTTAAACTA
-+
-%/;7-222265366-6977035:::;626;
- at machine1:HiMom:abcdeACXX:9:1:2:943 :Y:0:
-NAATACCAATAAACCTAGAATGTCTCATAC
-+
-%08<9646<6378744774:1005799<4#
- at machine1:HiMom:abcdeACXX:9:1:2:974 :Y:0:
-NGATCAATGATCACATCTTTGGATATGTAT
-+
-%/9979<99:999::9;;:7511<<<77<<
- at machine1:HiMom:abcdeACXX:9:1:2:988 :Y:0:
-NAAAGGAATGTTCAGCTCTGTGAGTTGAAC
-+
-%/92/04:2-2785-3875/404362-162
- at machine1:HiMom:abcdeACXX:9:1:3:1233 :N:0:
-NAACCAATTTCTTTACATACCAAATACGCC
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:3:1294 :N:0:
-TGTAACTTTACTTTAGTTGCTTATTTGTAG
-+
-BA############################
- at machine1:HiMom:abcdeACXX:9:1:3:405 :N:0:
-AAAAAACATAGAACGGGGTCAATATTTTAT
-+
-(?A>8(7B?<(:')?@)8(:(*:<8:0>'>
- at machine1:HiMom:abcdeACXX:9:1:3:579 :N:0:
-NGAAAAATGACCACACTTGCCTCCTGAGAA
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:3:673 :N:0:
-TCCTCAAAAACAAGATAAAACGGTTGAAAT
-+
->()>)''85BBC?#################
- at machine1:HiMom:abcdeACXX:9:1:3:890 :N:0:
-TGCTTCTGTTTCCGTTAGCTAGATAAAGTT
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:3:905 :N:0:
-TGTTATGTTTAATTTTCTTTAGCACCCTTC
-+
->7>?A:-<BA at 0>@:@8=A;5%7;9?=:9@
- at machine1:HiMom:abcdeACXX:9:1:3:918 :N:0:
-TTTTCATTCCTAGTCATCCACCCCATCAGA
-+
-0()@A=:2>3:>(/((<22A>:0(20:@)@
- at machine1:HiMom:abcdeACXX:9:2:0:1073 :N:0:
-NNNNNANCACNNNCNNNCNCANNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:1135 :N:0:
-NNNNNGNNGTNNNANNNTNTANNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:1198 :N:0:
-NNNNNTNCTANNNTNNNCNCANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:1278 :N:0:
-NNNNNNNNTANNNTNNNCNNANNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:135 :N:0:
-NNNNNNNNANNNNNNNNNNNGNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:1547 :N:0:
-NNNNNNNNCNNNNNNNNNNNGNNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:1598 :N:0:
-NNNNNNNNATNNNTNNNANNGNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:1620 :N:0:
-NNNNNNNNCANNNNNNNANNCNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:1668 :N:0:
-NNNNNANATANNNANNNGNTGNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:186 :N:0:
-NNNNNNNNCCNNNANNNTNNTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:205 :N:0:
-NNNNNNNNANNNNNNNNTNNCNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:287 :N:0:
-NNNNNNNNCCNNNCNNNTNNANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:382 :N:0:
-NNNNNNNNCANNNTNNNTNNANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:441 :N:0:
-NNNNNNNNTTNNNANNNANNTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:50 :N:0:
-NNNNNNNNTNNNNNNNNTNNGNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:501 :N:0:
-NNNNNGNNAGNNNANNNCNCTNNNCNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:73 :N:0:
-NNNNNANCATNNNGNNNANACNNNGNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:740 :N:0:
-NNNNNNNNTTNNNANNNTNNANNNANNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:766 :N:0:
-NNNNNNNNTGNNNANNNANNTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:0:87 :N:0:
-NNNNNNNNGNNNNNNNNANNTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1004 :N:0:
-NATTTATCACTANANATCCGCAAACCCTCC
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1034 :N:0:
-NATCATTTTCATNCNTTTCACTGATACATT
-+
-%.737:887471%-%1:8555545;696::
- at machine1:HiMom:abcdeACXX:9:2:1:1159 :N:0:
-NNACTTNTAGNNNGNNNAAATNNCCNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1168 :N:0:
-NNTCTANCTTNNNTNNNATTGNNTTNTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1180 :N:0:
-NNATGGNCTTNNNCNNNAGAANNTCNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1214 :N:0:
-NAAAAAAAAAAANANTATAAGAAAGAATCA
-+
-%035:#########################
- at machine1:HiMom:abcdeACXX:9:2:1:1221 :N:0:
-NGGTCACACTCACATAGTGTTCAGAGCACT
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1306 :N:0:
-NNACATNAAANNNTNNNAACANNGTNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1351 :N:0:
-NNNNNCNATANNNTNNNANAANNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1424 :N:0:
-NNTCATNTAGNNNCNNNATGGNNGTNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1452 :N:0:
-NGAAATTTGTAAAANCACCTGCAGAATACT
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1515 :N:0:
-NATTAAATATNANANNGTAATAATAATANN
-+
-%/9###########################
- at machine1:HiMom:abcdeACXX:9:2:1:1521 :N:0:
-NNACACNAAANNNGNNNATCTNNTTNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1536 :N:0:
-NAGCAAAGACTTNGNACCAACCCAAATGTT
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1543 :N:0:
-NNTTGANATCNNNANNNAATANNTANCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1617 :N:0:
-NNCCATNATCNNNGNNNCCAGNNGTNTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1627 :N:0:
-NNTGGTNAGANNNCNNNAAAANNCANTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1646 :N:0:
-NTTAATTATANNNANNTAAACATTCTAANN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1653 :N:0:
-NNAATTNAAANNNTNNNATCTNNAGNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1682 :N:0:
-NNTCTTNTTTNNNGNNNAAAANNAANTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:170 :Y:0:
-NAGAAGAAATGGGATCCTGCTGTGGCCAGT
-+
-%/888865284168866767663(6874/5
- at machine1:HiMom:abcdeACXX:9:2:1:1731 :N:0:
-NNTATANGAANNNTNNNTGCTNNAGNTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1755 :N:0:
-NNGTNANTCTNNNCNNNCNTGNNNGNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1812 :N:0:
-NNTTGCNCACNNNCNNNCCATNNAANGNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1853 :N:0:
-NNATCTNTTCNNNANNNAGTGNNATNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1919 :N:0:
-NNAATTNAAANNNANNNAGAANNAGNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1924 :N:0:
-NATATTCTGAAGNANNCCAATGAACCAAAN
-+
-%116<9579<7###################
- at machine1:HiMom:abcdeACXX:9:2:1:1933 :N:0:
-NAGGGTACATNTNCNNAATGTGCGGGTTNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1938 :Y:0:
-NAGTCCAGTGTCTCTGCTTCCGCAGGGACA
-+
-%/818865/058858644866457646668
- at machine1:HiMom:abcdeACXX:9:2:1:1950 :N:0:
-NNTTNANAAANNNCNNNTNCANNNTNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:1959 :N:0:
-NGACACATTCCTACNACAGAGAAAAATTTA
-+
-%*77;;<;<<:<;,%.::;:6:9::<4488
- at machine1:HiMom:abcdeACXX:9:2:1:1987 :N:0:
-NNATNGNACANNNCNNNTNGTNNNTNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:2006 :N:0:
-NNGTATNTGANNNGNNNCCTTNNAGNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:211 :N:0:
-NNCTGANACANNNGNNNTGCANNACNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:234 :N:0:
-NAAGCCTGTGGGNANNCCCAGTGGGAGCGN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:242 :N:0:
-NNGCTCNAGCNNNANNNATATNNTTNGNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:262 :N:0:
-NNATTGNAATNNNCNNNTTCCNNATNTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:298 :N:0:
-NNTCAANTTGNNNTNNNCTGCNNTTNTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:312 :N:0:
-NNTTGCNAGANNNANNNAACTNNTGNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:363 :Y:0:
-NGAAAGGTTTTGCAGCATGTGCAAACTCAC
-+
-%-5565678:8177656503512/377856
- at machine1:HiMom:abcdeACXX:9:2:1:37 :N:0:
-NTGTAAACGANNNCNNTTCCTGTTCAGCNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:370 :N:0:
-NNCTGGNAGCNNNTNNNCATANNAANCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:377 :N:0:
-NNAGAANGTGNNNTNNNAAATNNAANANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:414 :N:0:
-NNTAGANAGCNNNANNNTCAGNNACNGNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:421 :N:0:
-NNGTTANTTCNNNANNNCGTGNNATNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:428 :N:0:
-NATGTGAATANTNANNTAGTTGGGATTCAN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:44 :N:0:
-NACTACCTCANGNANNAAGCAGGTTCTAAN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:466 :N:0:
-NACACTCACANCNANNTGTTTGGAATGANN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:555 :N:0:
-NNCAATNTCTNNNGNNNTACANNCTNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:558 :N:0:
-NAAAATATCANTNANNAATAAATAATCANN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:56 :N:0:
-NNGCCANGGTNNNANNNTCACNNGGNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:569 :N:0:
-NNAGGCNAGTNNNGNNNGTCCNNGTNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:604 :N:0:
-NATGATGAAACTCTNTCTCTACTAAAAATA
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:628 :N:0:
-NAGTATGCCCNCNCNNACCACTCCTATTNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:64 :N:0:
-NATTAATCTTNNNTNNGCACAATTCATTNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:684 :N:0:
-NAAAAATCAAATGANCATAATTTTATAAAA
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:699 :N:0:
-NNAATTNTTGNNNTNNNATTTNNGANTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:714 :N:0:
-NATTAACTTANANTNNACCACAACCTAANN
-+
-%.:###########################
- at machine1:HiMom:abcdeACXX:9:2:1:722 :N:0:
-NNCCTCNCTGNNNCNNNCTGTNNTGNCNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:749 :N:0:
-NNAGTGNTACNNNTNNNCTTGNNCTNTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:760 :N:0:
-NGTCTGTTTTATGTNAAATATTTTGTTTAA
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:8 :N:0:
-NNTGCGNTGGNNNCNNNAGGCNNTTNTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:833 :N:0:
-NNGAGCNCCTNNNANNNCTCCNNGANGNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:848 :N:0:
-NNTACTNAGTNNNGNNNTGTTNNGCNTNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:893 :N:0:
-NGAGACAGAGTCTCNCTCTGTTCCCTAGCC
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:1:998 :N:0:
-NNATGTNTGCNNNANNNTATANNGGNANNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:2:0 :N:0:
-NATTCCTTNANNNNNNNNNNNNNNNNNNNN
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:2:131 :Y:0:
-NATATATTGACAGCAGTCATGTTGTTGAAG
-+
-%0<<<:<959874492:96999969:7784
- at machine1:HiMom:abcdeACXX:9:2:2:1636 :N:0:
-NGTGTAAAAGTAGGGAAATACTATAGCAAG
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:2:1974 :N:0:
-NACGCCAATACAAAAATGTTGAAGCTAGCT
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:2:351 :N:0:
-NGGGGTTGAGGTGTAAATAGAACATTTGTA
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:2:646 :N:0:
-NGAATCTAAGAAGACACAAAACTAAGGAAA
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:2:828 :N:0:
-NTCAAGTCAATTTGGGACTTGAAACAGCTC
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:1529 :N:0:
-NTTATATGAATAGATAAATAAATAATCAAT
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:179 :N:0:
-CATTATTGTTAGACTGATTTTTTATAATCT
-+
-B@)104..*0-A(@@(<A9A<(+9)-=6(B
- at machine1:HiMom:abcdeACXX:9:2:3:198 :N:0:
-TGTCATTTTCTTTGCCTTAATTGTTCTTCT
-+
-5 at CBB7-*<=####################
- at machine1:HiMom:abcdeACXX:9:2:3:2030 :N:0:
-CGAGATAATTTTTTAAAAAAAGTCCAAAAA
-+
-((@;()@==*7<(5A@<C>###########
- at machine1:HiMom:abcdeACXX:9:2:3:247 :N:0:
-TGTACATGACCAGGTAATTTGGTTATGTGA
-+
-<@596353;)>@A7=:,A0'6>########
- at machine1:HiMom:abcdeACXX:9:2:3:4 :N:0:
-AGAGGCAATAAGTTTTAANNNNNNNNNNNN
-+
-A>BA at 9BAB3AA##################
- at machine1:HiMom:abcdeACXX:9:2:3:862 :N:0:
-NCTTTAAGAAATCATTCATTCTGCAAACAC
-+
-##############################
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.barcode_1.fastq
deleted file mode 100644
index d03e8d4..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.barcode_1.fastq
+++ /dev/null
@@ -1,892 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:0:1038 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1093 :N:0:
-NNNNNTGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:113 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1193 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1291 :N:0:
-NNNNNGNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1307 :N:0:
-NNNNNTAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1434 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1475 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1690 :N:0:
-NNNNNANN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1703 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1940 :N:0:
-NNNNNCNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:2001 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:205 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:275 :N:0:
-NNNNNATN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:324 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:37 :N:0:
-NNNNNGNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:464 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:586 :N:0:
-NNNNNCNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:841 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:879 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1013 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:111 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1153 :N:0:
-NNNNNCTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1184 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1241 :N:0:
-NNNNNCTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1243 :N:0:
-NNNNNTGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1247 :N:0:
-NNNNNACN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1282 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:132 :N:0:
-NNNNNTGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1320 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1372 :N:0:
-NNNGNTTA
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1379 :N:0:
-NNNCNGAT
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1391 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:140 :N:0:
-NNNNNCAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1513 :N:0:
-NNNNNCTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1521 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:155 :N:0:
-NNNNNCAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1555 :N:0:
-NNNNNCAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:164 :N:0:
-NNNNNTTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1684 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1696 :N:0:
-NNNNNCTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:170 :N:0:
-NNNNNACN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:173 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1733 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1770 :N:0:
-NNNNNTCN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:18 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1815 :N:0:
-NNNTNGAC
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1836 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:184 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1886 :Y:0:
-NNNGNGCC
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1906 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1917 :N:0:
-NNNNNACN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:195 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1954 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:2 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:2011 :N:0:
-NNNGNTAG
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:240 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:262 :N:0:
-NNNNNCAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:264 :N:0:
-NNNNNCGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:299 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:30 :N:0:
-NNNNNACN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:353 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:367 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:41 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:416 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:483 :N:0:
-NNNNNTAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:486 :N:0:
-NNNNNTGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:495 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:508 :N:0:
-NNNNNCTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:517 :N:0:
-NNNCNAGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:535 :N:0:
-NNNCNCGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:55 :N:0:
-NNNGNTTA
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:554 :N:0:
-NNNNNTAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:567 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:59 :N:0:
-NNNNNACN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:613 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:622 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:627 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:684 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:72 :N:0:
-NNNTNGAC
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:812 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:874 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:931 :N:0:
-NNNNNCAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:965 :N:0:
-NNNTNTAA
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:994 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1158 :Y:0:
-NNCTTAGC
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1238 :N:0:
-NNCTAAGC
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1275 :Y:0:
-NNNANCTG
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1301 :N:0:
-NNNTAACA
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1453 :Y:0:
-NNACCAGG
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:150 :N:0:
-NNNANCCT
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1592 :Y:0:
-NNNGAGCC
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1706 :Y:0:
-NNNCNGAT
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1722 :N:0:
-NNNTCGAC
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1727 :N:0:
-NNNTNCTT
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1753 :N:0:
-NNTGCTTA
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1782 :Y:0:
-NNNTNAGC
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1827 :Y:0:
-NNCAACTG
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1932 :Y:0:
-NNNCNAGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1946 :N:0:
-NNNTNGAC
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:209 :N:0:
-NNCATTTC
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:246 :N:0:
-NNNANTTC
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:25 :N:0:
-NNNGATGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:307 :N:0:
-NNNTNGAC
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:363 :N:0:
-NNNTNCTT
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:449 :N:0:
-NNNGNTGT
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:546 :N:0:
-NNNANGTT
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:605 :Y:0:
-NNNTNGAC
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:69 :N:0:
-NNGGAGCC
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:747 :N:0:
-NNNCCAGG
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:786 :Y:0:
-NNNGATGT
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:858 :Y:0:
-NNACATCT
-+
-%%/57799
- at machine1:HiMom:abcdeACXX:9:1:2:943 :Y:0:
-NNACCAGG
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:974 :Y:0:
-NNTATGTT
-+
-%%0::::<
- at machine1:HiMom:abcdeACXX:9:1:2:988 :Y:0:
-NNTGGCGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:3:1233 :N:0:
-CCAACAGG
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:3:1294 :N:0:
-TCACAATG
-+
-*37<<@5<
- at machine1:HiMom:abcdeACXX:9:1:3:405 :N:0:
-ACACAAGA
-+
-0(><=###
- at machine1:HiMom:abcdeACXX:9:1:3:579 :N:0:
-AATCATGT
-+
-73######
- at machine1:HiMom:abcdeACXX:9:1:3:673 :N:0:
-TGCCCAAA
-+
-(<######
- at machine1:HiMom:abcdeACXX:9:1:3:890 :N:0:
-GTCACCAT
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:3:905 :N:0:
-ACATCCTA
-+
-AA78/<:#
- at machine1:HiMom:abcdeACXX:9:1:3:918 :N:0:
-ACTACCTT
-+
-)?4B>###
- at machine1:HiMom:abcdeACXX:9:2:0:1073 :N:0:
-NNNNNCAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:1135 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:1198 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:1278 :N:0:
-NNNNNTAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:135 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:1547 :N:0:
-NNNNNCAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:1598 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:1620 :N:0:
-NNNNNTGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:1668 :N:0:
-NNNNNCTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:186 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:205 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:287 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:382 :N:0:
-NNNNNTAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:441 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:50 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:501 :N:0:
-NNNNNTAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:73 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:740 :N:0:
-NNNNNGGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:766 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:87 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1004 :N:0:
-NNNGCCGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1034 :N:0:
-NNNAGCCT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1159 :N:0:
-NNNTNGAC
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1168 :N:0:
-NNNGNTAG
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1180 :N:0:
-NNNTNAGC
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1214 :N:0:
-NNNCATGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1221 :N:0:
-NNGGATGT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1306 :N:0:
-NNNANCTG
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1351 :N:0:
-NNNNNTTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1424 :N:0:
-NNNCNTCT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1452 :N:0:
-NNAGATCC
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1515 :N:0:
-NNNGNATG
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1521 :N:0:
-NNNCNAGG
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1536 :N:0:
-NNACATCT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1543 :N:0:
-NNNANTTC
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1617 :N:0:
-NNNCNAGG
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1627 :N:0:
-NNNANCTG
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1646 :N:0:
-NNNTNGAC
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1653 :N:0:
-NNNGNTGT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1682 :N:0:
-NNNGNGCC
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:170 :Y:0:
-NNGAGCCT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1731 :N:0:
-NNNTNAGC
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1755 :N:0:
-NNNNNCAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1812 :N:0:
-NNNCNTAT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1853 :N:0:
-NNNCNCGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1919 :N:0:
-NNNANCTG
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1924 :N:0:
-NNNAACTG
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1933 :N:0:
-NNNTTAGC
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1938 :Y:0:
-NNCTCGAC
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1950 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1959 :N:0:
-NNTGCTTA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1987 :N:0:
-NNNNNTAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:2006 :N:0:
-NNNGNGCC
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:211 :N:0:
-NNNGNTGT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:234 :N:0:
-NNNGCTTA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:242 :N:0:
-NNNCNCGC
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:262 :N:0:
-NNNCNAGG
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:298 :N:0:
-NNNGNTAG
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:312 :N:0:
-NNNANGTT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:363 :Y:0:
-NNTATGTT
-+
-%%.99999
- at machine1:HiMom:abcdeACXX:9:2:1:37 :N:0:
-NNNGNCGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:370 :N:0:
-NNNANCAT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:377 :N:0:
-NNNCNTCT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:414 :N:0:
-NNNGNTTA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:421 :N:0:
-NNNANCCT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:428 :N:0:
-NNNATGTT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:44 :N:0:
-NNNAGCGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:466 :N:0:
-NNNTNACA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:555 :N:0:
-NNNCNGAT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:558 :N:0:
-NNNANCGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:56 :N:0:
-NNNTNAGC
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:569 :N:0:
-NNNANCTG
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:604 :N:0:
-NNCAACTG
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:628 :N:0:
-NNNTAACA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:64 :N:0:
-NNNANGTT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:684 :N:0:
-NNAAACGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:699 :N:0:
-NNNCNCGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:714 :N:0:
-NNNAGCGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:722 :N:0:
-NNNCNAGG
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:749 :N:0:
-NNNTNGAC
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:760 :N:0:
-NNACAACA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:8 :N:0:
-NNNANNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:833 :N:0:
-NNNANCCT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:848 :N:0:
-NNNANCGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:893 :N:0:
-NNCAATTC
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:998 :N:0:
-NNNANGTT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:2:0 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:2:131 :Y:0:
-CACAATCC
-+
-AACCBCA@
- at machine1:HiMom:abcdeACXX:9:2:2:1636 :N:0:
-ATCAACCC
-+
-368?####
- at machine1:HiMom:abcdeACXX:9:2:2:1974 :N:0:
-AGCAATCT
-+
->#######
- at machine1:HiMom:abcdeACXX:9:2:2:351 :N:0:
-TGATAGAA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:2:646 :N:0:
-ATCAATTA
-+
-((>4/406
- at machine1:HiMom:abcdeACXX:9:2:2:828 :N:0:
-TATATCGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:3:1529 :N:0:
-TAGAACCT
-+
-9)@73?B=
- at machine1:HiMom:abcdeACXX:9:2:3:179 :N:0:
-GTTTATTA
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:3:198 :N:0:
-CAGGATCT
-+
-5)0*@782
- at machine1:HiMom:abcdeACXX:9:2:3:2030 :N:0:
-GATCAAGA
-+
-(((>(<@<
- at machine1:HiMom:abcdeACXX:9:2:3:247 :N:0:
-CGGTAGCT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:3:4 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:3:862 :N:0:
-TAACAAGA
-+
-4)=69)=@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.barcode_2.fastq
deleted file mode 100644
index 70b0ee2..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/NN.barcode_2.fastq
+++ /dev/null
@@ -1,892 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:0:1038 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1093 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:113 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1193 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1291 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1307 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1434 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1475 :N:0:
-NNNNNCNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1690 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1703 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:1940 :N:0:
-NNNNNCNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:2001 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:205 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:275 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:324 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:37 :N:0:
-NNNNNGNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:464 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:586 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:841 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:0:879 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1013 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:111 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1153 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1184 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1241 :N:0:
-NNNNNCNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1243 :N:0:
-NNNNNTGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1247 :N:0:
-NNNNNANN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1282 :N:0:
-NNNNNCNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:132 :N:0:
-NNNNNTNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1320 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1372 :N:0:
-NNNGNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1379 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1391 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:140 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1513 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1521 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:155 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1555 :N:0:
-NNNNNCNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:164 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1684 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1696 :N:0:
-NNNNNCTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:170 :N:0:
-NNNNNACN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:173 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1733 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1770 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:18 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1815 :N:0:
-NNNTNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1836 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:184 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1886 :Y:0:
-NNNGNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1906 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1917 :N:0:
-NNNNNACN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:195 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:1954 :N:0:
-NNNNNCNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:2 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:2011 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:240 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:262 :N:0:
-NNNNNCNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:264 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:299 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:30 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:353 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:367 :N:0:
-NNNNNANN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:41 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:416 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:483 :N:0:
-NNNNNTAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:486 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:495 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:508 :N:0:
-NNNNNCNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:517 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:535 :N:0:
-NNNCNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:55 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:554 :N:0:
-NNNNNTAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:567 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:59 :N:0:
-NNNNNANN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:613 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:622 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:627 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:684 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:72 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:812 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:874 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:931 :N:0:
-NNNNNCNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:965 :N:0:
-NNNTNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:1:994 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1158 :Y:0:
-NNNNTANN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1238 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1275 :Y:0:
-NNNANNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1301 :N:0:
-NNNTANNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1453 :Y:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:150 :N:0:
-NNNANNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1592 :Y:0:
-NNNGANNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1706 :Y:0:
-NNNCNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1722 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1727 :N:0:
-NNNTNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1753 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1782 :Y:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1827 :Y:0:
-NNNNACNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1932 :Y:0:
-NNNCNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:1946 :N:0:
-NNNNNGNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:209 :N:0:
-NNNATNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:246 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:25 :N:0:
-NNNGNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:307 :N:0:
-NNNTNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:363 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:449 :N:0:
-NNNGNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:546 :N:0:
-NNNNNGNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:605 :Y:0:
-NNNTNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:69 :N:0:
-NNNNAGNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:747 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:786 :Y:0:
-NNNGNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:858 :Y:0:
-NNNNATNN
-+
-%%/57799
- at machine1:HiMom:abcdeACXX:9:1:2:943 :Y:0:
-NNNCCNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:974 :Y:0:
-NNNATNNN
-+
-%%0::::<
- at machine1:HiMom:abcdeACXX:9:1:2:988 :Y:0:
-NNNGGNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:3:1233 :N:0:
-NNNACNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:3:1294 :N:0:
-TCNNNNNN
-+
-*37<<@5<
- at machine1:HiMom:abcdeACXX:9:1:3:405 :N:0:
-NNNNNAGN
-+
-0(><=###
- at machine1:HiMom:abcdeACXX:9:1:3:579 :N:0:
-NNNNATNN
-+
-73######
- at machine1:HiMom:abcdeACXX:9:1:3:673 :N:0:
-NNNCCNNN
-+
-(<######
- at machine1:HiMom:abcdeACXX:9:1:3:890 :N:0:
-NNCANNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:3:905 :N:0:
-ACNNNNNN
-+
-AA78/<:#
- at machine1:HiMom:abcdeACXX:9:1:3:918 :N:0:
-NNNNNCTN
-+
-)?4B>###
- at machine1:HiMom:abcdeACXX:9:2:0:1073 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:1135 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:1198 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:1278 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:135 :N:0:
-NNNNNCNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:1547 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:1598 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:1620 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:1668 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:186 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:205 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:287 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:382 :N:0:
-NNNNNTNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:441 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:50 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:501 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:73 :N:0:
-NNNNNCNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:740 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:766 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:0:87 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1004 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1034 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1159 :N:0:
-NNNTNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1168 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1180 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1214 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1221 :N:0:
-NNNNNTGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1306 :N:0:
-NNNNNCNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1351 :N:0:
-NNNNNTNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1424 :N:0:
-NNNCNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1452 :N:0:
-NNNNATNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1515 :N:0:
-NNNNNANN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1521 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1536 :N:0:
-NNANNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1543 :N:0:
-NNNANNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1617 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1627 :N:0:
-NNNANNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1646 :N:0:
-NNNTNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1653 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1682 :N:0:
-NNNNNGNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:170 :Y:0:
-NNNAGNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1731 :N:0:
-NNNNNAGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1755 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1812 :N:0:
-NNNCNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1853 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1919 :N:0:
-NNNANNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1924 :N:0:
-NNNAANNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1933 :N:0:
-NNNTNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1938 :Y:0:
-NNCTNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1950 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1959 :N:0:
-NNNNCTNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:1987 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:2006 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:211 :N:0:
-NNNNNTGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:234 :N:0:
-NNNNCTNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:242 :N:0:
-NNNCNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:262 :N:0:
-NNNCNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:298 :N:0:
-NNNGNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:312 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:363 :Y:0:
-NNTNNNNN
-+
-%%.99999
- at machine1:HiMom:abcdeACXX:9:2:1:37 :N:0:
-NNNGNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:370 :N:0:
-NNNANNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:377 :N:0:
-NNNNNTNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:414 :N:0:
-NNNGNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:421 :N:0:
-NNNANNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:428 :N:0:
-NNNANNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:44 :N:0:
-NNNAGNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:466 :N:0:
-NNNTNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:555 :N:0:
-NNNCNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:558 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:56 :N:0:
-NNNNNANN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:569 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:604 :N:0:
-NNCNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:628 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:64 :N:0:
-NNNNNGTN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:684 :N:0:
-NNAANNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:699 :N:0:
-NNNCNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:714 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:722 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:749 :N:0:
-NNNNNGNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:760 :N:0:
-NNNNAANN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:8 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:833 :N:0:
-NNNNNCCN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:848 :N:0:
-NNNANNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:893 :N:0:
-NNNAANNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:1:998 :N:0:
-NNNNNGNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:2:0 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:2:131 :Y:0:
-NNNAANNN
-+
-AACCBCA@
- at machine1:HiMom:abcdeACXX:9:2:2:1636 :N:0:
-NNNAANNN
-+
-368?####
- at machine1:HiMom:abcdeACXX:9:2:2:1974 :N:0:
-NGCNNNNN
-+
->#######
- at machine1:HiMom:abcdeACXX:9:2:2:351 :N:0:
-NNNNNGAN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:2:646 :N:0:
-NTCNNNNN
-+
-((>4/406
- at machine1:HiMom:abcdeACXX:9:2:2:828 :N:0:
-NNNNNCGN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:3:1529 :N:0:
-NAGNNNNN
-+
-9)@73?B=
- at machine1:HiMom:abcdeACXX:9:2:3:179 :N:0:
-NNNTANNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:3:198 :N:0:
-NNNNNTCN
-+
-5)0*@782
- at machine1:HiMom:abcdeACXX:9:2:3:2030 :N:0:
-NNNCANNN
-+
-(((>(<@<
- at machine1:HiMom:abcdeACXX:9:2:3:247 :N:0:
-CGNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:3:4 :N:0:
-NNNNNNNN
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:3:862 :N:0:
-TANNNNNN
-+
-4)=69)=@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGC.1.fastq
deleted file mode 100644
index e93c230..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGC.1.fastq
+++ /dev/null
@@ -1,32 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:737 :N:0:TACTTAGC
-NAAAACAATTAAAATAAATGCTTAAAATCA
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:2:85 :N:0:TACTTAGC
-NGATAAAGTACAATGCTAATCACTTAAGAT
-+
-%.52353046874+'01999975;:9255;
- at machine1:HiMom:abcdeACXX:7:1:3:1574 :Y:0:TACTTAGC
-NTTATTCCTTAGGAAATTTTAAATTCTGTA
-+
-%0955357999999:99::99102::9:3:
- at machine1:HiMom:abcdeACXX:7:2:2:101 :Y:0:TACTTAGC
-NGTTAATTTAGGGAAATTTGTTTGTATTTT
-+
-%,3:969;<52718;<<<768;::9;999;
- at machine1:HiMom:abcdeACXX:7:2:2:12 :N:0:TACTTAGC
-NATGCATTGTAATTTAATAGAGTGAAATGG
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:1844 :N:0:TACTTAGC
-NGGACTACAAGCGCACGCCACATGCTCAGC
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:728 :N:0:TACTTAGC
-TGCCTCCTTGGAGAGGGCCGCAAAGCCAGG
-+
-=>=7?A?7'50>/996:;<+>AA at 7+8B67
- at machine1:HiMom:abcdeACXX:7:2:3:80 :Y:0:TACTTAGC
-AGGCAGGATGAAATTTTGTCTATTTATTCA
-+
- at 9:B at B@?B at ABABBBB??7AABBBBBB?A
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGC.barcode_1.fastq
deleted file mode 100644
index 6fd2760..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGC.barcode_1.fastq
+++ /dev/null
@@ -1,32 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:737 :N:0:TACTTAGC
-TACTTAGC
-+
-BCCCBCBB
- at machine1:HiMom:abcdeACXX:7:1:2:85 :N:0:TACTTAGC
-TACTTAGC
-+
-B>(>B=B2
- at machine1:HiMom:abcdeACXX:7:1:3:1574 :Y:0:TACTTAGC
-TACTTAGC
-+
- at ACBBC@A
- at machine1:HiMom:abcdeACXX:7:2:2:101 :Y:0:TACTTAGC
-TACTTAGC
-+
-BB=CCCC?
- at machine1:HiMom:abcdeACXX:7:2:2:12 :N:0:TACTTAGC
-TACTTAGC
-+
-A8%9<=##
- at machine1:HiMom:abcdeACXX:7:2:3:1844 :N:0:TACTTAGC
-TACTTAGC
-+
-B?BC>:@@
- at machine1:HiMom:abcdeACXX:7:2:3:728 :N:0:TACTTAGC
-TACTTAGC
-+
-BBCA>B7#
- at machine1:HiMom:abcdeACXX:7:2:3:80 :Y:0:TACTTAGC
-TACTTAGC
-+
-B at 9ABA@8
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.1.fastq
deleted file mode 100644
index 9536869..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.1.fastq
+++ /dev/null
@@ -1,32 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:737 :N:0:TACTTAGCCACATCCT
-NAAAACAATTAAAATAAATGCTTAAAATCA
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:2:85 :N:0:TACTTAGCCACATCCT
-NGATAAAGTACAATGCTAATCACTTAAGAT
-+
-%.52353046874+'01999975;:9255;
- at machine1:HiMom:abcdeACXX:9:1:3:1574 :Y:0:TACTTAGCCACATCCT
-NTTATTCCTTAGGAAATTTTAAATTCTGTA
-+
-%0955357999999:99::99102::9:3:
- at machine1:HiMom:abcdeACXX:9:2:2:101 :Y:0:TACTTAGCCACATCCT
-NGTTAATTTAGGGAAATTTGTTTGTATTTT
-+
-%,3:969;<52718;<<<768;::9;999;
- at machine1:HiMom:abcdeACXX:9:2:2:12 :N:0:TACTTAGCCACATCCT
-NATGCATTGTAATTTAATAGAGTGAAATGG
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:1844 :N:0:TACTTAGCCACATCCT
-NGGACTACAAGCGCACGCCACATGCTCAGC
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:728 :N:0:TACTTAGCCACATCCT
-TGCCTCCTTGGAGAGGGCCGCAAAGCCAGG
-+
-=>=7?A?7'50>/996:;<+>AA at 7+8B67
- at machine1:HiMom:abcdeACXX:9:2:3:80 :Y:0:TACTTAGCCACATCCT
-AGGCAGGATGAAATTTTGTCTATTTATTCA
-+
- at 9:B at B@?B at ABABBBB??7AABBBBBB?A
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.barcode_1.fastq
deleted file mode 100644
index 431c08a..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.barcode_1.fastq
+++ /dev/null
@@ -1,32 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:737 :N:0:TACTTAGCCACATCCT
-TACTTAGC
-+
-BCCCBCBB
- at machine1:HiMom:abcdeACXX:9:1:2:85 :N:0:TACTTAGCCACATCCT
-TACTTAGC
-+
-B>(>B=B2
- at machine1:HiMom:abcdeACXX:9:1:3:1574 :Y:0:TACTTAGCCACATCCT
-TACTTAGC
-+
- at ACBBC@A
- at machine1:HiMom:abcdeACXX:9:2:2:101 :Y:0:TACTTAGCCACATCCT
-TACTTAGC
-+
-BB=CCCC?
- at machine1:HiMom:abcdeACXX:9:2:2:12 :N:0:TACTTAGCCACATCCT
-TACTTAGC
-+
-A8%9<=##
- at machine1:HiMom:abcdeACXX:9:2:3:1844 :N:0:TACTTAGCCACATCCT
-TACTTAGC
-+
-B?BC>:@@
- at machine1:HiMom:abcdeACXX:9:2:3:728 :N:0:TACTTAGCCACATCCT
-TACTTAGC
-+
-BBCA>B7#
- at machine1:HiMom:abcdeACXX:9:2:3:80 :Y:0:TACTTAGCCACATCCT
-TACTTAGC
-+
-B at 9ABA@8
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.barcode_2.fastq
deleted file mode 100644
index 35c71fa..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TACTTAGCCACATCCT.barcode_2.fastq
+++ /dev/null
@@ -1,32 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:737 :N:0:TACTTAGCCACATCCT
-CACATCCT
-+
-BCCCBCBB
- at machine1:HiMom:abcdeACXX:9:1:2:85 :N:0:TACTTAGCCACATCCT
-CACATCCT
-+
-B>(>B=B2
- at machine1:HiMom:abcdeACXX:9:1:3:1574 :Y:0:TACTTAGCCACATCCT
-CACATCCT
-+
- at ACBBC@A
- at machine1:HiMom:abcdeACXX:9:2:2:101 :Y:0:TACTTAGCCACATCCT
-CACATCCT
-+
-BB=CCCC?
- at machine1:HiMom:abcdeACXX:9:2:2:12 :N:0:TACTTAGCCACATCCT
-CACATCCT
-+
-A8%9<=##
- at machine1:HiMom:abcdeACXX:9:2:3:1844 :N:0:TACTTAGCCACATCCT
-CACATCCT
-+
-B?BC>:@@
- at machine1:HiMom:abcdeACXX:9:2:3:728 :N:0:TACTTAGCCACATCCT
-CACATCCT
-+
-BBCA>B7#
- at machine1:HiMom:abcdeACXX:9:2:3:80 :Y:0:TACTTAGCCACATCCT
-CACATCCT
-+
-B at 9ABA@8
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATG.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATG.1.fastq
deleted file mode 100644
index a6de675..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATG.1.fastq
+++ /dev/null
@@ -1,28 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1328 :N:0:TCGGAATG
-GCTACCAACCCCACTCCTAGATGAAAGACC
-+
-068,=@)=AA82 at C@8;;@3;8/<<#####
- at machine1:HiMom:abcdeACXX:7:1:3:2037 :N:0:TCGGAATG
-CATCCTGTAACAAAGTGTTTATAGTTTTCA
-+
-:@9 at B6<?A>(>AB@<*)=<CBA:>51:7A
- at machine1:HiMom:abcdeACXX:7:1:3:695 :Y:0:TCGGAATG
-TGATACTGCCTTTGCAAAAATTATAACAGT
-+
-;>ABBCC<?ACCBBBCCCCBBACBAABB<A
- at machine1:HiMom:abcdeACXX:7:2:2:220 :Y:0:TCGGAATG
-NAATAAACCTCTTTCTTTGATAAATTACCC
-+
-%.5:78335567:525<736:9868;8###
- at machine1:HiMom:abcdeACXX:7:2:3:567 :Y:0:TCGGAATG
-TATCTTCACATAAAAACTACACAAAGCATT
-+
-BCB<ACBB at BCCBBCB<BB<@;?BB>=BBB
- at machine1:HiMom:abcdeACXX:7:2:3:663 :N:0:TCGGAATG
-AAAAGCATGTTGCTCAGTAAAAGCAAATAG
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:3:922 :Y:0:TCGGAATG
-ATTTCTGTCTGACTTTTCCAAATGTGCTAT
-+
-AABB@>>>@>9@>AAAA>;@BB@@53;BBB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATG.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATG.barcode_1.fastq
deleted file mode 100644
index a0c3335..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATG.barcode_1.fastq
+++ /dev/null
@@ -1,28 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1328 :N:0:TCGGAATG
-TCGGAATG
-+
-A@@2=?83
- at machine1:HiMom:abcdeACXX:7:1:3:2037 :N:0:TCGGAATG
-TCGGAATG
-+
-?<):=@=@
- at machine1:HiMom:abcdeACXX:7:1:3:695 :Y:0:TCGGAATG
-TCGGAATG
-+
-B?;BBB=?
- at machine1:HiMom:abcdeACXX:7:2:2:220 :Y:0:TCGGAATG
-TCGGAATG
-+
-BA==@@?;
- at machine1:HiMom:abcdeACXX:7:2:3:567 :Y:0:TCGGAATG
-TCGGAATG
-+
-@?@?AB@<
- at machine1:HiMom:abcdeACXX:7:2:3:663 :N:0:TCGGAATG
-TCGGAATG
-+
-=<23<C=8
- at machine1:HiMom:abcdeACXX:7:2:3:922 :Y:0:TCGGAATG
-TCGGAATG
-+
-BA<ABC?;
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.1.fastq
deleted file mode 100644
index 89321f1..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.1.fastq
+++ /dev/null
@@ -1,28 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1328 :N:0:TCGGAATGATTATGTT
-GCTACCAACCCCACTCCTAGATGAAAGACC
-+
-068,=@)=AA82 at C@8;;@3;8/<<#####
- at machine1:HiMom:abcdeACXX:9:1:3:2037 :N:0:TCGGAATGATTATGTT
-CATCCTGTAACAAAGTGTTTATAGTTTTCA
-+
-:@9 at B6<?A>(>AB@<*)=<CBA:>51:7A
- at machine1:HiMom:abcdeACXX:9:1:3:695 :Y:0:TCGGAATGATTATGTT
-TGATACTGCCTTTGCAAAAATTATAACAGT
-+
-;>ABBCC<?ACCBBBCCCCBBACBAABB<A
- at machine1:HiMom:abcdeACXX:9:2:2:220 :Y:0:TCGGAATGATTATGTT
-NAATAAACCTCTTTCTTTGATAAATTACCC
-+
-%.5:78335567:525<736:9868;8###
- at machine1:HiMom:abcdeACXX:9:2:3:567 :Y:0:TCGGAATGATTATGTT
-TATCTTCACATAAAAACTACACAAAGCATT
-+
-BCB<ACBB at BCCBBCB<BB<@;?BB>=BBB
- at machine1:HiMom:abcdeACXX:9:2:3:663 :N:0:TCGGAATGATTATGTT
-AAAAGCATGTTGCTCAGTAAAAGCAAATAG
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:3:922 :Y:0:TCGGAATGATTATGTT
-ATTTCTGTCTGACTTTTCCAAATGTGCTAT
-+
-AABB@>>>@>9@>AAAA>;@BB@@53;BBB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.barcode_1.fastq
deleted file mode 100644
index 90a3a06..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.barcode_1.fastq
+++ /dev/null
@@ -1,28 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1328 :N:0:TCGGAATGATTATGTT
-TCGGAATG
-+
-A@@2=?83
- at machine1:HiMom:abcdeACXX:9:1:3:2037 :N:0:TCGGAATGATTATGTT
-TCGGAATG
-+
-?<):=@=@
- at machine1:HiMom:abcdeACXX:9:1:3:695 :Y:0:TCGGAATGATTATGTT
-TCGGAATG
-+
-B?;BBB=?
- at machine1:HiMom:abcdeACXX:9:2:2:220 :Y:0:TCGGAATGATTATGTT
-TCGGAATG
-+
-BA==@@?;
- at machine1:HiMom:abcdeACXX:9:2:3:567 :Y:0:TCGGAATGATTATGTT
-TCGGAATG
-+
-@?@?AB@<
- at machine1:HiMom:abcdeACXX:9:2:3:663 :N:0:TCGGAATGATTATGTT
-TCGGAATG
-+
-=<23<C=8
- at machine1:HiMom:abcdeACXX:9:2:3:922 :Y:0:TCGGAATGATTATGTT
-TCGGAATG
-+
-BA<ABC?;
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.barcode_2.fastq
deleted file mode 100644
index 08a7f9f..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCGGAATGATTATGTT.barcode_2.fastq
+++ /dev/null
@@ -1,28 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1328 :N:0:TCGGAATGATTATGTT
-ATTATGTT
-+
-A@@2=?83
- at machine1:HiMom:abcdeACXX:9:1:3:2037 :N:0:TCGGAATGATTATGTT
-ATTATGTT
-+
-?<):=@=@
- at machine1:HiMom:abcdeACXX:9:1:3:695 :Y:0:TCGGAATGATTATGTT
-ATTATGTT
-+
-B?;BBB=?
- at machine1:HiMom:abcdeACXX:9:2:2:220 :Y:0:TCGGAATGATTATGTT
-ATTATGTT
-+
-BA==@@?;
- at machine1:HiMom:abcdeACXX:9:2:3:567 :Y:0:TCGGAATGATTATGTT
-ATTATGTT
-+
-@?@?AB@<
- at machine1:HiMom:abcdeACXX:9:2:3:663 :N:0:TCGGAATGATTATGTT
-ATTATGTT
-+
-=<23<C=8
- at machine1:HiMom:abcdeACXX:9:2:3:922 :Y:0:TCGGAATGATTATGTT
-ATTATGTT
-+
-BA<ABC?;
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGA.1.fastq
deleted file mode 100644
index 9af8df3..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGA.1.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1406 :N:0:TCTGGCGA
-NAAAATGCCAGATAAATTTTATGTAAAACC
-+
-%1<<97227467::77(7;;;503<9:972
- at machine1:HiMom:abcdeACXX:7:1:3:1717 :Y:0:TCTGGCGA
-NAAACAGACTTGTTTCTTGTAATAATTATG
-+
-%/;;89689:999<76:8399:9:::::##
- at machine1:HiMom:abcdeACXX:7:2:3:2004 :N:0:TCTGGCGA
-NAAGACTACCTTGCTGAAATAGGGCATTTA
-+
-%.:875459;4-743(29;;5139266###
- at machine1:HiMom:abcdeACXX:7:2:3:695 :Y:0:TCTGGCGA
-NCAACTCCAAGACACATAATTGTCAGATTC
-+
-%/:::95578589969:::;6559748;82
- at machine1:HiMom:abcdeACXX:7:2:3:987 :N:0:TCTGGCGA
-AAGAGCAATATTTTCTTTCACTATATTATT
-+
-*@<@@?A at 0)7448)?C@)@4)9:@#####
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGA.barcode_1.fastq
deleted file mode 100644
index f2ad3a3..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGA.barcode_1.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1406 :N:0:TCTGGCGA
-TCTGGCGA
-+
-AA=;5@=@
- at machine1:HiMom:abcdeACXX:7:1:3:1717 :Y:0:TCTGGCGA
-TCTGGCGA
-+
-AB=11;A@
- at machine1:HiMom:abcdeACXX:7:2:3:2004 :N:0:TCTGGCGA
-TCTGGCGA
-+
-@?>/>BBB
- at machine1:HiMom:abcdeACXX:7:2:3:695 :Y:0:TCTGGCGA
-TCTGGCGA
-+
-AA?>9=@A
- at machine1:HiMom:abcdeACXX:7:2:3:987 :N:0:TCTGGCGA
-TCTCGCGA
-+
-0<(.(;1@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.1.fastq
deleted file mode 100644
index 83ca136..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.1.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1406 :N:0:TCTGGCGAAGTTGCTT
-NAAAATGCCAGATAAATTTTATGTAAAACC
-+
-%1<<97227467::77(7;;;503<9:972
- at machine1:HiMom:abcdeACXX:9:1:3:1717 :Y:0:TCTGGCGAAGTTGCTT
-NAAACAGACTTGTTTCTTGTAATAATTATG
-+
-%/;;89689:999<76:8399:9:::::##
- at machine1:HiMom:abcdeACXX:9:2:3:2004 :N:0:TCTGGCGAAGTTGCTT
-NAAGACTACCTTGCTGAAATAGGGCATTTA
-+
-%.:875459;4-743(29;;5139266###
- at machine1:HiMom:abcdeACXX:9:2:3:695 :Y:0:TCTGGCGAAGTTGCTT
-NCAACTCCAAGACACATAATTGTCAGATTC
-+
-%/:::95578589969:::;6559748;82
- at machine1:HiMom:abcdeACXX:9:2:3:987 :N:0:TCTGGCGAAGTTGCTT
-AAGAGCAATATTTTCTTTCACTATATTATT
-+
-*@<@@?A at 0)7448)?C@)@4)9:@#####
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.barcode_1.fastq
deleted file mode 100644
index 80e639a..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.barcode_1.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1406 :N:0:TCTGGCGAAGTTGCTT
-TCTGGCGA
-+
-AA=;5@=@
- at machine1:HiMom:abcdeACXX:9:1:3:1717 :Y:0:TCTGGCGAAGTTGCTT
-TCTGGCGA
-+
-AB=11;A@
- at machine1:HiMom:abcdeACXX:9:2:3:2004 :N:0:TCTGGCGAAGTTGCTT
-TCTGGCGA
-+
-@?>/>BBB
- at machine1:HiMom:abcdeACXX:9:2:3:695 :Y:0:TCTGGCGAAGTTGCTT
-TCTGGCGA
-+
-AA?>9=@A
- at machine1:HiMom:abcdeACXX:9:2:3:987 :N:0:TCTGGCGAAGTTGCTT
-TCTCGCGA
-+
-0<(.(;1@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.barcode_2.fastq
deleted file mode 100644
index deecd6b..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TCTGGCGAAGTTGCTT.barcode_2.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1406 :N:0:TCTGGCGAAGTTGCTT
-AGTTGCTT
-+
-AA=;5@=@
- at machine1:HiMom:abcdeACXX:9:1:3:1717 :Y:0:TCTGGCGAAGTTGCTT
-AGTTGCTT
-+
-AB=11;A@
- at machine1:HiMom:abcdeACXX:9:2:3:2004 :N:0:TCTGGCGAAGTTGCTT
-AGTTGCTT
-+
-@?>/>BBB
- at machine1:HiMom:abcdeACXX:9:2:3:695 :Y:0:TCTGGCGAAGTTGCTT
-AGTTGCTT
-+
-AA?>9=@A
- at machine1:HiMom:abcdeACXX:9:2:3:987 :N:0:TCTGGCGAAGTTGCTT
-AGTTGCTT
-+
-0<(.(;1@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGAC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGAC.1.fastq
deleted file mode 100644
index 9037a85..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGAC.1.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:52 :N:0:TGCTCGAC
-NAAGTATAATGTAGAGACGCTTGTATTGTC
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:1:3:1348 :Y:0:TGCTCGAC
-NATATTGATTCTTCCTACCCATGAGTATGG
-+
-%1;;78.+389999888;;89118;7;8##
- at machine1:HiMom:abcdeACXX:7:1:3:1981 :Y:0:TGCTCGAC
-AGCCTGTCTGTAGAAAAAATACAAAAATTA
-+
- at 3;=;8/@=:8B8=BBBBB:B?BBABB?:B
- at machine1:HiMom:abcdeACXX:7:2:2:115 :N:0:TGCTCGAC
-NGATGTGCTACACACTTTCAAACAAACAGA
-+
-%0:500&/99;69727::995313374484
- at machine1:HiMom:abcdeACXX:7:2:3:317 :Y:0:TGCTCGAC
-AGAGAGAAATGTGGCATATGAGTATCACCT
-+
- at 4>BBB?ABCAB@>>ACBB?B<AABBCBBB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGAC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGAC.barcode_1.fastq
deleted file mode 100644
index 70798ff..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGAC.barcode_1.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:52 :N:0:TGCTCGAC
-TGCTCGAC
-+
-:;;;:;=;
- at machine1:HiMom:abcdeACXX:7:1:3:1348 :Y:0:TGCTCGAC
-TGCTCGAC
-+
-B9??@7 at 5
- at machine1:HiMom:abcdeACXX:7:1:3:1981 :Y:0:TGCTCGAC
-TGCTCGAC
-+
-=*@1;@BB
- at machine1:HiMom:abcdeACXX:7:2:2:115 :N:0:TGCTCGAC
-TGCTCGAC
-+
-BA=>=@@=
- at machine1:HiMom:abcdeACXX:7:2:3:317 :Y:0:TGCTCGAC
-TGCTCGAC
-+
-BAABBA<=
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.1.fastq
deleted file mode 100644
index 2710293..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.1.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:52 :N:0:TGCTCGACAGCAATTC
-NAAGTATAATGTAGAGACGCTTGTATTGTC
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:1:3:1348 :Y:0:TGCTCGACAGCAATTC
-NATATTGATTCTTCCTACCCATGAGTATGG
-+
-%1;;78.+389999888;;89118;7;8##
- at machine1:HiMom:abcdeACXX:9:1:3:1981 :Y:0:TGCTCGACAGCAATTC
-AGCCTGTCTGTAGAAAAAATACAAAAATTA
-+
- at 3;=;8/@=:8B8=BBBBB:B?BBABB?:B
- at machine1:HiMom:abcdeACXX:9:2:2:115 :N:0:TGCTCGACAGCAATTC
-NGATGTGCTACACACTTTCAAACAAACAGA
-+
-%0:500&/99;69727::995313374484
- at machine1:HiMom:abcdeACXX:9:2:3:317 :Y:0:TGCTCGACAGCAATTC
-AGAGAGAAATGTGGCATATGAGTATCACCT
-+
- at 4>BBB?ABCAB@>>ACBB?B<AABBCBBB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.barcode_1.fastq
deleted file mode 100644
index 62cf80e..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.barcode_1.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:52 :N:0:TGCTCGACAGCAATTC
-TGCTCGAC
-+
-:;;;:;=;
- at machine1:HiMom:abcdeACXX:9:1:3:1348 :Y:0:TGCTCGACAGCAATTC
-TGCTCGAC
-+
-B9??@7 at 5
- at machine1:HiMom:abcdeACXX:9:1:3:1981 :Y:0:TGCTCGACAGCAATTC
-TGCTCGAC
-+
-=*@1;@BB
- at machine1:HiMom:abcdeACXX:9:2:2:115 :N:0:TGCTCGACAGCAATTC
-TGCTCGAC
-+
-BA=>=@@=
- at machine1:HiMom:abcdeACXX:9:2:3:317 :Y:0:TGCTCGACAGCAATTC
-TGCTCGAC
-+
-BAABBA<=
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.barcode_2.fastq
deleted file mode 100644
index bf38ef7..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGCTCGACAGCAATTC.barcode_2.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:52 :N:0:TGCTCGACAGCAATTC
-AGCAATTC
-+
-:;;;:;=;
- at machine1:HiMom:abcdeACXX:9:1:3:1348 :Y:0:TGCTCGACAGCAATTC
-AGCAATTC
-+
-B9??@7 at 5
- at machine1:HiMom:abcdeACXX:9:1:3:1981 :Y:0:TGCTCGACAGCAATTC
-AGCAATTC
-+
-=*@1;@BB
- at machine1:HiMom:abcdeACXX:9:2:2:115 :N:0:TGCTCGACAGCAATTC
-AGCAATTC
-+
-BA=>=@@=
- at machine1:HiMom:abcdeACXX:9:2:3:317 :Y:0:TGCTCGACAGCAATTC
-AGCAATTC
-+
-BAABBA<=
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGAT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGAT.1.fastq
deleted file mode 100644
index 610e71c..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGAT.1.fastq
+++ /dev/null
@@ -1,16 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:950 :Y:0:TGTCGGAT
-NGTGTGTGTTTTTAGAGATGCCTTTTAGAA
-+
-%-7463817999<999998876999;6579
- at machine1:HiMom:abcdeACXX:7:2:3:1389 :Y:0:TGTCGGAT
-TATCGATCTCCTGACCTCGTGATCCACCCA
-+
-ACBCBCB?CBB at 6ABCB@)B>CBBCC at 4;5
- at machine1:HiMom:abcdeACXX:7:2:3:143 :Y:0:TGTCGGAT
-AAAATCAATTCTGAAATGATTACATATTTT
-+
-BBBACBBACB=B?BBBBCBBCBBBBBBCBB
- at machine1:HiMom:abcdeACXX:7:2:3:898 :Y:0:TGTCGGAT
-TAACATTCCCACAGTGCTTGCCACAGAGCC
-+
-ACCCCCC at C@@B@);>;BBCC=@BC?B@;>
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGAT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGAT.barcode_1.fastq
deleted file mode 100644
index 8c96032..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGAT.barcode_1.fastq
+++ /dev/null
@@ -1,16 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:950 :Y:0:TGTCGGAT
-TGTCGGAT
-+
-@@=A:AAA
- at machine1:HiMom:abcdeACXX:7:2:3:1389 :Y:0:TGTCGGAT
-TGTCGGAT
-+
-?2ACA at B<
- at machine1:HiMom:abcdeACXX:7:2:3:143 :Y:0:TGTCGGAT
-TGTCGGAT
-+
-A>AB??=B
- at machine1:HiMom:abcdeACXX:7:2:3:898 :Y:0:TGTCGGAT
-TGTCGGAT
-+
->8>A@=<@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.1.fastq
deleted file mode 100644
index 97566b5..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.1.fastq
+++ /dev/null
@@ -1,16 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:950 :Y:0:TGTCGGATACCAACTG
-NGTGTGTGTTTTTAGAGATGCCTTTTAGAA
-+
-%-7463817999<999998876999;6579
- at machine1:HiMom:abcdeACXX:9:2:3:1389 :Y:0:TGTCGGATACCAACTG
-TATCGATCTCCTGACCTCGTGATCCACCCA
-+
-ACBCBCB?CBB at 6ABCB@)B>CBBCC at 4;5
- at machine1:HiMom:abcdeACXX:9:2:3:143 :Y:0:TGTCGGATACCAACTG
-AAAATCAATTCTGAAATGATTACATATTTT
-+
-BBBACBBACB=B?BBBBCBBCBBBBBBCBB
- at machine1:HiMom:abcdeACXX:9:2:3:898 :Y:0:TGTCGGATACCAACTG
-TAACATTCCCACAGTGCTTGCCACAGAGCC
-+
-ACCCCCC at C@@B@);>;BBCC=@BC?B@;>
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.barcode_1.fastq
deleted file mode 100644
index 780d300..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.barcode_1.fastq
+++ /dev/null
@@ -1,16 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:950 :Y:0:TGTCGGATACCAACTG
-TGTCGGAT
-+
-@@=A:AAA
- at machine1:HiMom:abcdeACXX:9:2:3:1389 :Y:0:TGTCGGATACCAACTG
-TGTCGGAT
-+
-?2ACA at B<
- at machine1:HiMom:abcdeACXX:9:2:3:143 :Y:0:TGTCGGATACCAACTG
-TGTCGGAT
-+
-A>AB??=B
- at machine1:HiMom:abcdeACXX:9:2:3:898 :Y:0:TGTCGGATACCAACTG
-TGTCGGAT
-+
->8>A@=<@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.barcode_2.fastq
deleted file mode 100644
index 1a9029a..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TGTCGGATACCAACTG.barcode_2.fastq
+++ /dev/null
@@ -1,16 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:950 :Y:0:TGTCGGATACCAACTG
-ACCAACTG
-+
-@@=A:AAA
- at machine1:HiMom:abcdeACXX:9:2:3:1389 :Y:0:TGTCGGATACCAACTG
-ACCAACTG
-+
-?2ACA at B<
- at machine1:HiMom:abcdeACXX:9:2:3:143 :Y:0:TGTCGGATACCAACTG
-ACCAACTG
-+
-A>AB??=B
- at machine1:HiMom:abcdeACXX:9:2:3:898 :Y:0:TGTCGGATACCAACTG
-ACCAACTG
-+
->8>A@=<@
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGA.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGA.1.fastq
deleted file mode 100644
index d696f12..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGA.1.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:309 :Y:0:TTCGCTGA
-NAATGGCCATGCTGCCCAAAGTATTTTATA
-+
-%.705699:5-227759996717:::9:9:
- at machine1:HiMom:abcdeACXX:7:1:2:63 :Y:0:TTCGCTGA
-NGAGTGGAATGGAATGGAGTGGAATGGCTT
-+
-%,/66818682811553536525875686#
- at machine1:HiMom:abcdeACXX:7:1:3:880 :N:0:TTCGCTGA
-ATGAGTGAGAAATAGAAGTCCTAAGTAGAT
-+
-B@=;/75>)>?B@=3>@=<.2=B at 2@>49B
- at machine1:HiMom:abcdeACXX:7:2:2:669 :N:0:TTCGCTGA
-NGGCTGAAGCAGGAGGGTCACTTGAGCCAA
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:2:775 :Y:0:TTCGCTGA
-NGTTTATAATTGTGAGTTAAAAATCTAAAA
-+
-%,-78:8:968:45524<<636;<:<<<<<
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGA.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGA.barcode_1.fastq
deleted file mode 100644
index 6a7b76c..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGA.barcode_1.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:2:309 :Y:0:TTCGCTGA
-NTCGCTGA
-+
-########
- at machine1:HiMom:abcdeACXX:7:1:2:63 :Y:0:TTCGCTGA
-TTCGCTGA
-+
-7@=B<C@#
- at machine1:HiMom:abcdeACXX:7:1:3:880 :N:0:TTCGCTGA
-TTCGCTGA
-+
->@62;A==
- at machine1:HiMom:abcdeACXX:7:2:2:669 :N:0:TTCGCTGA
-TTCGCTGA
-+
-B>BB at BB9
- at machine1:HiMom:abcdeACXX:7:2:2:775 :Y:0:TTCGCTGA
-TTCGCTGA
-+
-BCC6ABBC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.1.fastq
deleted file mode 100644
index 68353f1..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.1.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:309 :Y:0:TTCGCTGAAAGGATGT
-NAATGGCCATGCTGCCCAAAGTATTTTATA
-+
-%.705699:5-227759996717:::9:9:
- at machine1:HiMom:abcdeACXX:9:1:2:63 :Y:0:TTCGCTGAAAGGATGT
-NGAGTGGAATGGAATGGAGTGGAATGGCTT
-+
-%,/66818682811553536525875686#
- at machine1:HiMom:abcdeACXX:9:1:3:880 :N:0:TTCGCTGAAAGGATGT
-ATGAGTGAGAAATAGAAGTCCTAAGTAGAT
-+
-B@=;/75>)>?B@=3>@=<.2=B at 2@>49B
- at machine1:HiMom:abcdeACXX:9:2:2:669 :N:0:TTCGCTGAAAGGATGT
-NGGCTGAAGCAGGAGGGTCACTTGAGCCAA
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:2:775 :Y:0:TTCGCTGAAAGGATGT
-NGTTTATAATTGTGAGTTAAAAATCTAAAA
-+
-%,-78:8:968:45524<<636;<:<<<<<
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.barcode_1.fastq
deleted file mode 100644
index 233f520..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.barcode_1.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:309 :Y:0:TTCGCTGAAAGGATGT
-NTCGCTGA
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:63 :Y:0:TTCGCTGAAAGGATGT
-TTCGCTGA
-+
-7@=B<C@#
- at machine1:HiMom:abcdeACXX:9:1:3:880 :N:0:TTCGCTGAAAGGATGT
-TTCGCTGA
-+
->@62;A==
- at machine1:HiMom:abcdeACXX:9:2:2:669 :N:0:TTCGCTGAAAGGATGT
-TTCGCTGA
-+
-B>BB at BB9
- at machine1:HiMom:abcdeACXX:9:2:2:775 :Y:0:TTCGCTGAAAGGATGT
-TTCGCTGA
-+
-BCC6ABBC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.barcode_2.fastq
deleted file mode 100644
index 491006d..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTCGCTGAAAGGATGT.barcode_2.fastq
+++ /dev/null
@@ -1,20 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:2:309 :Y:0:TTCGCTGAAAGGATGT
-AAGGATGT
-+
-########
- at machine1:HiMom:abcdeACXX:9:1:2:63 :Y:0:TTCGCTGAAAGGATGT
-AAGGATGT
-+
-7@=B<C@#
- at machine1:HiMom:abcdeACXX:9:1:3:880 :N:0:TTCGCTGAAAGGATGT
-AAGGATGT
-+
->@62;A==
- at machine1:HiMom:abcdeACXX:9:2:2:669 :N:0:TTCGCTGAAAGGATGT
-AAGGATGT
-+
-B>BB at BB9
- at machine1:HiMom:abcdeACXX:9:2:2:775 :Y:0:TTCGCTGAAAGGATGT
-AAGGATGT
-+
-BCC6ABBC
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCT.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCT.1.fastq
deleted file mode 100644
index 644b059..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCT.1.fastq
+++ /dev/null
@@ -1,24 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1155 :N:0:TTGAGCCT
-NCAGCGAAAGAAGTACCAGGGTATGGGAAG
-+
-##############################
- at machine1:HiMom:abcdeACXX:7:2:2:1559 :Y:0:TTGAGCCT
-NACAGAAGGGAAAAGGTCACAGACTAAAGA
-+
-%//6;;;8849;:91,35::757:4:;:9:
- at machine1:HiMom:abcdeACXX:7:2:2:488 :Y:0:TTGAGCCT
-NTGGGAAACTAAACCCCATGAGGGCAGAGC
-+
-%/2/156666785445255551/12545/4
- at machine1:HiMom:abcdeACXX:7:2:3:1101 :Y:0:TTGAGCCT
-AAGATTATATGAGTATAATGGAGCTATTTG
-+
-B<38>B=>>B==30ABBA886;?;AAA@@>
- at machine1:HiMom:abcdeACXX:7:2:3:1123 :N:0:TTGAGCCT
-NCCTCTTCCACAACTTCCTTCTTCTCCTTT
-+
-%.23)7475776876486:;67348867:8
- at machine1:HiMom:abcdeACXX:7:2:3:782 :Y:0:TTGAGCCT
-AGCCATGGGCATATAGAATCACTGTAAACA
-+
-B at BBBB>7;BCBCBB at BBB?BB>:=BAB at B
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCT.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCT.barcode_1.fastq
deleted file mode 100644
index 33c23ba..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCT.barcode_1.fastq
+++ /dev/null
@@ -1,24 +0,0 @@
- at machine1:HiMom:abcdeACXX:7:1:3:1155 :N:0:TTGAGCCT
-TTGAGCCT
-+
-########
- at machine1:HiMom:abcdeACXX:7:2:2:1559 :Y:0:TTGAGCCT
-TTGAGCCT
-+
-A at 5@@4BC
- at machine1:HiMom:abcdeACXX:7:2:2:488 :Y:0:TTGAGCCT
-TTGAGCCT
-+
-@>=@@;@A
- at machine1:HiMom:abcdeACXX:7:2:3:1101 :Y:0:TTGAGCCT
-TTGAGCCT
-+
-7 at 57<*5=
- at machine1:HiMom:abcdeACXX:7:2:3:1123 :N:0:TTGAGCCT
-TTGAGCCT
-+
-B at 67(.AA
- at machine1:HiMom:abcdeACXX:7:2:3:782 :Y:0:TTGAGCCT
-TTGAGCCT
-+
-BAAA<;B?
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.1.fastq
deleted file mode 100644
index 0377752..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.1.fastq
+++ /dev/null
@@ -1,24 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1155 :N:0:TTGAGCCTAACTTGAC
-NCAGCGAAAGAAGTACCAGGGTATGGGAAG
-+
-##############################
- at machine1:HiMom:abcdeACXX:9:2:2:1559 :Y:0:TTGAGCCTAACTTGAC
-NACAGAAGGGAAAAGGTCACAGACTAAAGA
-+
-%//6;;;8849;:91,35::757:4:;:9:
- at machine1:HiMom:abcdeACXX:9:2:2:488 :Y:0:TTGAGCCTAACTTGAC
-NTGGGAAACTAAACCCCATGAGGGCAGAGC
-+
-%/2/156666785445255551/12545/4
- at machine1:HiMom:abcdeACXX:9:2:3:1101 :Y:0:TTGAGCCTAACTTGAC
-AAGATTATATGAGTATAATGGAGCTATTTG
-+
-B<38>B=>>B==30ABBA886;?;AAA@@>
- at machine1:HiMom:abcdeACXX:9:2:3:1123 :N:0:TTGAGCCTAACTTGAC
-NCCTCTTCCACAACTTCCTTCTTCTCCTTT
-+
-%.23)7475776876486:;67348867:8
- at machine1:HiMom:abcdeACXX:9:2:3:782 :Y:0:TTGAGCCTAACTTGAC
-AGCCATGGGCATATAGAATCACTGTAAACA
-+
-B at BBBB>7;BCBCBB at BBB?BB>:=BAB at B
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.barcode_1.fastq
deleted file mode 100644
index 2f53965..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.barcode_1.fastq
+++ /dev/null
@@ -1,24 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1155 :N:0:TTGAGCCTAACTTGAC
-TTGAGCCT
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:2:1559 :Y:0:TTGAGCCTAACTTGAC
-TTGAGCCT
-+
-A at 5@@4BC
- at machine1:HiMom:abcdeACXX:9:2:2:488 :Y:0:TTGAGCCTAACTTGAC
-TTGAGCCT
-+
-@>=@@;@A
- at machine1:HiMom:abcdeACXX:9:2:3:1101 :Y:0:TTGAGCCTAACTTGAC
-TTGAGCCT
-+
-7 at 57<*5=
- at machine1:HiMom:abcdeACXX:9:2:3:1123 :N:0:TTGAGCCTAACTTGAC
-TTGAGCCT
-+
-B at 67(.AA
- at machine1:HiMom:abcdeACXX:9:2:3:782 :Y:0:TTGAGCCTAACTTGAC
-TTGAGCCT
-+
-BAAA<;B?
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.barcode_2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.barcode_2.fastq
deleted file mode 100644
index e424db6..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/TTGAGCCTAACTTGAC.barcode_2.fastq
+++ /dev/null
@@ -1,24 +0,0 @@
- at machine1:HiMom:abcdeACXX:9:1:3:1155 :N:0:TTGAGCCTAACTTGAC
-AACTTGAC
-+
-########
- at machine1:HiMom:abcdeACXX:9:2:2:1559 :Y:0:TTGAGCCTAACTTGAC
-AACTTGAC
-+
-A at 5@@4BC
- at machine1:HiMom:abcdeACXX:9:2:2:488 :Y:0:TTGAGCCTAACTTGAC
-AACTTGAC
-+
-@>=@@;@A
- at machine1:HiMom:abcdeACXX:9:2:3:1101 :Y:0:TTGAGCCTAACTTGAC
-AACTTGAC
-+
-7 at 57<*5=
- at machine1:HiMom:abcdeACXX:9:2:3:1123 :N:0:TTGAGCCTAACTTGAC
-AACTTGAC
-+
-B at 67(.AA
- at machine1:HiMom:abcdeACXX:9:2:3:782 :Y:0:TTGAGCCTAACTTGAC
-AACTTGAC
-+
-BAAA<;B?
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/barcode.params b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/barcode.params
deleted file mode 100644
index dd3a1ac..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/barcode.params
+++ /dev/null
@@ -1,26 +0,0 @@
-BARCODE_1
-AACTTGAC
-AAGGATGT
-ACCAACTG
-AGCAATTC
-AGTTGCTT
-ATTATGTT
-CACATCCT
-CAGGAGCC
-CATAGCGA
-CATGCTTA
-CCAGTTAG
-CCTACCAT
-CTACCAGG
-GCACACGA
-GCACATCT
-GGTCCAGA
-GTATAACA
-TACTTAGC
-TCGGAATG
-TCTGGCGA
-TGCTCGAC
-TGTCGGAT
-TTCGCTGA
-TTGAGCCT
-N
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/barcode_double.params b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/barcode_double.params
deleted file mode 100644
index fff0849..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/barcode_double.params
+++ /dev/null
@@ -1,26 +0,0 @@
-BARCODE_1 BARCODE_2
-AACTTGAC TTGAGCCT
-AAGGATGT TTCGCTGA
-ACCAACTG TGTCGGAT
-AGCAATTC TGCTCGAC
-AGTTGCTT TCTGGCGA
-ATTATGTT TCGGAATG
-CACATCCT TACTTAGC
-CAGGAGCC GTATAACA
-CATAGCGA GGTCCAGA
-CATGCTTA GCACATCT
-CCAGTTAG GCACACGA
-CCTACCAT CTACCAGG
-CTACCAGG CCTACCAT
-GCACACGA CCAGTTAG
-GCACATCT CATGCTTA
-GGTCCAGA CATAGCGA
-GTATAACA CAGGAGCC
-TACTTAGC CACATCCT
-TCGGAATG ATTATGTT
-TCTGGCGA AGTTGCTT
-TGCTCGAC AGCAATTC
-TGTCGGAT ACCAACTG
-TTCGCTGA AAGGATGT
-TTGAGCCT AACTTGAC
-N N
\ No newline at end of file
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/nonBarcoded.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/nonBarcoded.1.fastq
deleted file mode 100644
index 4d09170..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/nonBarcoded.1.fastq
+++ /dev/null
@@ -1,240 +0,0 @@
- at machine1:HiMom:abcdeACXX:1:1:1793:1011 1:N:0:
-ANNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
-+
-(%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%1%%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1420 1:N:0:
-GNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNN
-+
-=%%%%%%%%%%%%%%%%%%%%=%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1441 1:N:0:
-CNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
-+
-(%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%+%%%%%%%%%%%%%%%%%%%%%5%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1483 1:N:0:
-GNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNANNNNNNNNNN
-+
-:%%%%%%%%%%%%%%%%%%%%=%%%%%%%%%%%%%%%%%%%%%/%%%%%%%%%%%%%%%%%%%%%8%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1495 1:N:0:
-GNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
-+
-7%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1527 1:N:0:
-GNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNN
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-.%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%
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-CNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
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-)%%%%%%%%%%%%%%%%%%%%)%%%%%%%%%%%%%%%%%%%%%)%%%%%%%%%%%%%%%%%%%%%1%%%%%%%%%%
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-GNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNN
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-:%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%
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-GNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNN
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-5%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%5%%%%%%%%%%
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-CNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNN
-+
-<%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1658 1:N:0:
-CNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNN
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-(%%%%%%%%%%%%%%%%%%%%=%%%%%%%%%%%%%%%%%%%%%=%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1681 1:N:0:
-CNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNANNNNNNNNNN
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-?%%%%%%%%%%%%%%%%%%%%)%%%%%%%%%%%%%%%%%%%%%&%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1718 1:N:0:
-GNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
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-:%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%)%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1745 1:N:0:
-CNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNN
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-1%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%7%%%%%%%%%%%%%%%%%%%%%1%%%%%%%%%%
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-GNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
-+
-:%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%:%%%%%%%%%%%%%%%%%%%%%1%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1813 1:N:0:
-GNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
-+
-7%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%1%%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1916 1:N:0:
-GNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
-+
-<%%%%%%%%%%%%%%%%%%%%6%%%%%%%%%%%%%%%%%%%%%=%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1959 1:N:0:
-GNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
-+
-<%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:602 1:N:0:
-TNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNANNNNNNNNNN
-+
-<%%%%%%%%%%%%%%%%%%%%>%%%%%%%%%%%%%%%%%%%%%7%%%%%%%%%%%%%%%%%%%%%2%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:808 1:N:0:
-TNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNN
-+
-:%%%%%%%%%%%%%%%%%%%%?%%%%%%%%%%%%%%%%%%%%%?%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:2:1793:1117 1:N:0:
-GNGGGNNNNNNNCNGGTCGTTAGCAAGTGATGGCTGTGTTCTGTATCTTTATTGTGGCGACACTTACATGACTGGA
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-3%;B7%%%%%%%=%9C*'5@?BCB><.9>?@BA)>>(B<3@)@4?B<8)5>67<6A5+5-0.(84-8637,7/7%)
- at machine1:HiMom:abcdeACXX:1:2:1793:1329 1:N:0:
-CNTCTNNNNNNNTNGATGCAGTAACTGGAAATATAGAAGATGCTGTGACTCCATTTGAATCTATAAAAAGCGTTGT
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-8%805%%%%%%%3%9?*7?(1(90'80;4(:??<<+9:5+/=A85,/=?3)=')6-+*,5=/902-2-0+5-%,-0
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-TNGCTNNNNNNNGNGGCGCCGCGAAGCGCACGGCGCCGACGCAGGGGGAAGGCGGGACATACACGACCCGCGAGCG
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-1%;A;%%%%%%%8%(5;@B7;(;*8;(8@;@<9/81((77*<(8 at -3<'(5=;(7((<')'<.0(/*(7/.2(9>1
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-CNTTCNNNNNNNGNGACTGCAGTTGCTGTTGCCCATTAAGACCTTGAGAAAAGGCTTGCCTGCCCTTCGTCTGACT
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-?%8=?%%%%%%%:%9'=?@C*@2'=B<;/(;=%?,89'80(=B9=>7145.-(7B-)38/5)'=%5-=:/57)%6%
- at machine1:HiMom:abcdeACXX:1:2:1793:1478 1:N:0:
-TNTTTNNNNNNNCNAATTTTACCTCATAAAATTTTTTGAGGTTTGATGTATGTCTCTGTCTTATCAATAATGAGGC
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-=%?C?%%%%%%%*%+, at CCB>BCBBA@=778BCBCBCB?BC?BCA4AC@;@C at CBCBBACA:)=B>';64=>6=AC
- at machine1:HiMom:abcdeACXX:1:2:1793:1793 1:N:0:
-CNCCANNNNNNNCNGGGCCCTTTGTCTAAAGTCTGAATCAGCATTTGGATTTAGCCCTAATAGAGCCTGTTCATCC
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-=%?%)%%%%%%%=%68>BBB9?>@:B:)2(7:A84'67>5;>/67889'385,9@?=-+(327+3@>8777</15@
- at machine1:HiMom:abcdeACXX:1:2:1793:1812 1:N:0:
-CNCTCNNNNNNNCNGCATACTTAACAAGTCTGATCTTGCTTATAGAAATTGGATCTTACTACTTCATTCTCAGAAT
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-(%?B>%%%%%%%?%>B7=- at BB;=@07B at CBB5?CBBBCB?+>:B944?BB at 1@CBB9/=7B at AB=@@BB@(>(8<
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-GNTCCNNNNNNNANTCCCCGTGGATGAAAATGCTGTACATGTTCTTGTTGATAACAATGGGCAAGGTCTAGGACAG
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-0%;C<%%%%%%%)%9CC@(>?C at 1=A7(00=BCAB96A><A?@CAAB at AA5>7AB1'6>7>B9.9B7B5)7;5B<>
- at machine1:HiMom:abcdeACXX:1:2:1793:1909 1:N:0:
-GNCCTNNNNNNNCNCTCACACCGCCCCCCTTCTCACCTGCCCTGCGTAACCTGTACTGACTGCCCACTCCTCACCC
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-(%<@8%%%%%%%*%;(8@;*>7;*.(<B>5(.5@/*>93;(2@=-:'5>)0=+1;'5:';/(;1@*>,(;';((:)
- at machine1:HiMom:abcdeACXX:1:2:1793:1931 1:N:0:
-GNCTANNNNNNNTNCACTGTCGACACCGCACACGGGGCATACCCACATCAAAGCAGTCCCCCAAGTCCCTGCGCAG
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-<%8.'%%%%%%%&%.(<B**(>3*775(*(;'.6''+;'&1(9.).*(7;5/'2(64A70>0.,23@)0%'5=<*'
- at machine1:HiMom:abcdeACXX:1:2:1793:1969 1:N:0:
-TNCGCNNNNNNNANCCCTGACTGGCAAGGCGGTGGCGGCTCCAGTGAAGGCTCCCCGTGTTCTTAAAGACTAGCGC
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-5%8((%%%%%%%1%;BBB>+)7BBB?-?10 at B7BBB9A@@A379'?*39BA4@>);'5:'BBAA;>2>A6+9+@*<
- at machine1:HiMom:abcdeACXX:1:2:1793:2004 1:N:0:
-GNGTTNNNNNNNCNTACTGGCATTTACTGTTTAACATCACACACCAAGCCAGGTTATTTCACACTCCTGCTACTGG
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-8%13<%%%%%%%:%?CCBBB?(>CCCCCBA@*9+ at +@C at +*1?;8 at +3*@*8C4 at 4>C>7 at 8115?),CC<7@?:A
- at machine1:HiMom:abcdeACXX:1:2:1793:2031 1:N:0:
-CNCCGNNNNNNNGNGGTGCATGGGCTCCAACGTGGTGTCCTGTGGAGCTGTTGGGCCTGGGCAGGCGGCACAGATC
-+
-:%'*:%%%%%%%:%:B;B@(<BBAB9BA3AAB9A@,B1(==A6 at A/??;=5=?A3%273<4A,;7;:=;+&&/,/3
- at machine1:HiMom:abcdeACXX:1:2:1793:2038 1:N:0:
-GNGCGNNNNNNNGNCACCTTGGTACTGGGTGATGGGGAGGCACTGAATGGGCTTCAAGTCCTCAAACGCCTGATCT
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-?%:-;%%%%%%%.%=)@CCACB=8ABCB?7@&>B?AC=?CB9C4AAA>>6==>>;%5>3%:/:%,3.;@0,9*-1;
- at machine1:HiMom:abcdeACXX:1:2:1793:310 1:N:0:
-CNGGANNNNNNNTNGAACCTTTGGCAAGGCTGCTCTTACGAGTCCTCTCGCCCTGTTCCACCTATCCCCATAGCTA
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-(%5;'%%%%%%%(%.*0 at 99@AB>CA5):=:A1;A<3':-''.'3';('5>BC at B=A(A<>511(6B?,''(<&-*
- at machine1:HiMom:abcdeACXX:1:2:1793:404 1:N:0:
-CNCCCNNNNNNNTNCAATGCTATGCAGTATGTCTTCTTATCTCTGTCTTCAAGAGCATCCTCTGTCAGTCCTACAT
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-:%)?0%%%%%%%9%*/0%,8.-->>>>9@?=975(=4/%0?74'/''39%-?8828,4412=0168;2+9A:74'5
- at machine1:HiMom:abcdeACXX:1:2:1793:475 1:N:0:
-CNGGGNNNNNNNCNCCCCCCTAGGCAATATGCTACTGCATATATATTTGGTCTAGATATATAACAAGTTACTACTG
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-?%9?3%%%%%%%0%<<%5;(2*7<@?(1')6>7?,7=7@*)6)35'7:7)%%,'3(.(+2++482.:))-%0-''2
- at machine1:HiMom:abcdeACXX:1:2:1793:666 1:N:0:
-CNGAGNNNNNNNTNGGGTAGGAAACACAGCCTTGCTCCACAGCGCACTGTCAGCAAGACGCTCCTTTCTTCGGAGA
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-?%9(9%%%%%%%%%7)9..<::>3>1;77<B05??)B>0=12(2A6=4:4956?/%5-%-;1;6542;/-&(26,(
- at machine1:HiMom:abcdeACXX:1:2:1793:829 1:N:0:
-TNGGCNNNNNNNCNTGGGCAAGCACCTGACCAGCAACAGCCCCCGCCTGGTGCAGCACTGCCTGTGGACCCTGCGC
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-;%;>*%%%%%%%<%:BAB at 0;BBBBBB@;@B at A@;*@*>BBBBBABBA?@3@@;<(5 at AAB@:>.=;,<BB;<BAB
- at machine1:HiMom:abcdeACXX:1:2:1794:490 1:N:0:
-CNTCCNNNNNNNTNTATTTACTATTTTCTGATTTTTAAAATGACAGTGGCAATTACCATTTATACTGTGTTATTTG
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-?%8C?%%%%%%%9%6(=?:(=@BAA@@B at A<<<<=@=;5?@9+?A@:?9 at 5&1=>A?+:6668=A9?7?9?=<9=6
- at machine1:HiMom:abcdeACXX:1:3:1793:1031 1:N:0:
-CNACTNNNNNNNGNNGCATTGGAGAAGAACCAAGCTGGCTCTCTAAGGAAGTGCACACGAGTTGGAACACATATTC
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-?%<?(%%%%%%%:%%=B47?B=6?=2?/00 at 8), at BB=3,>).'50;:72))1)5=:)<19%)+(%5?:=;7.)1'
- at machine1:HiMom:abcdeACXX:1:3:1793:1143 1:N:0:
-TNGGGNNNNNNNTNCATGGTGAGGAAGAGTCGGAAGCAGGCATGCGGCTGCAGGGAATGCAACTTCTTCTCCATCG
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-:%(B3%%%%%%%:%=BCCC<CBBB<CCB3*@?BBBAA*=B at 9@?B?8<3;>3;A;+2:9<43:<;?9>A:8<+%<%
- at machine1:HiMom:abcdeACXX:1:3:1793:1282 1:N:0:
-GNTAGNNNNNNNCNGGACTCTGGCGTCACCTTTGGCGCTGAGCGCCCCAGGCCCGCCAGCCCGCCCGCCCACTGCC
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-<%;(.%%%%%%%(%.6.(;B at 55+9>*8@(>*@;(.;@75'5';;@;;*4<5<2*@;/><@5>5(16;1;7)',..
- at machine1:HiMom:abcdeACXX:1:3:1793:1301 1:N:0:
-GNAGGNNNNNNNTNCAGGGTTGAGGTATTCTTAGGTTAGCCGAGCTCTTTCCTCCTTTCCCCCCCCCTCTCCCCCA
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-?%*:3%%%%%%%(%;*9)>3+-*-@=)3?CCBAA;)A8 at 2*25;A7,52=B;(=)47)=BC;+:C@)2 at 0=BA9(9
- at machine1:HiMom:abcdeACXX:1:3:1793:1311 1:N:0:
-GNTATNNNNNNNTNTTCCTTCAGTCTGCACAAAGATTAAGGTAATTTACAGTCAATCTGTGAATGAATGTTGAGAC
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-<%()<%%%%%%%7%<<BCBCCCABCCCC at CBB?BCCCCCBC>AACC?*@.BAB8*@CCCBC@:@?7?ABAA??B8B
- at machine1:HiMom:abcdeACXX:1:3:1793:1326 1:N:0:
-GNCCANNNNNNNCNTCTTGGGCTCCACACCATTACCAGCATCAGAGGCAGGGGAACACAATCTGCTGCCTTATAAG
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-?%?@7%%%%%%%?%3C=+;.<@+@@8A?AC@@ABBB at BCB?+?;?-5- at BA92-7B<?-2/,*@A2?BB;A5?1'4
- at machine1:HiMom:abcdeACXX:1:3:1793:1389 1:N:0:
-GNGGGNNNNNNNGNCGCAGGTGGGGATGGGCACCCTCACAGCTTCCCTGGACCTTAGTTTTGTTGGGGTTCAGTCC
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-:%<B;%%%%%%%7%;A at 1@>.>BB@:;ABAABBBBB<+<7?@8 at BBBBA72@>2<(>5+=7906A<;5*3<2 at -(4
- at machine1:HiMom:abcdeACXX:1:3:1793:1405 1:N:0:
-GNTGGNNNNNNNTNGCTGAGATGCTCTTTAACCAAAGGAGGAAAGAGAGGAGACCAAGGGCCAGCTGGTTGGTTGT
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-7%1C=%%%%%%%8%8CA=2@?ABB6BABBABBC;:>BB>B at 9(;A=@?B>3?)@A?=5(7?@1>B=A;(=@@,1=3
- at machine1:HiMom:abcdeACXX:1:3:1793:141 1:N:0:
-TNCTCNNNNNNNCNCTTAGCAGTGCGCCCCCCGAGCGCGGCACAGGGGCCAGGGAGACAGAGGACACCGGGATCTC
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-;%;9,%%%%%%%,%52(((3.8(+/*/B at 1<1((=.&4+9+/(::11+(&7600+.+A4'*%%%-%:/,%%,'9'B
- at machine1:HiMom:abcdeACXX:1:3:1793:1507 1:N:0:
-GNGTGNNNNNNNTNGTTGCCAGCCTGCTGCCCGCCATCCTGGTCTTCATTCTCATCTTCATGGAGACACAGATCAC
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-=%==8%%%%%%%?%5ABABBABCCBBCBBCCCBC at 09ACB==;CBB at 0;>ABBBACA>?'9A==>)@)?9;63?5@
- at machine1:HiMom:abcdeACXX:1:3:1793:1557 1:N:0:
-GNGGANNNNNNNCNTCGAGCCATTCCACTCCCGCCCGGGCACCAACAGCCAAACGCACGCTCATCAAAAAGGCCGA
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-(%;*(%%%%%%%;%5>/(4?A;=6(><1*@1*-@@>/*0 at 9)9?>2.=8'<,8<,1((%:1<?+(.08'+55B?:%
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-GNTCTNNNNNNNTNTCTCCACTCTGCTGCCCTACCTCTCGGAGTCTTCTACCGCGTCTAACTAGTCATATTTACAA
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-6%3B6%%%%%%%,%'C@@BC>1?B at CC?C at CAB@B@?6&BACA4,?*<B@>1'13,<B;)@BB3'?%)+:A@;CB@
- at machine1:HiMom:abcdeACXX:1:3:1793:1617 1:N:0:
-CNGAANNNNNNNTNCGCCTTCTTCTTCAACTCGGAGCTGCTGAGCGCTGTGCGCTTCGCCCTGGGCAAGGGCCGCG
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-:%75'%%%%%%%3%;;BA><A;=B;7 at 84>'9>:90<,7<,61132%*8//3471'349+6,36+:&+462+.&.%
- at machine1:HiMom:abcdeACXX:1:3:1793:1709 1:N:0:
-GNGGGNNNNNNNTNCCATTGGTTTCTGAAAGTATTCACATCATTTGGGATACCAGATAGCTCAATACTCTCTGAGT
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-8%>B<%%%%%%%:%?B8BBBB?BBCAC?@6 at 1;AB@*@<>B9>?@@B?9<4BB8 at 82)<C at CA:?8B at C@C@?/='
- at machine1:HiMom:abcdeACXX:1:3:1793:1738 1:N:0:
-GNGCCNNNNNNNGNCTCTTGGGGAATATCTGAGGCTCTGTGGTCACCCACAGACCCGTTACTCCTTTAGGTGTCTG
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-?%:C?%%%%%%%8%=BCABBBBC?BBCBCBBBBBC at C?A1AB.?3?A2)@880@@)0%96?9 at B;><+=>5 at 0>=@
- at machine1:HiMom:abcdeACXX:1:3:1793:1779 1:N:0:
-GNGCANNNNNNNCNTGCGTATATTTACAGATATATATACAGAATTGTTTGCTCTGAGCCATTTATAAGCACTTACT
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-=%5A0%%%%%%%?%)9*>'=@::>BBB:B@;7AAA at 7@=3/.*:?@8;,<*;B4=ABBC?).=4>(;BA=CA:-?;
- at machine1:HiMom:abcdeACXX:1:3:1793:1793 1:N:0:
-CNTCTNNNNNNNANNATGGGCTTTCTACAGCCTGCTTACCACTAACAGTAAGGAATCTTTCATAAACACACCTCAG
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-:%1 at 6%%%%%%%&%%'-;:)62(9=)=>3)0A9>@501??:=5:583466.451,9 at 952<,94.2;88+2=8;3,
- at machine1:HiMom:abcdeACXX:1:3:1793:1859 1:N:0:
-GNGAGNNNNNNNANCCAAGCATCTATCCCAGTGTGGGGGCTGAGGCTGCGAGAGGAAAGCGGGGACGGAAGACGGG
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-<%((;%%%%%%%<%(;=<B96<@B3?BBB=B11(A;BB/(0=-:?9)@-=,12<=2>>:@8@':%8<=.52(82(+
- at machine1:HiMom:abcdeACXX:1:3:1793:1898 1:N:0:
-GNACANNNNNNNGNAATATGGGCTTATCCAACCCAACCAAGATGGAGAGTGAGGGGGTTGTCCCTGGGCCCAAGGC
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-:%/=(%%%%%%%:%*/<1=5;BBBAAACCA8ABCAACB;)@?BBB+B6?4B:A7;??16@=BA?9509B?@-+844
- at machine1:HiMom:abcdeACXX:1:3:1793:456 1:N:0:
-CNTATNNNNNNNCNNCGGGTACCACAGTTGAGGACTGACATTCTGAACCCTGATGTTTCTAAAGAAACGACAGTAT
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-?%6 at 8%%%%%%%?%%?@?@6AAA??6<>>@6/7?A??6><<8=@252;>@84<9>58@?7.-6;78;<4'9-<:68
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/nonBarcoded.2.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/nonBarcoded.2.fastq
deleted file mode 100644
index 8e9b24a..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/nonBarcoded.2.fastq
+++ /dev/null
@@ -1,240 +0,0 @@
- at machine1:HiMom:abcdeACXX:1:1:1793:1011 2:N:0:
-ANNNTNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
-+
-3%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%%%%%%%%%%%%?%%%%%%%%%%%%%%%%%%%%%*%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1420 2:N:0:
-CNNNANNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNN
-+
-?%%%*%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1441 2:N:0:
-CNNNANNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
-+
-<%%%(%%%%%%%%%%%%%%%%'%%%%%%%%%%%%%%%%%%%%%:%%%%%%%%%%%%%%%%%%%%%&%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1483 2:N:0:
-GNNNANNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
-+
-<%%%%%%%%%%%%%%%%%%%%0%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%>%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1495 2:N:0:
-ANNNTNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
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-)%%%*%%%%%%%%%%%%%%%%(%%%%%%%%%%%%%%%%%%%%%:%%%%%%%%%%%%%%%%%%%%%4%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1527 2:N:0:
-CNNNCNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
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-:%%%*%%%%%%%%%%%%%%%%7%%%%%%%%%%%%%%%%%%%%%5%%%%%%%%%%%%%%%%%%%%%*%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1545 2:N:0:
-CNNNTNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
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-5%%%*%%%%%%%%%%%%%%%%2%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1583 2:N:0:
-CNNNTNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
-+
-<%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%&%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1596 2:N:0:
-CNNNCNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
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-<%%%+%%%%%%%%%%%%%%%%5%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%+%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1602 2:N:0:
-CNNNGNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
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-;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%8%%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1658 2:N:0:
-TNNNCNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
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-:%%%+%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1681 2:N:0:
-ANNNANNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
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-)%%%(%%%%%%%%%%%%%%%%7%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%%%%%%%%%%%%4%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1718 2:N:0:
-ANNNANNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
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-(%%%%%%%%%%%%%%%%%%%%/%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1745 2:N:0:
-ANNNTNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNN
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-(%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%%%%%%%%%%%%4%%%%%%%%%%%%%%%%%%%%%0%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1777 2:N:0:
-ANNNANNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
-+
-)%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1813 2:N:0:
-CNNNCNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
-+
-<%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%*%%%%%%%%%%%%%%%%%%%%%:%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1916 2:N:0:
-CNNNANNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
-+
-(%%%(%%%%%%%%%%%%%%%%0%%%%%%%%%%%%%%%%%%%%%5%%%%%%%%%%%%%%%%%%%%%4%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:1959 2:N:0:
-ANNNCNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNCNNNNNNNNNN
-+
-1%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:602 2:N:0:
-CNNNANNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
-+
-?%%%&%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%:%%%%%%%%%%%%%%%%%%%%%6%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:1:1793:808 2:N:0:
-CNNNANNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNN
-+
-<%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%
- at machine1:HiMom:abcdeACXX:1:2:1793:1117 2:N:0:
-TTCTTCAGCTGTATTGAAGTATAATTTACAATACAGTACAATTCATATATTTTAATTGTATAATTTAATGACTTTG
-+
-+4 at .:B=?<'<?@2+=38A4+;>.3:9A>(7??A09(0>((0=A::;,;+/(:+*769)..'09>.%+2-4>-'(7
- at machine1:HiMom:abcdeACXX:1:2:1793:1329 2:N:0:
-GAGCCCCGCGTCTGTCTCAGAGAACTTTTGCATTCTTCTTGTTCTCCAGGAGAAACGGCATCATCTTCCATGTCTT
-+
-A@=*BC at -+:6B8'6 at BC@C>,;2)5BBBBB>;BCBBC at 6@@BAACCB>B;8)07*<@=':C><<9A@(68@=B59
- at machine1:HiMom:abcdeACXX:1:2:1793:1354 2:N:0:
-CTGAACCTCAAGTCTCCACCAATCAGAATCTGGGGGAGGGCGCGCGTGCAGGGAGCCGCCTGCTCTCCACCTTCGC
-+
-A24(06/+.2(21?49?:-+(5&8&5**4?1'13..0'.'%,,98&%(60&.++1(&+A,,0..8.18(.0&+,,/
- at machine1:HiMom:abcdeACXX:1:2:1793:1455 2:N:0:
-GGAAACCAACCCCTCACATGGTAACCCGCTCCAACCCGCACGCCCTGTTCGGCCCCTGACCCGGCCCCCCGGCGCA
-+
->/,+'<:''',5'3(59'+.705,/8 at 94(,+'5@;'%7%%;3>86.*%04&'%17(&.5%%+%,>0624*%,*:%
- at machine1:HiMom:abcdeACXX:1:2:1793:1478 2:N:0:
-CAGCCATTCAAATCCAGTATTTTTTAAGCCTCATTATTGATAAGACAGAGACATACATCACACCTCAACACCTTTT
-+
-A:;C?'7<>(0*8B?*:4-4;A><8+-9BB>?/;;7:<702'+:(?/9(92<+12<,5;&'.>@<?*&%*&%3865
- at machine1:HiMom:abcdeACXX:1:2:1793:1793 2:N:0:
-GTTTATAACTTCTTCTGTGGGATCAGCGGGCACGCCTCTTCCCACCAGCACACTACACGTCTACCAGCGCGGATGG
-+
-B?A>.90)(<@CB?C at B8BA>?=?*<&:@?=%;ABB:&85&=+>A=%7&+'. at 3&9&,=2&810626B7'<5%->:
- at machine1:HiMom:abcdeACXX:1:2:1793:1812 2:N:0:
-TCCAGCATGAAGATAATGGCTAATACCAAAGCAGCCTTTTTGCTGTGGTAGGAAGATAATGGCTAATAAAAATGAG
-+
-BCCCCB9A at ++@4?7+?CBCA@)=)''/2)8@)=?(;??AA=&=B at BB02<9.)3).%0-2<5&/+*1%(:'*,%9
- at machine1:HiMom:abcdeACXX:1:2:1793:1893 2:N:0:
-GGGCAGGGGGCTTTTTCTCACTCTCTCTCATATCTTCTAGGGTAACTACATGAACACACGCTTCTCTCCCCTTCCG
-+
-ABBB4=BBB:)=B<AAC?C>)?C at C?CBB3;)<C at BC9(>?A3 at -@=)@6@=4'?4(425C9=B<C at CB@(07((:
- at machine1:HiMom:abcdeACXX:1:2:1793:1909 2:N:0:
-CTCACACCCACACCCCCCCCAATCCCACCCCCGGACACCACACCCCTCCAACTTCCCCCCCCGAGCGCAGCCGGGG
-+
-B16+:&3:(%+'4+&6;/2(%,/29.'5,,--,('&.''%%,&.1+%*:%%1%%%%,((%'&(%(247-*%+11&%
- at machine1:HiMom:abcdeACXX:1:2:1793:1931 2:N:0:
-CTGAAGCGCCACCGCCGCGGCGTGGCGGGCCCCGCGCACCACCTCTTCCCGTCCTCTACCGGCCCTGGCCACGCCC
-+
-9+&'411'41,0'1/.%'%&9(0,%,'--%%-'%%.''.,((.+,(%-3+++,/(*+&'3,+*-%%**.&%,0'*(
- at machine1:HiMom:abcdeACXX:1:2:1793:1969 2:N:0:
-GAGAACTCTCTGTGTAGTTGTGACTTCCATCCTTCCGCAACAGTAGTAAGGACCGCGACTTCTGACCACATTGACC
-+
-:%===(,=B>=:-;7<B/?@8@=:8==>'.,=86 at B@A,,+07-(9'35>?58//?;-'+.8(50'619('''+/9
- at machine1:HiMom:abcdeACXX:1:2:1793:2004 2:N:0:
-GAACTTGACTATCTCTTCTAATTTTATTGTTTATTTTGTGTTTACTGCCCAGCTACTTCCCACCTTCCACTTGCTT
-+
-B?4 at C@<+>=57'3B>=)?4>BBA?+=@B@>7-;@@@A=B::7?4<>?*?<8B83A?=>(>;BB1A.%-@@:8 at 5=
- at machine1:HiMom:abcdeACXX:1:2:1793:2031 2:N:0:
-TGCCAGTAGTTTTGGGTCAAGCCCTCACCTGATTCCACGCTTCATAGCTTCAGCCGTTCCCATCATACTACTAGCT
-+
-BBBC=>==B=@@@@BB5@)-=CBA9'/B@=>16 at BB)(8'4=A54-=B:8@(;?(9'0?A7'1A.96>3/'4235-
- at machine1:HiMom:abcdeACXX:1:2:1793:2038 2:N:0:
-CCTGTGTCTCAGTGAGCCTTCAGTGCAACATACGGGTAAGAGCAGCCTTCTCTTCACTGAGATGAGACCCCCCCAC
-+
-B>626.288?89.5'5??60,477.3'%%)+112.21.&21330/75*)55(5+./,2*%-,/1)162/2'55662
- at machine1:HiMom:abcdeACXX:1:2:1793:310 2:N:0:
-CGAAACTTGGGTCAGTAAACTGGTGAAGCTGACCTATTTGGCAAGCAGCATGATTCGGAAGCGCGGCAGGCAGAGT
-+
-?(5 at BB*>57 at 6B@*34)?=6B@()'18%'?=@A*:@?4 at +(4>A;8<'/@=366A@;/7@(-'()7(1(8(2'''
- at machine1:HiMom:abcdeACXX:1:2:1793:404 2:N:0:
-ACATGAATCCTCTCCCACAGGAATTATTCAGCTTACCGCGAGTACGCTTCCGTGTTGGAAAGATTCAACTCACCCC
-+
-;'7B62:2(=/8<>A at 9A=88>6<==:4?%5A8=;>@*73,.%6?<'%%5;+)%%-2'1)&%5(-937&0)%%0=B
- at machine1:HiMom:abcdeACXX:1:2:1793:475 2:N:0:
-AACTTTTTTACGCAATGTTAATATTCAACTCTTCCTTCCAATAGAAATTTTCTGCTGCTTTTCTTGCTCGTGCTAG
-+
-BCB77433)@1)@*:>A9+>401>@?:*@6=(6C8*/2@<(2A8%)6?;97 at 9+9;<'3/4)-15:34+)'8'2--
- at machine1:HiMom:abcdeACXX:1:2:1793:666 2:N:0:
-ATTTTTGCTTTCCTTGGCCCCCACCAATTTATACATCTCCATTTTCCGACCTCTGGACTAACTGCTTGCTCAGCAC
-+
-6;BAC?AB@@>@8;@>@BBBBA:@B8=?;1>6 at AA<B4AB:94<;=,0'<@<A87)7B=73@;3)'/69(<,67'%
- at machine1:HiMom:abcdeACXX:1:2:1793:829 2:N:0:
-TCGCTGTTGTTGCATGTCAGGTTGGAGAGTGTGCCCGTGGCCCCGGTGCGGCCGGTGGCCGCCCCCCCCCCCCGCC
-+
-AB at BBA=AB?AA@)8@=@)>=>=A>3=0>4A3ABB at 6+<><(<'88*8%:8%:4%52(8%(55%4>2<7;*;2%7%
- at machine1:HiMom:abcdeACXX:1:2:1794:490 2:N:0:
-ATAAACTTGAAAATAATTTTCTATGATACAGCTTTCAGGTAGAAAAATGAATTTTCGTCGTGTTTAACAATGTTGT
-+
-ABBCBCAAC@;5@@77BBB?CCBBB?@BCBBCAB@@3<A6>>)99?0<B at 6?>@@BB6A9>B5A<@6<%+>@<<:0
- at machine1:HiMom:abcdeACXX:1:3:1793:1031 2:N:0:
-CCCATACCAGCACAGAGCATACAGAAACACAGAAAAAATATTCCCAGTAAAACATGTGCAACTGTCCAGGCAGTCG
-+
-+5AA at 92+>4AABBA6@;'(-;<=22)B8@@@7>A@<583498 at 62-45:-8>8;:0081*956-;7.)*%.4))0
- at machine1:HiMom:abcdeACXX:1:3:1793:1143 2:N:0:
-CTGCAGAGCAGTTGTGGCACTGGGCTTTGGCCACTCAAACTCAGGCTGGTCCGGAACCTCCCCCACCCCGCCCCAC
-+
-A==B59>>A at 8/7=,19:+:'344A..366?A9=4>168?1:113;42,%7:3-&177&59=;8&,=2%(8+7%%2
- at machine1:HiMom:abcdeACXX:1:3:1793:1282 2:N:0:
-AAGCACACCAAGCTTCCCGCAGCTGCGGCGCCCCCGCTCCAAGGCCAGCAGCTGCCCCCTCTGCCCCCACCCCCTC
-+
-(*579.1(.//>B at -17+=../@9=*=(.(.;<.1'>;<:'''7=;'.':==:551938*7.7;:%7:'';@;609
- at machine1:HiMom:abcdeACXX:1:3:1793:1301 2:N:0:
-GCATTGCGTCCATCTCTTTACAGAAGAACTCAGCCCACACCCTAGAATGTACACCTTTGGAAAAAGGAGAAGTGCT
-+
-=(6;9*AA;*BCBCCCABB at CB@)??@>@BBBCCCA6 at 8?CC>9@>=?@-2)9AB;6>>;5334=3=7+6-14?=-
- at machine1:HiMom:abcdeACXX:1:3:1793:1311 2:N:0:
-CAGCAAAAGTGCCGGCTAGTCCGGTTTGTTGAAAATACAGTAGAAAAGCTGATTCTGGTTATCTCTCTCAGGACAA
-+
-B<ABBA4=A1?CCBB*B9?:>'>@)?A@<AA74;A@?B=>)'6'61<58(:/75A?7(0===@=@4*7%355/>40
- at machine1:HiMom:abcdeACXX:1:3:1793:1326 2:N:0:
-CAAGATCATACTAACACACTCCAGCCTGGGCAACAGAGTGGGACTCTGTATCCAAAAAAAATTCTCTACCAACTAC
-+
-BABB==BA?@CB??BBCCCCBB- at AC0B<,CCCCA at 4<@A;;AC+CBCA,BCA1=A:=9<=A,C?+<?B?3<B,?C
- at machine1:HiMom:abcdeACXX:1:3:1793:1389 2:N:0:
-ACCACAGGCACCACCAGCCACGGACCCACGCCTGCCACTCCCCACCCCCCCCCCCCCAGCCACGCCACCGTCCCAC
-+
-7@>*@0:3 at 2@@7BB=ABB3B=5%;B>(>0%:;<A=0@=8';&(:?A>2>7%<;%:A;3@>+.*%%.+<0/:)>-)
- at machine1:HiMom:abcdeACXX:1:3:1793:1405 2:N:0:
-GCCTTGTTTGGCCCTGATCTCTGACTTCTAGAGCCCCAGCTGCTGGCGGCTGCTGGGATATCCTCCCCGCTCGGGT
-+
- at BBBBBA@@9BBBBA11=BBBBBABBBBB9=9BBBBB9ABABB@*=B@@719.2=33%822@>'':A5%1+%77%(
- at machine1:HiMom:abcdeACXX:1:3:1793:141 2:N:0:
-CTCTCCCGCGCCTGCTACGGAGCCCGCTCGGGGGGGCCACGCCGCTCCCGAGGACGTAGCACCTCCTCCACTCACG
-+
-4:-*695*:&7(.333?9*'(@(6.((%%,;62+*..(./0(>3/&%14(,1((0-6&15%%.6>(&'%+20&+3(
- at machine1:HiMom:abcdeACXX:1:3:1793:1507 2:N:0:
-CAGAGCGCGTTGGCGTGAGTGACAGAGCGGCCAGTGGCCGCCGCCCACCCGCCCACGCCCCCGAGGGCCCCCCTGC
-+
- at 11+1?4>44344=533,252.;11,->4.&7.**,-5++.,(.7*&,1*%%%.*(%...,*%*+,%%+1(&+%,.
- at machine1:HiMom:abcdeACXX:1:3:1793:1557 2:N:0:
-CGGCTTTTTTTTTATTGAGACCAGCTCCTGCCCTACCCCCGCGGCTGCGGAGCAAGGTCCCCTTCATGCGCCCCCC
-+
-5&0/(7*3>96=9)<*+%'+5,/%'&7%7+675%'%%+09*(*'2(5%%,&(.&,%%(,6%(&'7&+&,&-,+554
- at machine1:HiMom:abcdeACXX:1:3:1793:1570 2:N:0:
-CAGACACCTTTCATATCTTTATGGCAACTTAATTTTTGGCCTTTTATCACTCTGTCATACCAGCATTCTGCCGTCA
-+
-A@>;B at CB549'34=9B;?>/A@?8@@;=<(9/5++<74B;B<%..;C-(.8?@(>'9@>><6>(4;<%*.(.*=:
- at machine1:HiMom:abcdeACXX:1:3:1793:1617 2:N:0:
-GTGGTCATAACTGTTTCTGGACCCATTTGAACTTCATCTGAATATAGAAATCTCAGCAGCGCCCGGACGGCTGCGG
-+
-A<CBAB4>=, at BB@BAC at B=*A@*+>ABB94BB at B;>B?;>@@5A;B=046C@@(6A9;A2A<'90'(:-?%3:/:
- at machine1:HiMom:abcdeACXX:1:3:1793:1709 2:N:0:
-AGCCACTGTCCCGTGTATAACTTGGCATTAGAGCACCAGGTCTGTTGGATGGTGGTGGCAGGCCCAATTAATTTTT
-+
-,?@)7 at B@6BCCC;C?@A;+ at A;BBB=;BA at 6@B6B@(>B8CAA6<B?69B?(B=-:@>-7 at 85:%.))3&73-%)
- at machine1:HiMom:abcdeACXX:1:3:1793:1738 2:N:0:
-TCCCTGACTGGATACAGGCAGCTGACCCCTTCTCCCGACACCTCAAGGAGTAACTGGGCTGTTGGTGACCCCCGAC
-+
-ABBBBA at BBBA<B7B at ABBAB;(:';BBA=A at 0@@*90@)@B<(>)>>(>(+;@9@:%;*<(54 at +.%3@(>5(%'
- at machine1:HiMom:abcdeACXX:1:3:1793:1779 2:N:0:
-CACTGAAATGTTTAGGACCATATTATAAGTAAGTACTTATCAATGTACTTTAGGACCATATTATAAGTAAGTGCTT
-+
-=:AB>(>64A=;27A@=B@)=64@@:5)@9<)=:BBB@:='?'9B*BC>)67B at AC@;=9>)0@*8?:40:<BC=<
- at machine1:HiMom:abcdeACXX:1:3:1793:1793 2:N:0:
-GCTCAAATTTGTGCTACCAATGATATCGAGTTTATAGCAAATTTTCTACGGGAAGTCTATGCGGCAATTTTCTCAT
-+
-BCA=8+3?C=A-8A@:ACB?,@;8;@+@*@;C3,8)8C?+9=;2*=+='2A?898*+0%())18)42:?A7B>?':
- at machine1:HiMom:abcdeACXX:1:3:1793:1859 2:N:0:
-CGATTTTTAAGGACCCCGTGCCTCTGGGGGCCGATGAACTCCACGATGGGACGCACCTGGAGCTCTACCATCAATA
-+
-BB55A9?@>.(7AAAB?3,A>A=A>A6@?>29(434(.'0B?2:?266<2/,91:B9.1)06451//&&78A10,2
- at machine1:HiMom:abcdeACXX:1:3:1793:1898 2:N:0:
-CCGGCCAAGCAGGCATGTGTGAATGAACGTGGCCGCTGACTCAGAACAGAGGACATCCCAGGGCCGCAAGCGCGGA
-+
-BB>ABB3=;>&5(1%2=4=552-',37A=,41>1(1',+.37'1,&9/331(/9/'6.+''0,(%,2&(.1,//.(
- at machine1:HiMom:abcdeACXX:1:3:1793:456 2:N:0:
-TCCATCCACTTCCCTGAGCCTCAGAAAAGGGCAAGGCATGGCTCACATACTCTCAGCCACGGCCTGGCCTGCTGCC
-+
-BBB<ABB at BBBBBB=@@ABB?B5 at 777=;;ABA9A;B?=><BB at 6@AA?B>B9>*>AA9A53?>(%89(.9>;<:(
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/testMultiplex.1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/testMultiplex.1.fastq
deleted file mode 100644
index d91b64e..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/testMultiplex.1.fastq
+++ /dev/null
@@ -1,1600 +0,0 @@
- at HiMom:7:1:0:1038
-NNNNNCNNCANNNCNNNCNCCNNNCNNNNN
-+
-##############################
- at HiMom:7:1:0:1093
-NNNNNCNNGTNNNANNNGNAANNNANNNNN
-+
-##############################
- at HiMom:7:1:0:113
-NNNNNNNNGNNNNNNNNNNNANNNNNNNNN
-+
-##############################
- at HiMom:7:1:0:1193
-NNNNNNNNTNNNNTNNNTNNTNNNCNNNNN
-+
-##############################
- at HiMom:7:1:0:1291
-NNNNNNNNANNNNNNNNANNTNNNNNNNNN
-+
-##############################
- at HiMom:7:1:0:1307
-NNNNNNNNCNNNNANNNTNNTNNNCNNNNN
-+
-##############################
- at HiMom:7:1:0:1434
-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-+
-##############################
- at HiMom:7:1:0:1475
-NNNNNGNNANNNNANNNANNANNNANNNNN
-+
-##############################
- at HiMom:7:1:0:1690
-NNNNNNNNANNNNNNNNGNNCNNNCNNNNN
-+
-##############################
- at HiMom:7:1:0:1703
-NNNNNNNNANNNNNNNNNNNANNNNNNNNN
-+
-##############################
- at HiMom:7:1:0:1940
-NNNNNNNNCNNNNNNNNTNNTNNNNNNNNN
-+
-##############################
- at HiMom:7:1:0:2001
-NNNNNANNTGNNNGNNNANGCNNNANNNNN
-+
-##############################
- at HiMom:7:1:0:205
-NNNNNNNNANNNNNNNNANNTNNNANNNNN
-+
-##############################
- at HiMom:7:1:0:275
-NNNNNANNCANNNTNNNGNCCNNNANNNNN
-+
-##############################
- at HiMom:7:1:0:324
-NNNNNNNNTNNNNNNNNTNNANNNANNNNN
-+
-##############################
- at HiMom:7:1:0:37
-NNNNNNNNANNNNNNNNCNNTNNNCNNNNN
-+
-##############################
- at HiMom:7:1:0:464
-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-+
-##############################
- at HiMom:7:1:0:586
-NNNNNNNNCNNNNNNNNCNNCNNNANNNNN
-+
-##############################
- at HiMom:7:1:0:841
-NNNNNNNNCNNNNNNNNNNNTNNNNNNNNN
-+
-##############################
- at HiMom:7:1:0:879
-NNNNNNNNTNNNNNNNNNNNTNNNNNNNNN
-+
-##############################
- at HiMom:7:1:1:1013
-NNCNNTNCAGNNNCNNNANGTNNNGNNNNN
-+
-##############################
- at HiMom:7:1:1:111
-NNCNNTNGCGNNNTNNNANCTNNNTNNNNN
-+
-##############################
- at HiMom:7:1:1:1153
-NNTNNTNTGGNNNTNNNCNTCNNNTNNNNN
-+
-##############################
- at HiMom:7:1:1:1184
-NNANNGNTCGNNNANNNTNCANNNTNNNNN
-+
-##############################
- at HiMom:7:1:1:1241
-NNANNGNTGGNNNTNNNCNTGNNNANNNNN
-+
-##############################
- at HiMom:7:1:1:1243
-NNANNANGGANNNANNNCNTANNNTNNNNN
-+
-##############################
- at HiMom:7:1:1:1247
-NCCAGCNTTTNNNTNNNTNCTNNNGNNNNN
-+
-##############################
- at HiMom:7:1:1:1282
-NNANNANGGGNNNTNNNGNAGNNNCNNNNN
-+
-##############################
- at HiMom:7:1:1:132
-NNANNGNGGGNNNGNNNGNGGNNNGNNNNN
-+
-##############################
- at HiMom:7:1:1:1320
-NNANNTNAGTNNNGNNNGNTANNNCNNNNN
-+
-##############################
- at HiMom:7:1:1:1372
-NACATTTTTTAGNTNANTTGTTNACNANNN
-+
-##############################
- at HiMom:7:1:1:1379
-NAATATAATTNNNTNNNTTAGANTTNNNNN
-+
-##############################
- at HiMom:7:1:1:1391
-NNGNNTNTAANNNANNNTNATNNNTNNNNN
-+
-##############################
- at HiMom:7:1:1:140
-NNANNTNTAANNNGNNNCNTTNNNTNNNNN
-+
-##############################
- at HiMom:7:1:1:1513
-NNNNNANNTTNNNANNNANAANNNCNNNNN
-+
-##############################
- at HiMom:7:1:1:1521
-NAACAANATTNNNTNNNANTANNTANNNNN
-+
-##############################
- at HiMom:7:1:1:155
-NNGNNCNAGTNNNCNNNANTTNNNGNNNNN
-+
-##############################
- at HiMom:7:1:1:1555
-NNTNNGNAGANNNANNNCNTANNNANNNNN
-+
-##############################
- at HiMom:7:1:1:164
-NNANNANTAANNNTNNNTNATNNNTNNNNN
-+
-##############################
- at HiMom:7:1:1:1684
-NNGNNANGGTNNNGNNNTNTCNNNTNNNNN
-+
-##############################
- at HiMom:7:1:1:1696
-NNANNGNNGCNNNGNNNANACNNNTNNNNN
-+
-##############################
- at HiMom:7:1:1:170
-NNTNNCNCACNNNGNNNGNTCNNNGNNNNN
-+
-##############################
- at HiMom:7:1:1:173
-NNNNNANNATNNNTNNNCNTTNNNTNNNNN
-+
-##############################
- at HiMom:7:1:1:1733
-NNANNGNGTCNNNTNNNTNAGNNNANNNNN
-+
-##############################
- at HiMom:7:1:1:1770
-NNCNNTNCTGNNNGNNNGNCANNNANNNNN
-+
-##############################
- at HiMom:7:1:1:18
-NATCAGNCTGNNNANNNTNGTNNAANNNNN
-+
-##############################
- at HiMom:7:1:1:1815
-NATGAAAATANNNTNNNTAAATNATNNNNN
-+
-##############################
- at HiMom:7:1:1:1836
-NNNNNGNNTANNNGNNNTNCTNNNCNNNNN
-+
-##############################
- at HiMom:7:1:1:184
-NNCNNTNTAANNNANNNTNATNNNGNNNNN
-+
-##############################
- at HiMom:7:1:1:1886
-NACATATGCATACATATATAATAGATANNN
-+
-%.9:;<217;:999;<;;<<<;;#######
- at HiMom:7:1:1:1906
-NNTNNCNATANNNCNNNTNCTNNNGNNNNN
-+
-##############################
- at HiMom:7:1:1:1917
-NNNNNTNNGANNNCNNNANAANNNANNNNN
-+
-##############################
- at HiMom:7:1:1:195
-NNANNGNGTGNNNGNNNCNATNNNANNNNN
-+
-##############################
- at HiMom:7:1:1:1954
-NAGANTNCTTNNNGNNNGNAGNNNCNNNNN
-+
-##############################
- at HiMom:7:1:1:2
-NNANNGNGAANNNCNNNNNNNNNNNNNNNN
-+
-##############################
- at HiMom:7:1:1:2011
-NACAGCTGGCANNTNNNAGAGCNAGNANNN
-+
-##############################
- at HiMom:7:1:1:240
-NNGNNANGTANNNTNNNTNCCNNNCNNNNN
-+
-##############################
- at HiMom:7:1:1:262
-NNCNNGNCATNNNANNNCNTGNNNCNNNNN
-+
-##############################
- at HiMom:7:1:1:264
-NAACTGNAATNNNCNNNANCANNCTNNNNN
-+
-##############################
- at HiMom:7:1:1:299
-NNCNNTNGCANNNANNNCNAANNNTNNNNN
-+
-##############################
- at HiMom:7:1:1:30
-NNANNANTTTNNNTNNNGNTCNNNTNNNNN
-+
-##############################
- at HiMom:7:1:1:353
-NNANNTNTAGNNNANNNTNATNNNANNNNN
-+
-##############################
- at HiMom:7:1:1:367
-NNANNTNAGCNNNGNNNANGTNNNCNNNNN
-+
-##############################
- at HiMom:7:1:1:41
-NNANNCNAAANNNGNNNTNCANNNCNNNNN
-+
-##############################
- at HiMom:7:1:1:416
-NNANNCNAATNNNGNNNGNACNNNCNNNNN
-+
-##############################
- at HiMom:7:1:1:483
-NNGNNGNGGGNNNGNNNGNTTNNNTNNNNN
-+
-##############################
- at HiMom:7:1:1:486
-NNANNANTTTNNNANNNANAGNNNTNNNNN
-+
-##############################
- at HiMom:7:1:1:495
-NNCNNANCGTNNNTNNNTNAANNNCNNNNN
-+
-##############################
- at HiMom:7:1:1:508
-NNGNNCNCAGNNNTNNNCNCTNNNCNNNNN
-+
-##############################
- at HiMom:7:1:1:517
-NTCATAAAACATCANTATTGGAAAGGANNN
-+
-%.75:<999578##################
- at HiMom:7:1:1:535
-NGCCCAAGTATTGANTATGTGCTCTAANNN
-+
-%.599:7187:940%0::52599#######
- at HiMom:7:1:1:55
-NTTTATGTCCTTNANAACTTAGNAGTTNNN
-+
-%/9<<83599####################
- at HiMom:7:1:1:554
-NNANNGNAGANNNGNNNTNTCNNNANNNNN
-+
-##############################
- at HiMom:7:1:1:567
-NNCNNCNGTTNNNCNNNGNACNNNCNNNNN
-+
-##############################
- at HiMom:7:1:1:59
-NNANNGNTGCNNNTNNNTNACNNNANNNNN
-+
-##############################
- at HiMom:7:1:1:613
-NNGNNANTATNNNCNNNGNATNNNANNNNN
-+
-##############################
- at HiMom:7:1:1:622
-NNTNNCNAGTNNNCNNNANCTNNNTNNNNN
-+
-##############################
- at HiMom:7:1:1:627
-NNANNTNGACNNNTNNNANGCNNNCNNNNN
-+
-##############################
- at HiMom:7:1:1:684
-NNTNNTNAGANNNCNNNANAGNNNANNNNN
-+
-##############################
- at HiMom:7:1:1:72
-NACACACATATCACNCACATCATACACNNN
-+
-%..48696;5:6;.%)49;;;9########
- at HiMom:7:1:1:812
-NNANNCNAAGNNNTNNNANTCNNNANNNNN
-+
-##############################
- at HiMom:7:1:1:874
-NNANNANGCCNNNGNNNTNTANNNTNNNNN
-+
-##############################
- at HiMom:7:1:1:931
-NNTNNGNGATNNNGNNNCNTTNNNCNNNNN
-+
-##############################
- at HiMom:7:1:1:965
-NACTAATCTTCCGCNCATATCCCCAAANNN
-+
-##############################
- at HiMom:7:1:1:994
-NNANNTNGATNNNTNNNGNTTNNNCNNNNN
-+
-##############################
- at HiMom:7:1:2:11
-NAAATGAAAAAAGAAATGCATTGTCAGGTG
-+
-##############################
- at HiMom:7:1:2:1158
-NGGGTCCTTCATAGTTTTTTTCTACTTTCC
-+
-%0777646;099:::95;;;688::99###
- at HiMom:7:1:2:119
-NGATTGGAATCAACCCGAGTGGAATGGAAT
-+
-%06:75577786742-6-66///288517#
- at HiMom:7:1:2:1238
-NTCCTTATATTCAATTATTAATATTTTTAC
-+
-##############################
- at HiMom:7:1:2:1275
-NAGTGAAATAAGCCAGACACAGAAAGACAN
-+
-%/5204:99971773,44755-39717###
- at HiMom:7:1:2:1301
-NAGTAGACTGCATTAATTAATTGGAAGAGN
-+
-%0370)024263144:48;;##########
- at HiMom:7:1:2:1336
-NAAGTCTAAAATTATCTTGAAGTAAAAAGT
-+
-%.75795:89<<<<4-7::58579<<<8.7
- at HiMom:7:1:2:1417
-NATTCCATTCGATGATTCCATTCGAGTCCA
-+
-%-::567;93-510788014:8538122##
- at HiMom:7:1:2:1453
-NATATCTTATTTTCTTTTCTTTCAGGCTCT
-+
-%.:7,,395255##################
- at HiMom:7:1:2:1465
-NTTGTATTTCTGAAACCCCGAAGGGCATGG
-+
-##############################
- at HiMom:7:1:2:150
-NAAGACTTGATTATATCCCTTGTATGANNN
-+
-##############################
- at HiMom:7:1:2:1507
-NGGCTTGGAAAGTGTAGGAGGGAGAGTCAC
-+
-##############################
- at HiMom:7:1:2:1592
-NGAAAACTGGCACAAGACAAGGATGCCCTC
-+
-%,67786861,3466(8485868648583#
- at HiMom:7:1:2:1706
-NGATATGTGGATACAGCTCACAAAGAGNNN
-+
-%,99:6/566999/7###############
- at HiMom:7:1:2:1722
-NAAAGAAAATTAAAGAAAAATATACACGTN
-+
-##############################
- at HiMom:7:1:2:1727
-NTATTGAAGGACTTTTGTATCCTCCTTATN
-+
-##############################
- at HiMom:7:1:2:1753
-NGTTCACACAAGGATAATATTTTTGATTAT
-+
-##############################
- at HiMom:7:1:2:1782
-NACCAAGTGTTTGGAGTATGCTGCCTANNN
-+
-%0:::668885-5335/85###########
- at HiMom:7:1:2:1827
-NAACCGAGGATGTACACTGTCCCTGTGAAA
-+
-##############################
- at HiMom:7:1:2:1878
-NAATACTGAGATGTATTTAAGGCTGACACT
-+
-%.9:957/3767079:::7:5/57::9999
- at HiMom:7:1:2:1889
-NGAAATGTATCAAGGTTTGTATAATTGCTG
-+
-%-7<<:::<2:::8:4<<:07547765978
- at HiMom:7:1:2:1895
-NAAAACTTCTAAGTAATCATGAAGCTCTGC
-+
-%.7;9:::::<84:99989:<678<:6776
- at HiMom:7:1:2:190
-NATAAGTGTATATTTATTTGTACCATGACA
-+
-%-;8694777:8;;9<:<<<<99998:996
- at HiMom:7:1:2:1932
-NAGCGATCCTCCCGCCTCTGCCTCCCANNN
-+
-%,1545541455##################
- at HiMom:7:1:2:1946
-NATCTTCTGGAATTTCTAACAGCTTGGAAN
-+
-%0515.,.35<997################
- at HiMom:7:1:2:1995
-NATTTCCTGAACACAGCACAGGGAAGAGGA
-+
-%/78777738777:8877786776858225
- at HiMom:7:1:2:209
-NGACTCAACTCCTGGGCTCCCTACGACCAT
-+
-##############################
- at HiMom:7:1:2:246
-NGGAGGTTTCATTTAGCCGATATTGTGNNN
-+
-##############################
- at HiMom:7:1:2:25
-NGCTTTGGCAAGACAAATCTCCCGTCTGGN
-+
-##############################
- at HiMom:7:1:2:307
-NGGATGAACAGAAACTAAAATAACACANNN
-+
-##############################
- at HiMom:7:1:2:309
-NAATGGCCATGCTGCCCAAAGTATTTTATA
-+
-%.705699:5-227759996717:::9:9:
- at HiMom:7:1:2:358
-NTCTGTTGTTATTTCCCTGTTACTTTTGGT
-+
-##############################
- at HiMom:7:1:2:363
-NATATTCTTTTTTTTTATTTATCAGATNNN
-+
-##############################
- at HiMom:7:1:2:425
-NAATATATGCAAGACTCCTGTTATTAGAAA
-+
-%099:99055:726<<9<9977::9:::<<
- at HiMom:7:1:2:449
-NATTCTAATTCTAGGAAATTAACAATCNNN
-+
-%.9315<936970%0###############
- at HiMom:7:1:2:455
-NGCTTGAACTCAGGATTCACAATTTCAACC
-+
-##############################
- at HiMom:7:1:2:52
-NAAGTATAATGTAGAGACGCTTGTATTGTC
-+
-##############################
- at HiMom:7:1:2:546
-NGGTTGTGTCTCTCTCAGCCTTTGGGATCN
-+
-%,46888444685-35##############
- at HiMom:7:1:2:605
-NGCATTGAGCAGACGTGGCATCCAGATNNN
-+
-%)085222/55453################
- at HiMom:7:1:2:63
-NGAGTGGAATGGAATGGAGTGGAATGGCTT
-+
-%,/66818682811553536525875686#
- at HiMom:7:1:2:636
-NGATCATTTACTGTTGTCAACTACCAAAAT
-+
-%/72'+769621513-1-563202356557
- at HiMom:7:1:2:658
-NGATGCTTCTGTCCTAAGAAGCTTGAGACA
-+
-%%2632887412107753560555542255
- at HiMom:7:1:2:69
-NTCAGTCTGCTGTTTTAAAAAAATACTGTG
-+
-##############################
- at HiMom:7:1:2:737
-NAAAACAATTAAAATAAATGCTTAAAATCA
-+
-##############################
- at HiMom:7:1:2:747
-NAACAACAGCGGAAAATAATAAAAAAAAAN
-+
-##############################
- at HiMom:7:1:2:786
-NTAAACAATAATCTGATGATTTATAATCCN
-+
-%09<<<<;<;<8<9;<9<;<::<<::####
- at HiMom:7:1:2:802
-NAAGTTAATTGTGTATTATTAACATCATTC
-+
-%/627<<<<444358<<::::989957972
- at HiMom:7:1:2:85
-NGATAAAGTACAATGCTAATCACTTAAGAT
-+
-%.52353046874+'01999975;:9255;
- at HiMom:7:1:2:858
-NAAACGTTGCTGATCTTCTGTTTTAAACTA
-+
-%/;7-222265366-6977035:::;626;
- at HiMom:7:1:2:943
-NAATACCAATAAACCTAGAATGTCTCATAC
-+
-%08<9646<6378744774:1005799<4#
- at HiMom:7:1:2:950
-NGTGTGTGTTTTTAGAGATGCCTTTTAGAA
-+
-%-7463817999<999998876999;6579
- at HiMom:7:1:2:974
-NGATCAATGATCACATCTTTGGATATGTAT
-+
-%/9979<99:999::9;;:7511<<<77<<
- at HiMom:7:1:2:988
-NAAAGGAATGTTCAGCTCTGTGAGTTGAAC
-+
-%/92/04:2-2785-3875/404362-162
- at HiMom:7:1:3:1155
-NCAGCGAAAGAAGTACCAGGGTATGGGAAG
-+
-##############################
- at HiMom:7:1:3:1188
-GCGAATGCCATTATTTCATTCCTTTTCATG
-+
-=@CACA?AABCCCCCCCCAB??CBCBCCBB
- at HiMom:7:1:3:1219
-AGTTACTTATAGTGAATGGTTATTACTCCA
-+
-BA>BBBBBBA@?:?AA;;<8 at B9=97>9>A
- at HiMom:7:1:3:1222
-TGGCATCCAGCTTTGTACTCATGAAAATTG
-+
-A?=@CBA@=7A@>@9 at BBA?>B=;<=@?B@
- at HiMom:7:1:3:1233
-NAACCAATTTCTTTACATACCAAATACGCC
-+
-##############################
- at HiMom:7:1:3:1294
-TGTAACTTTACTTTAGTTGCTTATTTGTAG
-+
-BA############################
- at HiMom:7:1:3:131
-TAAAATAAAGTAAAAAGAAAGCAAGGTCCT
-+
-BBBBCCCBBA<CCCCA<<CBC>BBC=AC=C
- at HiMom:7:1:3:1311
-AGACATAAAACCAGAGAGAAGATAGTGGGT
-+
-@@@BBBBCBA;>B>ABBBBBBBBA?;9:3>
- at HiMom:7:1:3:1319
-TAAATGATTGCCTTCCACAGTATACATGTG
-+
-BAAA<::=B at 7:89)>=>B+)B at B@=####
- at HiMom:7:1:3:1328
-GCTACCAACCCCACTCCTAGATGAAAGACC
-+
-068,=@)=AA82 at C@8;;@3;8/<<#####
- at HiMom:7:1:3:1341
-TGAAGAGTTTCTGGCACATAGGCACTCAAC
-+
-B7AACB;>C7A??4AB<B>B:':@CAAAAB
- at HiMom:7:1:3:1348
-NATATTGATTCTTCCTACCCATGAGTATGG
-+
-%1;;78.+389999888;;89118;7;8##
- at HiMom:7:1:3:1358
-NTCCTTCCTCAAGGGGACCCCGCCTCCCCT
-+
-##############################
- at HiMom:7:1:3:1406
-NAAAATGCCAGATAAATTTTATGTAAAACC
-+
-%1<<97227467::77(7;;;503<9:972
- at HiMom:7:1:3:1450
-NGATTCGATTAGAATCATCGAATGGACTCG
-+
-##############################
- at HiMom:7:1:3:1488
-NATTCTGAGTAGCATGCTGGATCCCACCCC
-+
-%-445014,42/1666423###########
- at HiMom:7:1:3:1513
-CACGCCACTGCGCCTGCAGCCTGGGCAATA
-+
-B=55 at AA6@=;>;>/;@@9@<>52<?@ABA
- at HiMom:7:1:3:1525
-AGAAAATATCTGCATAGATGTGTTGAAGTC
-+
-BBBBBBAA@@?<3<:B=?B@@A at BAAA@=A
- at HiMom:7:1:3:1544
-CGTGGATGGTTTTGATGAGTCCCACTGCAC
-+
-=@=<)*@22375A9@?36(768@:'897<#
- at HiMom:7:1:3:1574
-NTTATTCCTTAGGAAATTTTAAATTCTGTA
-+
-%0955357999999:99::99102::9:3:
- at HiMom:7:1:3:162
-AATGAAGGCCACAGAGTGGTCCAAATAGCC
-+
-?@@5@@@>>A<0?;=0839:2<AAABA=##
- at HiMom:7:1:3:1677
-AGTGCAGTGGCGTGATCTTGGCTCACTGCA
-+
-A?7BBB@?9969A7B7;@;1>9:'=7;7 at B
- at HiMom:7:1:3:1688
-NCCTTCTTTACACACTGAGGAACTTAACCT
-+
-%..99999:9:7753564-357708:9777
- at HiMom:7:1:3:1717
-NAAACAGACTTGTTTCTTGTAATAATTATG
-+
-%/;;89689:999<76:8399:9:::::##
- at HiMom:7:1:3:176
-ATATTTCATGAAAGACATAAATTTACAGTT
-+
-BBBCCB at BBBABBBB?ABBBBBBBBABB at B
- at HiMom:7:1:3:1760
-ACAAGAGACCCTAACATTAGGTAGGAATAT
-+
-A:@@5A<B<48 at B@=>?A?:;:?5>AB?@@
- at HiMom:7:1:3:1764
-NTCTATGGGGTGTGTATCTGTTTCTGGACT
-+
-%09::845(4586/6666884;8851.314
- at HiMom:7:1:3:1861
-NGATTAATGAATAGAGTGAATAGTGTCTGA
-+
-%-07:::5.3<<7788529:<<530:9646
- at HiMom:7:1:3:1867
-AGAAGCATTCTCAGAAACTTATTTGTGATG
-+
-BB>81>BB?->?;07>4;B at BABB?:<@=:
- at HiMom:7:1:3:1927
-CACATCACCTTCTACTACATTTGAAATTCT
-+
-BCACA8B>C=BA?C8BC:'8=-5@)@=0=B
- at HiMom:7:1:3:1973
-NCTTTTATTGAATTAGCTTCTGTGGAAACC
-+
-%.<774<<145;105<<:6<7<:88;####
- at HiMom:7:1:3:198
-TATAATTTAATGGTTTTTATATATTCAGAG
-+
-BBC=BBCCA=@=8<BCBCBBABBCB=BB<9
- at HiMom:7:1:3:1981
-AGCCTGTCTGTAGAAAAAATACAAAAATTA
-+
- at 3;=;8/@=:8B8=BBBBB:B?BBABB?:B
- at HiMom:7:1:3:2027
-AATGTATTATGTTTCATAAGAAAACAAAAG
-+
-BA7/- at 8=@4,*1=>?:A@:>B at BBCB@8#
- at HiMom:7:1:3:2037
-CATCCTGTAACAAAGTGTTTATAGTTTTCA
-+
-:@9 at B6<?A>(>AB@<*)=<CBA:>51:7A
- at HiMom:7:1:3:273
-NAATTGACATAAATCAATATTGTTAAAATG
-+
-##############################
- at HiMom:7:1:3:277
-NGATGGGAAGGCCCCGGCCTGGGGAGGTGG
-+
-##############################
- at HiMom:7:1:3:289
-ATAGTGCTACAATAAACATGGGAGTGCAGA
-+
-BB=;>AABB at BBBBBB@ACBA>>BA;9@?A
- at HiMom:7:1:3:301
-NTACGTGTGTGGCTGGATAGTCTGGACCAT
-+
-##############################
- at HiMom:7:1:3:33
-CGGGCGCGGTGGATTCCGCCTTTAATCCTA
-+
-71@=>3?BA#####################
- at HiMom:7:1:3:347
-NGTGGTGTGAGGTGTATCTGGGTCAGCAGG
-+
-##############################
- at HiMom:7:1:3:389
-NGATGTTCAAACATGCATAACTCTAAGTAT
-+
-##############################
- at HiMom:7:1:3:405
-AAAAAACATAGAACGGGGTCAATATTTTAT
-+
-(?A>8(7B?<(:')?@)8(:(*:<8:0>'>
- at HiMom:7:1:3:471
-AGAAAAAGACAAGCAGGCCTCTCACAGAGC
-+
-@=B>CB@?8BBBA<B<@ABBAAA=<@>>3<
- at HiMom:7:1:3:579
-NGAAAAATGACCACACTTGCCTCCTGAGAA
-+
-##############################
- at HiMom:7:1:3:583
-GGCTTACACAGTCAAACTGGAGAGAAGTAG
-+
-(56=CCCC=B8BABBBC@:=BBAAA?, at A<
- at HiMom:7:1:3:608
-NTGTGCTTCAATGATGCTATCAGGTGTGTT
-+
-%.9675:747:766553::9:7119::8::
- at HiMom:7:1:3:673
-TCCTCAAAAACAAGATAAAACGGTTGAAAT
-+
->()>)''85BBC?#################
- at HiMom:7:1:3:676
-ATAAGAAAATGCCAACCCATTTACAGTTTT
-+
-?':7%68>?<(.9A7(=:68>A=2>(9@??
- at HiMom:7:1:3:683
-NAAGTTTTTATTTATACGTAGAATTTATAC
-+
-%.611<<:;<98;<<<93993789<;<;9:
- at HiMom:7:1:3:695
-TGATACTGCCTTTGCAAAAATTATAACAGT
-+
-;>ABBCC<?ACCBBBCCCCBBACBAABB<A
- at HiMom:7:1:3:699
-NTGTCTTCTTACACTATTTTTTTTAAAATC
-+
-##############################
- at HiMom:7:1:3:751
-CACTTTTATTCTTAAGTACCACCTTCTGGA
-+
-6A=CCCCBCCCAAA??@CC8@@CCBC:>)@
- at HiMom:7:1:3:795
-NGTAATGGAAGTCCTAGTACTAAAAATTAG
-+
-##############################
- at HiMom:7:1:3:880
-ATGAGTGAGAAATAGAAGTCCTAAGTAGAT
-+
-B@=;/75>)>?B@=3>@=<.2=B at 2@>49B
- at HiMom:7:1:3:890
-TGCTTCTGTTTCCGTTAGCTAGATAAAGTT
-+
-##############################
- at HiMom:7:1:3:900
-TGAATCTTTGTTCAACACAGATTATTCCAG
-+
-)>@+5*<B1':(5,23A>5)@:)(/>:=##
- at HiMom:7:1:3:905
-TGTTATGTTTAATTTTCTTTAGCACCCTTC
-+
->7>?A:-<BA at 0>@:@8=A;5%7;9?=:9@
- at HiMom:7:1:3:918
-TTTTCATTCCTAGTCATCCACCCCATCAGA
-+
-0()@A=:2>3:>(/((<22A>:0(20:@)@
- at HiMom:7:1:3:959
-NAAAGTTTCCTGTGAGAAGGCGCATGGCAT
-+
-%.52-487848866757#############
- at HiMom:7:1:3:985
-AGGTTTAATTGGTTCCAGGAGGTCACACTG
-+
-?898 at BBB?@6<;@>;B::>:-79BA at A@:
- at HiMom:7:1:3:996
-AAGGGAATTCTTGGACTTGATTAAATTGGT
-+
-=C9?6?BBB?6;6>;>A?BA?@2<@BB:##
- at HiMom:7:2:0:1073
-NNNNNANCACNNNCNNNCNCANNNCNNNNN
-+
-##############################
- at HiMom:7:2:0:1135
-NNNNNGNNGTNNNANNNTNTANNNGNNNNN
-+
-##############################
- at HiMom:7:2:0:1198
-NNNNNTNCTANNNTNNNCNCANNNANNNNN
-+
-##############################
- at HiMom:7:2:0:1278
-NNNNNNNNTANNNTNNNCNNANNNGNNNNN
-+
-##############################
- at HiMom:7:2:0:135
-NNNNNNNNANNNNNNNNNNNGNNNNNNNNN
-+
-##############################
- at HiMom:7:2:0:1547
-NNNNNNNNCNNNNNNNNNNNGNNNANNNNN
-+
-##############################
- at HiMom:7:2:0:1598
-NNNNNNNNATNNNTNNNANNGNNNCNNNNN
-+
-##############################
- at HiMom:7:2:0:1620
-NNNNNNNNCANNNNNNNANNCNNNCNNNNN
-+
-##############################
- at HiMom:7:2:0:1668
-NNNNNANATANNNANNNGNTGNNNTNNNNN
-+
-##############################
- at HiMom:7:2:0:186
-NNNNNNNNCCNNNANNNTNNTNNNTNNNNN
-+
-##############################
- at HiMom:7:2:0:205
-NNNNNNNNANNNNNNNNTNNCNNNTNNNNN
-+
-##############################
- at HiMom:7:2:0:287
-NNNNNNNNCCNNNCNNNTNNANNNANNNNN
-+
-##############################
- at HiMom:7:2:0:382
-NNNNNNNNCANNNTNNNTNNANNNANNNNN
-+
-##############################
- at HiMom:7:2:0:441
-NNNNNNNNTTNNNANNNANNTNNNTNNNNN
-+
-##############################
- at HiMom:7:2:0:50
-NNNNNNNNTNNNNNNNNTNNGNNNGNNNNN
-+
-##############################
- at HiMom:7:2:0:501
-NNNNNGNNAGNNNANNNCNCTNNNCNNNNN
-+
-##############################
- at HiMom:7:2:0:73
-NNNNNANCATNNNGNNNANACNNNGNNNNN
-+
-##############################
- at HiMom:7:2:0:740
-NNNNNNNNTTNNNANNNTNNANNNANNNNN
-+
-##############################
- at HiMom:7:2:0:766
-NNNNNNNNTGNNNANNNANNTNNNTNNNNN
-+
-##############################
- at HiMom:7:2:0:87
-NNNNNNNNGNNNNNNNNANNTNNNTNNNNN
-+
-##############################
- at HiMom:7:2:1:1004
-NATTTATCACTANANATCCGCAAACCCTCC
-+
-##############################
- at HiMom:7:2:1:1034
-NATCATTTTCATNCNTTTCACTGATACATT
-+
-%.737:887471%-%1:8555545;696::
- at HiMom:7:2:1:1159
-NNACTTNTAGNNNGNNNAAATNNCCNANNN
-+
-##############################
- at HiMom:7:2:1:1168
-NNTCTANCTTNNNTNNNATTGNNTTNTNNN
-+
-##############################
- at HiMom:7:2:1:1180
-NNATGGNCTTNNNCNNNAGAANNTCNANNN
-+
-##############################
- at HiMom:7:2:1:1214
-NAAAAAAAAAAANANTATAAGAAAGAATCA
-+
-%035:#########################
- at HiMom:7:2:1:1221
-NGGTCACACTCACATAGTGTTCAGAGCACT
-+
-##############################
- at HiMom:7:2:1:1306
-NNACATNAAANNNTNNNAACANNGTNANNN
-+
-##############################
- at HiMom:7:2:1:1351
-NNNNNCNATANNNTNNNANAANNNTNNNNN
-+
-##############################
- at HiMom:7:2:1:1424
-NNTCATNTAGNNNCNNNATGGNNGTNCNNN
-+
-##############################
- at HiMom:7:2:1:1452
-NGAAATTTGTAAAANCACCTGCAGAATACT
-+
-##############################
- at HiMom:7:2:1:1515
-NATTAAATATNANANNGTAATAATAATANN
-+
-%/9###########################
- at HiMom:7:2:1:1521
-NNACACNAAANNNGNNNATCTNNTTNCNNN
-+
-##############################
- at HiMom:7:2:1:1536
-NAGCAAAGACTTNGNACCAACCCAAATGTT
-+
-##############################
- at HiMom:7:2:1:1543
-NNTTGANATCNNNANNNAATANNTANCNNN
-+
-##############################
- at HiMom:7:2:1:1617
-NNCCATNATCNNNGNNNCCAGNNGTNTNNN
-+
-##############################
- at HiMom:7:2:1:1627
-NNTGGTNAGANNNCNNNAAAANNCANTNNN
-+
-##############################
- at HiMom:7:2:1:1646
-NTTAATTATANNNANNTAAACATTCTAANN
-+
-##############################
- at HiMom:7:2:1:1653
-NNAATTNAAANNNTNNNATCTNNAGNANNN
-+
-##############################
- at HiMom:7:2:1:1682
-NNTCTTNTTTNNNGNNNAAAANNAANTNNN
-+
-##############################
- at HiMom:7:2:1:170
-NAGAAGAAATGGGATCCTGCTGTGGCCAGT
-+
-%/888865284168866767663(6874/5
- at HiMom:7:2:1:1731
-NNTATANGAANNNTNNNTGCTNNAGNTNNN
-+
-##############################
- at HiMom:7:2:1:1755
-NNGTNANTCTNNNCNNNCNTGNNNGNANNN
-+
-##############################
- at HiMom:7:2:1:1812
-NNTTGCNCACNNNCNNNCCATNNAANGNNN
-+
-##############################
- at HiMom:7:2:1:1853
-NNATCTNTTCNNNANNNAGTGNNATNCNNN
-+
-##############################
- at HiMom:7:2:1:1919
-NNAATTNAAANNNANNNAGAANNAGNANNN
-+
-##############################
- at HiMom:7:2:1:1924
-NATATTCTGAAGNANNCCAATGAACCAAAN
-+
-%116<9579<7###################
- at HiMom:7:2:1:1933
-NAGGGTACATNTNCNNAATGTGCGGGTTNN
-+
-##############################
- at HiMom:7:2:1:1938
-NAGTCCAGTGTCTCTGCTTCCGCAGGGACA
-+
-%/818865/058858644866457646668
- at HiMom:7:2:1:1950
-NNTTNANAAANNNCNNNTNCANNNTNCNNN
-+
-##############################
- at HiMom:7:2:1:1959
-NGACACATTCCTACNACAGAGAAAAATTTA
-+
-%*77;;<;<<:<;,%.::;:6:9::<4488
- at HiMom:7:2:1:1987
-NNATNGNACANNNCNNNTNGTNNNTNNNNN
-+
-##############################
- at HiMom:7:2:1:2006
-NNGTATNTGANNNGNNNCCTTNNAGNANNN
-+
-##############################
- at HiMom:7:2:1:211
-NNCTGANACANNNGNNNTGCANNACNCNNN
-+
-##############################
- at HiMom:7:2:1:234
-NAAGCCTGTGGGNANNCCCAGTGGGAGCGN
-+
-##############################
- at HiMom:7:2:1:242
-NNGCTCNAGCNNNANNNATATNNTTNGNNN
-+
-##############################
- at HiMom:7:2:1:262
-NNATTGNAATNNNCNNNTTCCNNATNTNNN
-+
-##############################
- at HiMom:7:2:1:298
-NNTCAANTTGNNNTNNNCTGCNNTTNTNNN
-+
-##############################
- at HiMom:7:2:1:312
-NNTTGCNAGANNNANNNAACTNNTGNANNN
-+
-##############################
- at HiMom:7:2:1:363
-NGAAAGGTTTTGCAGCATGTGCAAACTCAC
-+
-%-5565678:8177656503512/377856
- at HiMom:7:2:1:37
-NTGTAAACGANNNCNNTTCCTGTTCAGCNN
-+
-##############################
- at HiMom:7:2:1:370
-NNCTGGNAGCNNNTNNNCATANNAANCNNN
-+
-##############################
- at HiMom:7:2:1:377
-NNAGAANGTGNNNTNNNAAATNNAANANNN
-+
-##############################
- at HiMom:7:2:1:414
-NNTAGANAGCNNNANNNTCAGNNACNGNNN
-+
-##############################
- at HiMom:7:2:1:421
-NNGTTANTTCNNNANNNCGTGNNATNCNNN
-+
-##############################
- at HiMom:7:2:1:428
-NATGTGAATANTNANNTAGTTGGGATTCAN
-+
-##############################
- at HiMom:7:2:1:44
-NACTACCTCANGNANNAAGCAGGTTCTAAN
-+
-##############################
- at HiMom:7:2:1:466
-NACACTCACANCNANNTGTTTGGAATGANN
-+
-##############################
- at HiMom:7:2:1:555
-NNCAATNTCTNNNGNNNTACANNCTNCNNN
-+
-##############################
- at HiMom:7:2:1:558
-NAAAATATCANTNANNAATAAATAATCANN
-+
-##############################
- at HiMom:7:2:1:56
-NNGCCANGGTNNNANNNTCACNNGGNCNNN
-+
-##############################
- at HiMom:7:2:1:569
-NNAGGCNAGTNNNGNNNGTCCNNGTNANNN
-+
-##############################
- at HiMom:7:2:1:604
-NATGATGAAACTCTNTCTCTACTAAAAATA
-+
-##############################
- at HiMom:7:2:1:628
-NAGTATGCCCNCNCNNACCACTCCTATTNN
-+
-##############################
- at HiMom:7:2:1:64
-NATTAATCTTNNNTNNGCACAATTCATTNN
-+
-##############################
- at HiMom:7:2:1:684
-NAAAAATCAAATGANCATAATTTTATAAAA
-+
-##############################
- at HiMom:7:2:1:699
-NNAATTNTTGNNNTNNNATTTNNGANTNNN
-+
-##############################
- at HiMom:7:2:1:714
-NATTAACTTANANTNNACCACAACCTAANN
-+
-%.:###########################
- at HiMom:7:2:1:722
-NNCCTCNCTGNNNCNNNCTGTNNTGNCNNN
-+
-##############################
- at HiMom:7:2:1:749
-NNAGTGNTACNNNTNNNCTTGNNCTNTNNN
-+
-##############################
- at HiMom:7:2:1:760
-NGTCTGTTTTATGTNAAATATTTTGTTTAA
-+
-##############################
- at HiMom:7:2:1:8
-NNTGCGNTGGNNNCNNNAGGCNNTTNTNNN
-+
-##############################
- at HiMom:7:2:1:833
-NNGAGCNCCTNNNANNNCTCCNNGANGNNN
-+
-##############################
- at HiMom:7:2:1:848
-NNTACTNAGTNNNGNNNTGTTNNGCNTNNN
-+
-##############################
- at HiMom:7:2:1:893
-NGAGACAGAGTCTCNCTCTGTTCCCTAGCC
-+
-##############################
- at HiMom:7:2:1:998
-NNATGTNTGCNNNANNNTATANNGGNANNN
-+
-##############################
- at HiMom:7:2:2:0
-NATTCCTTNANNNNNNNNNNNNNNNNNNNN
-+
-##############################
- at HiMom:7:2:2:101
-NGTTAATTTAGGGAAATTTGTTTGTATTTT
-+
-%,3:969;<52718;<<<768;::9;999;
- at HiMom:7:2:2:1012
-NAGAAATACCATTTGACCCACCAATCCCAT
-+
-%066:::9636963567778::88895-58
- at HiMom:7:2:2:1038
-NATGGAATCAACCTGAGTGGAATGAAATGG
-+
-##############################
- at HiMom:7:2:2:115
-NGATGTGCTACACACTTTCAAACAAACAGA
-+
-%0:500&/99;69727::995313374484
- at HiMom:7:2:2:12
-NATGCATTGTAATTTAATAGAGTGAAATGG
-+
-##############################
- at HiMom:7:2:2:1298
-NGATTCCATTCAATGAATCCATTCGATTCC
-+
-%.235+22976###################
- at HiMom:7:2:2:131
-NATATATTGACAGCAGTCATGTTGTTGAAG
-+
-%0<<<:<959874492:96999969:7784
- at HiMom:7:2:2:1365
-NATAAAGATTATCCGTGAATGGCGCCTCCA
-+
-##############################
- at HiMom:7:2:2:1402
-NGGATGGCTTCCAGTATGGGAACCTTTTCA
-+
-%.5484-/858865/78/(/62'/886555
- at HiMom:7:2:2:1559
-NACAGAAGGGAAAAGGTCACAGACTAAAGA
-+
-%//6;;;8849;:91,35::757:4:;:9:
- at HiMom:7:2:2:1567
-NAGACAGCAGTAACCTCTGCAGACTTAAAC
-+
-%,67:720544;4667:62-5667::6877
- at HiMom:7:2:2:1636
-NGTGTAAAAGTAGGGAAATACTATAGCAAG
-+
-##############################
- at HiMom:7:2:2:1662
-NACTAAAGACCTTATTCATGTAGCCAAATA
-+
-%.2556331)%079799::9:71855<88:
- at HiMom:7:2:2:1671
-NGGGAATTACATGGAAAATGATCAAAGGAA
-+
-##############################
- at HiMom:7:2:2:1723
-NGAAGCTGACATTACAGGTTTCAGACACCA
-+
-##############################
- at HiMom:7:2:2:1745
-NGGGAGCTAAGTAACTGGAACAAGTTTTTG
-+
-%-5237789999:8886689:9:9569887
- at HiMom:7:2:2:184
-NGAAACGTTTTTCGGTTGAGGAAACTTTTT
-+
-##############################
- at HiMom:7:2:2:1842
-NGGTGGATCCCCTGAGGTCAGGAGTTCAAG
-+
-##############################
- at HiMom:7:2:2:1874
-NGGCATATATCCTTTTACATACCCAACACA
-+
-%,0137:949699;9;88798789717996
- at HiMom:7:2:2:1944
-NATTAAATATATATTTTATTCTGAACATAA
-+
-%09::<<<<<;:<<<:99<<9<<;<;<:<<
- at HiMom:7:2:2:1974
-NACGCCAATACAAAAATGTTGAAGCTAGCT
-+
-##############################
- at HiMom:7:2:2:1985
-NGACTATCACTCTAGGGCCTCCACCCTTGC
-+
-%%2266466667186(66############
- at HiMom:7:2:2:220
-NAATAAACCTCTTTCTTTGATAAATTACCC
-+
-%.5:78335567:525<736:9868;8###
- at HiMom:7:2:2:255
-NGGGTCCAAATAAGAGAAGGAGAAAAACAG
-+
-%00412036893057554167465;98977
- at HiMom:7:2:2:303
-NAGATCTTGTCTTTCAATCTTTTTAAATTC
-+
-##############################
- at HiMom:7:2:2:351
-NGGGGTTGAGGTGTAAATAGAACATTTGTA
-+
-##############################
- at HiMom:7:2:2:463
-NGTGCTTGGGGGCGTCTGTGTTGATGCGTG
-+
-##############################
- at HiMom:7:2:2:488
-NTGGGAAACTAAACCCCATGAGGGCAGAGC
-+
-%/2/156666785445255551/12545/4
- at HiMom:7:2:2:599
-NAAACAAAAAAGCTGATGGCCTGGCGGGGT
-+
-%.836844751583,38-)/8638######
- at HiMom:7:2:2:61
-NTTTCGATGGTGTTTCCATTTGATTCATTC
-+
-%0;:9:;799:8:97779:<679<977;::
- at HiMom:7:2:2:611
-NGGAACCAGGCAGGGCCACACACAGGTAGC
-+
-##############################
- at HiMom:7:2:2:646
-NGAATCTAAGAAGACACAAAACTAAGGAAA
-+
-##############################
- at HiMom:7:2:2:669
-NGGCTGAAGCAGGAGGGTCACTTGAGCCAA
-+
-##############################
- at HiMom:7:2:2:679
-NCTCTGTCTCAAAAAATAAAAATAAAAATA
-+
-##############################
- at HiMom:7:2:2:775
-NGTTTATAATTGTGAGTTAAAAATCTAAAA
-+
-%,-78:8:968:45524<<636;<:<<<<<
- at HiMom:7:2:2:828
-NTCAAGTCAATTTGGGACTTGAAACAGCTC
-+
-##############################
- at HiMom:7:2:2:904
-NTTAGACACCATGAAGGTAACTTCCTACTC
-+
-%0:62667999/&.6058::5978489366
- at HiMom:7:2:2:953
-NGTTTAGTACATACTAGGTTTCACCAAATT
-+
-##############################
- at HiMom:7:2:3:1016
-TGGCTCTGTCCTAATATCTTATTCTTACAA
-+
-<3=@BBA?@<=BBCC@>6>BBBBB at B?@AC
- at HiMom:7:2:3:1025
-NAATGGAAAGGAGTCCAATGGAAGGGAATC
-+
-%/4626885-+3-3777:532570313837
- at HiMom:7:2:3:1053
-NTTTGATCATGATTCCATTCGAGACCATTC
-+
-%.;;##########################
- at HiMom:7:2:3:1094
-CATATGGTATCACCACTCAGATACATAAAG
-+
-AABB<:=1CBBCBC@?AA@)>CCBBCCB?=
- at HiMom:7:2:3:1101
-AAGATTATATGAGTATAATGGAGCTATTTG
-+
-B<38>B=>>B==30ABBA886;?;AAA@@>
- at HiMom:7:2:3:112
-NATGGAGTCTTGCTCTATTGCCCAGGCTGG
-+
-##############################
- at HiMom:7:2:3:1123
-NCCTCTTCCACAACTTCCTTCTTCTCCTTT
-+
-%.23)7475776876486:;67348867:8
- at HiMom:7:2:3:1133
-AGAAGCTTTCTATTCTGATCCCCAAGGAGT
-+
-BACBA>BB=1;?BA??5A>:@25<=.43;?
- at HiMom:7:2:3:1179
-ATTTAATAAATAAAGCAACCTGACAACTGA
-+
- at 15;'88?A at 1/3='106/9A7.*:/08##
- at HiMom:7:2:3:1209
-NTTGAGGATGTTACTACATTATTATACAAA
-+
-%/3370/010.55#################
- at HiMom:7:2:3:1290
-NTCACCTGAATCCACGTTAGCTGGGGAAGA
-+
-##############################
- at HiMom:7:2:3:1326
-AGGAGGGAATGATGAACCAGTAGGTTAAGG
-+
-B>=<28+<B5%9:/;A78>+/=A#######
- at HiMom:7:2:3:1352
-AAAGTGGCCCTTTCTGCATAATTCTTCTTG
-+
- at B@>2:@@:>B at AAA:AA>?B?>:=<1=<#
- at HiMom:7:2:3:1387
-NCGATTATGACTCTGAGAGAAAGTAGGGCA
-+
-##############################
- at HiMom:7:2:3:1389
-TATCGATCTCCTGACCTCGTGATCCACCCA
-+
-ACBCBCB?CBB at 6ABCB@)B>CBBCC at 4;5
- at HiMom:7:2:3:143
-AAAATCAATTCTGAAATGATTACATATTTT
-+
-BBBACBBACB=B?BBBBCBBCBBBBBBCBB
- at HiMom:7:2:3:1484
-CATCAACCTGTCACAAAATGACAAAACCTA
-+
-=A at 5@CB?B5@?B@@BBBB?ABCCBC at ABB
- at HiMom:7:2:3:151
-AGAGAACAGATAGGTCTGTCAGGGCTGACC
-+
-?>=99B>BA?B>)?;5AB;89;=6??<73>
- at HiMom:7:2:3:1529
-NTTATATGAATAGATAAATAAATAATCAAT
-+
-##############################
- at HiMom:7:2:3:157
-TGGGTGGTTCAAACTAAGCAGTCCAACTGC
-+
-BACC at BBABBBBCBBCBBBBBB?AAB?B?A
- at HiMom:7:2:3:1576
-NGAAACCACGTGCCCATTTTCAGTTCTGGT
-+
-%*/%.55663117868788787/765####
- at HiMom:7:2:3:1581
-NATAGGCAGGGAGCAAACCTCAATAAAAAG
-+
-##############################
- at HiMom:7:2:3:16
-AGCTGGGCATGGTGATGCGCCCCTGTAATC
-+
-A;?;<<?@9?@@@@4=3)1 at 59??9<5.<2
- at HiMom:7:2:3:1602
-AATTCATGAATACTTTTCAGTCTTTAAAAA
-+
-BCBAAABBBBB?<@BAB?AA=?BBBBBBBB
- at HiMom:7:2:3:1712
-AGTGCTGTGGCCTGGATGGATGTCAGGATT
-+
->91:?5:=5:77>305>/;=>1:<B9694;
- at HiMom:7:2:3:1733
-NTTAAATGAGTGTAAATATTCAATTATGCA
-+
-%,:6::2/5;393<<9:<;919<97#####
- at HiMom:7:2:3:1775
-NAATCCGACAATTATGTGTCTTGGAGTTGC
-+
-%.22301499988866456250*.424955
- at HiMom:7:2:3:179
-CATTATTGTTAGACTGATTTTTTATAATCT
-+
-B@)104..*0-A(@@(<A9A<(+9)-=6(B
- at HiMom:7:2:3:1807
-NGCATACTTCTTTCTTTCTTATTTTTCTTT
-+
-##############################
- at HiMom:7:2:3:1844
-NGGACTACAAGCGCACGCCACATGCTCAGC
-+
-##############################
- at HiMom:7:2:3:1898
-NTTGAATTGCTGGACTTCAATGTGTGTGGG
-+
-%08868:64680+0-5:8765255647522
- at HiMom:7:2:3:1917
-NTCCACAAAAAAAAAAAAAATTAGTTGGGT
-+
-%*6<737<4756##################
- at HiMom:7:2:3:1941
-TGTACTCGTGTAGCCTTTCACAGGCACAGC
-+
-B<.ACBBB2;9C>@5ABBBCBCBABCCC5B
- at HiMom:7:2:3:1952
-NATAGATGATAAAAACATTTGACAGTGAAA
-+
-%.8737868:::<;<;9;9979::9858;;
- at HiMom:7:2:3:1962
-ACTAAATCCAAGAGCACATCAAAATGTTAA
-+
-B5;BBB@@8 at BAB9>BBBABACB@@B;@BB
- at HiMom:7:2:3:1970
-NTAATACTCTTTGAGAAAGGACTGAGGGAA
-+
-%.:77558:68862.3;8455:0057535;
- at HiMom:7:2:3:198
-TGTCATTTTCTTTGCCTTAATTGTTCTTCT
-+
-5 at CBB7-*<=####################
- at HiMom:7:2:3:2004
-NAAGACTACCTTGCTGAAATAGGGCATTTA
-+
-%.:875459;4-743(29;;5139266###
- at HiMom:7:2:3:2013
-AGCAGAAGCCTGCTGTGGGAACACTCAGTC
-+
-B?B###########################
- at HiMom:7:2:3:2030
-CGAGATAATTTTTTAAAAAAAGTCCAAAAA
-+
-((@;()@==*7<(5A@<C>###########
- at HiMom:7:2:3:2038
-NANAGATAGATAGATAGATAGATAGATAGA
-+
-##############################
- at HiMom:7:2:3:207
-AGTTAGAAACAGAATACGGGTAATAATGTA
-+
-BBCCCA at BA@AAABC at CC@AACBCBBBCBC
- at HiMom:7:2:3:247
-TGTACATGACCAGGTAATTTGGTTATGTGA
-+
-<@596353;)>@A7=:,A0'6>########
- at HiMom:7:2:3:274
-AGTGAAGTGCTTAGCACCTGGGCCAGCAGC
-+
-:57.:@@>96=@97>@=;=>;@;@=@9=9;
- at HiMom:7:2:3:317
-AGAGAGAAATGTGGCATATGAGTATCACCT
-+
- at 4>BBB?ABCAB@>>ACBB?B<AABBCBBB
- at HiMom:7:2:3:328
-AGCTTAATATAGCATAGCAGATAAGATTTG
-+
-(:*8>=,3:))<)?A<(8>###########
- at HiMom:7:2:3:386
-NTGAATAAATAAATATCTGTATTATTCCTA
-+
-%156;99:999:5773,4-57973851.48
- at HiMom:7:2:3:399
-AGGGTATGTAAACCGAGTTTTGCGGGGGAT
-+
-A@@@>BBBBBAA>@;?B?BBAA>@:@:?AB
- at HiMom:7:2:3:4
-AGAGGCAATAAGTTTTAANNNNNNNNNNNN
-+
-A>BA at 9BAB3AA##################
- at HiMom:7:2:3:470
-TGTGGATTCCATTCGAATTCATTCGATTAT
-+
-BBCBBACC at CCCC>)@CBA>@CB?BCCCCC
- at HiMom:7:2:3:490
-NCTAATTGATGGGTAAGAGGCAAAGCATGA
-+
-##############################
- at HiMom:7:2:3:495
-NTCCGTTTTTATAACTGTAAATTTATCACT
-+
-##############################
- at HiMom:7:2:3:567
-TATCTTCACATAAAAACTACACAAAGCATT
-+
-BCB<ACBB at BCCBBCB<BB<@;?BB>=BBB
- at HiMom:7:2:3:577
-NTTCAACTCTGGGAGTTGAATGCAAACATC
-+
-##############################
- at HiMom:7:2:3:584
-AAAGTCCTGGGATTACAGGCATGAGCCACT
-+
-ABC2<@=>8;6=>?>3>-3<>B9@/=9A;<
- at HiMom:7:2:3:589
-TGAATGCAGGTGCCAGGGAGACGTGACTTC
-+
-=8ACBB??>@=?<ACB9<;?A>??;A<>?3
- at HiMom:7:2:3:640
-AGATTAAAAAAAAATGACGTGACAAATTAA
-+
-=6CBC at CABCBBCBC@>@=@ABBCCBBBCC
- at HiMom:7:2:3:663
-AAAAGCATGTTGCTCAGTAAAAGCAAATAG
-+
-##############################
- at HiMom:7:2:3:691
-ATTTTCAAATCATAAATATGGATTGCTGTG
-+
-BBBABACBBA at ABBBBBBB727AB8+;B55
- at HiMom:7:2:3:695
-NCAACTCCAAGACACATAATTGTCAGATTC
-+
-%/:::95578589969:::;6559748;82
- at HiMom:7:2:3:72
-CTAGTCTTTGACTTATATCAATTCAGTATT
-+
-BBC?ACCCCCB at CCCCCCCBCCCCCA@BCC
- at HiMom:7:2:3:728
-TGCCTCCTTGGAGAGGGCCGCAAAGCCAGG
-+
-=>=7?A?7'50>/996:;<+>AA at 7+8B67
- at HiMom:7:2:3:782
-AGCCATGGGCATATAGAATCACTGTAAACA
-+
-B at BBBB>7;BCBCBB at BBB?BB>:=BAB at B
- at HiMom:7:2:3:80
-AGGCAGGATGAAATTTTGTCTATTTATTCA
-+
- at 9:B at B@?B at ABABBBB??7AABBBBBB?A
- at HiMom:7:2:3:808
-NGAGTGTAATACAATGGTATGGATTTTAAC
-+
-##############################
- at HiMom:7:2:3:862
-NCTTTAAGAAATCATTCATTCTGCAAACAC
-+
-##############################
- at HiMom:7:2:3:875
-AGGCAGTAGTCTAATCCCGAGGATCCCAAG
-+
-:,73=@?<.=@;??@::3?8)5<=9%:?>7
- at HiMom:7:2:3:889
-NTTTTTATAACACCTCAGGCATCGTCAAAC
-+
-##############################
- at HiMom:7:2:3:898
-TAACATTCCCACAGTGCTTGCCACAGAGCC
-+
-ACCCCCC at C@@B@);>;BBCC=@BC?B@;>
- at HiMom:7:2:3:922
-ATTTCTGTCTGACTTTTCCAAATGTGCTAT
-+
-AABB@>>>@>9@>AAAA>;@BB@@53;BBB
- at HiMom:7:2:3:932
-AGAAAGACAGACAGACAAACTGACTCTCAG
-+
-@>@C at 4A=?2 at B@.>ABABBBB>=A:;>@#
- at HiMom:7:2:3:983
-TGTTTTTTATTTTAACAGATGAAGTACCAA
-+
-B=BCCCCCCCCCCCA>AACCBCC at AC@>BC
- at HiMom:7:2:3:987
-AAGAGCAATATTTTCTTTCACTATATTATT
-+
-*@<@@?A at 0)7448)?C@)@4)9:@#####
- at HiMom:7:2:3:99
-CATATCTGTGTTATTTTAGCATAAATTTGA
-+
-1 at +@31?('4(A;73>)?73))@))@C?##
- at HiMom:7:2:3:991
-TGGAAGCCAGCCAAAGATACACTCTTGGCA
-+
-BABC>6BBCBBBBCAAA at BACB<<?BABBB
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/testMultiplex.barcode_1.fastq b/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/testMultiplex.barcode_1.fastq
deleted file mode 100644
index b42cd1a..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToFastqTest/testMultiplex.barcode_1.fastq
+++ /dev/null
@@ -1,1600 +0,0 @@
- at HiMom:7:1:0:1038
-NNNNNGTN
-+
-########
- at HiMom:7:1:0:1093
-NNNNNTGN
-+
-########
- at HiMom:7:1:0:113
-NNNNNNNN
-+
-########
- at HiMom:7:1:0:1193
-NNNNNGTN
-+
-########
- at HiMom:7:1:0:1291
-NNNNNGNN
-+
-########
- at HiMom:7:1:0:1307
-NNNNNTAN
-+
-########
- at HiMom:7:1:0:1434
-NNNNNNNN
-+
-########
- at HiMom:7:1:0:1475
-NNNNNCCN
-+
-########
- at HiMom:7:1:0:1690
-NNNNNANN
-+
-########
- at HiMom:7:1:0:1703
-NNNNNNNN
-+
-########
- at HiMom:7:1:0:1940
-NNNNNCNN
-+
-########
- at HiMom:7:1:0:2001
-NNNNNGAN
-+
-########
- at HiMom:7:1:0:205
-NNNNNCGN
-+
-########
- at HiMom:7:1:0:275
-NNNNNATN
-+
-########
- at HiMom:7:1:0:324
-NNNNNGTN
-+
-########
- at HiMom:7:1:0:37
-NNNNNGNN
-+
-########
- at HiMom:7:1:0:464
-NNNNNNNN
-+
-########
- at HiMom:7:1:0:586
-NNNNNCNN
-+
-########
- at HiMom:7:1:0:841
-NNNNNNNN
-+
-########
- at HiMom:7:1:0:879
-NNNNNNNN
-+
-########
- at HiMom:7:1:1:1013
-NNNNNGAN
-+
-########
- at HiMom:7:1:1:111
-NNNNNCGN
-+
-########
- at HiMom:7:1:1:1153
-NNNNNCTN
-+
-########
- at HiMom:7:1:1:1184
-NNNNNAGN
-+
-########
- at HiMom:7:1:1:1241
-NNNNNCTN
-+
-########
- at HiMom:7:1:1:1243
-NNNNNTGN
-+
-########
- at HiMom:7:1:1:1247
-NNNNNACN
-+
-########
- at HiMom:7:1:1:1282
-NNNNNCCN
-+
-########
- at HiMom:7:1:1:132
-NNNNNTGN
-+
-########
- at HiMom:7:1:1:1320
-NNNNNCGN
-+
-########
- at HiMom:7:1:1:1372
-NNNGNTTA
-+
-########
- at HiMom:7:1:1:1379
-NNNCNGAT
-+
-########
- at HiMom:7:1:1:1391
-NNNNNAGN
-+
-########
- at HiMom:7:1:1:140
-NNNNNCAN
-+
-########
- at HiMom:7:1:1:1513
-NNNNNCTN
-+
-########
- at HiMom:7:1:1:1521
-NNNNNCCN
-+
-########
- at HiMom:7:1:1:155
-NNNNNCAN
-+
-########
- at HiMom:7:1:1:1555
-NNNNNCAN
-+
-########
- at HiMom:7:1:1:164
-NNNNNTTN
-+
-########
- at HiMom:7:1:1:1684
-NNNNNCGN
-+
-########
- at HiMom:7:1:1:1696
-NNNNNCTN
-+
-########
- at HiMom:7:1:1:170
-NNNNNACN
-+
-########
- at HiMom:7:1:1:173
-NNNNNCCN
-+
-########
- at HiMom:7:1:1:1733
-NNNNNGAN
-+
-########
- at HiMom:7:1:1:1770
-NNNNNTCN
-+
-########
- at HiMom:7:1:1:18
-NNNNNCGN
-+
-########
- at HiMom:7:1:1:1815
-NNNTNGAC
-+
-########
- at HiMom:7:1:1:1836
-NNNNNGTN
-+
-########
- at HiMom:7:1:1:184
-NNNNNGTN
-+
-########
- at HiMom:7:1:1:1886
-NNNGNGCC
-+
-########
- at HiMom:7:1:1:1906
-NNNNNCGN
-+
-########
- at HiMom:7:1:1:1917
-NNNNNACN
-+
-########
- at HiMom:7:1:1:195
-NNNNNCGN
-+
-########
- at HiMom:7:1:1:1954
-NNNNNCCN
-+
-########
- at HiMom:7:1:1:2
-NNNNNNNN
-+
-########
- at HiMom:7:1:1:2011
-NNNGNTAG
-+
-########
- at HiMom:7:1:1:240
-NNNNNGAN
-+
-########
- at HiMom:7:1:1:262
-NNNNNCAN
-+
-########
- at HiMom:7:1:1:264
-NNNNNCGA
-+
-########
- at HiMom:7:1:1:299
-NNNNNCGN
-+
-########
- at HiMom:7:1:1:30
-NNNNNACN
-+
-########
- at HiMom:7:1:1:353
-NNNNNCGN
-+
-########
- at HiMom:7:1:1:367
-NNNNNAGN
-+
-########
- at HiMom:7:1:1:41
-NNNNNGAN
-+
-########
- at HiMom:7:1:1:416
-NNNNNGAN
-+
-########
- at HiMom:7:1:1:483
-NNNNNTAN
-+
-########
- at HiMom:7:1:1:486
-NNNNNTGN
-+
-########
- at HiMom:7:1:1:495
-NNNNNGAN
-+
-########
- at HiMom:7:1:1:508
-NNNNNCTN
-+
-########
- at HiMom:7:1:1:517
-NNNCNAGA
-+
-########
- at HiMom:7:1:1:535
-NNNCNCGA
-+
-########
- at HiMom:7:1:1:55
-NNNGNTTA
-+
-########
- at HiMom:7:1:1:554
-NNNNNTAN
-+
-########
- at HiMom:7:1:1:567
-NNNNNCCN
-+
-########
- at HiMom:7:1:1:59
-NNNNNACN
-+
-########
- at HiMom:7:1:1:613
-NNNNNAGN
-+
-########
- at HiMom:7:1:1:622
-NNNNNAGN
-+
-########
- at HiMom:7:1:1:627
-NNNNNGAN
-+
-########
- at HiMom:7:1:1:684
-NNNNNGAN
-+
-########
- at HiMom:7:1:1:72
-NNNTNGAC
-+
-########
- at HiMom:7:1:1:812
-NNNNNGAN
-+
-########
- at HiMom:7:1:1:874
-NNNNNGTN
-+
-########
- at HiMom:7:1:1:931
-NNNNNCAN
-+
-########
- at HiMom:7:1:1:965
-NNNTNTAA
-+
-########
- at HiMom:7:1:1:994
-NNNNNCGN
-+
-########
- at HiMom:7:1:2:11
-GTATAAGA
-+
- at 7==@7##
- at HiMom:7:1:2:1158
-NNCTTAGC
-+
-########
- at HiMom:7:1:2:119
-CATAGCGA
-+
-?@>=;<CB
- at HiMom:7:1:2:1238
-NNCTAAGC
-+
-########
- at HiMom:7:1:2:1275
-NNNANCTG
-+
-########
- at HiMom:7:1:2:1301
-NNNTAACA
-+
-########
- at HiMom:7:1:2:1336
-CAGGAGCC
-+
-7 at 9=B=7@
- at HiMom:7:1:2:1417
-AAGGATGT
-+
-B?5??BC?
- at HiMom:7:1:2:1453
-NNACCAGG
-+
-########
- at HiMom:7:1:2:1465
-CACATCCT
-+
-<:@=BB@@
- at HiMom:7:1:2:150
-NNNANCCT
-+
-########
- at HiMom:7:1:2:1507
-AGCAATTC
-+
-?2=@9A<>
- at HiMom:7:1:2:1592
-NNNGAGCC
-+
-########
- at HiMom:7:1:2:1706
-NNNCNGAT
-+
-########
- at HiMom:7:1:2:1722
-NNNTCGAC
-+
-########
- at HiMom:7:1:2:1727
-NNNTNCTT
-+
-########
- at HiMom:7:1:2:1753
-NNTGCTTA
-+
-########
- at HiMom:7:1:2:1782
-NNNTNAGC
-+
-########
- at HiMom:7:1:2:1827
-NNCAACTG
-+
-########
- at HiMom:7:1:2:1878
-CAGGAGCC
-+
-B<81<=7;
- at HiMom:7:1:2:1889
-NAGGATGT
-+
-%.46:;;9
- at HiMom:7:1:2:1895
-CATAGCGA
-+
-?@CC@>BC
- at HiMom:7:1:2:190
-CATAGCGA
-+
-AACC==@B
- at HiMom:7:1:2:1932
-NNNCNAGA
-+
-########
- at HiMom:7:1:2:1946
-NNNTNGAC
-+
-########
- at HiMom:7:1:2:1995
-CTACCAGG
-+
-B=AA?BBA
- at HiMom:7:1:2:209
-NNCATTTC
-+
-########
- at HiMom:7:1:2:246
-NNNANTTC
-+
-########
- at HiMom:7:1:2:25
-NNNGATGA
-+
-########
- at HiMom:7:1:2:307
-NNNTNGAC
-+
-########
- at HiMom:7:1:2:309
-NTCGCTGA
-+
-########
- at HiMom:7:1:2:358
-AACTTGAC
-+
-A?;65173
- at HiMom:7:1:2:363
-NNNTNCTT
-+
-########
- at HiMom:7:1:2:425
-CAGGAGCC
-+
-AA@@=9;<
- at HiMom:7:1:2:449
-NNNGNTGT
-+
-########
- at HiMom:7:1:2:455
-GTATAACT
-+
-,@######
- at HiMom:7:1:2:52
-TGCTCGAC
-+
-:;;;:;=;
- at HiMom:7:1:2:546
-NNNANGTT
-+
-########
- at HiMom:7:1:2:605
-NNNTNGAC
-+
-########
- at HiMom:7:1:2:63
-TTCGCTGA
-+
-7@=B<C@#
- at HiMom:7:1:2:636
-CCTACCAT
-+
-63<@A?B=
- at HiMom:7:1:2:658
-AGCAATTC
-+
- at 7=@@@=;
- at HiMom:7:1:2:69
-NNGGAGCC
-+
-########
- at HiMom:7:1:2:737
-TACTTAGC
-+
-BCCCBCBB
- at HiMom:7:1:2:747
-NNNCCAGG
-+
-########
- at HiMom:7:1:2:786
-NNNGATGT
-+
-########
- at HiMom:7:1:2:802
-CAGGAGCC
-+
-=>0>?7>#
- at HiMom:7:1:2:85
-TACTTAGC
-+
-B>(>B=B2
- at HiMom:7:1:2:858
-NNACATCT
-+
-%%/57799
- at HiMom:7:1:2:943
-NNACCAGG
-+
-########
- at HiMom:7:1:2:950
-TGTCGGAT
-+
-@@=A:AAA
- at HiMom:7:1:2:974
-NNTATGTT
-+
-%%0::::<
- at HiMom:7:1:2:988
-NNTGGCGA
-+
-########
- at HiMom:7:1:3:1155
-TTGAGCCT
-+
-########
- at HiMom:7:1:3:1188
-GTATAACA
-+
-BBBCBCCB
- at HiMom:7:1:3:1219
-ACCAACTG
-+
-B?@@A??9
- at HiMom:7:1:3:1222
-AACTTGAC
-+
- at CC=@@>B
- at HiMom:7:1:3:1233
-CCAACAGG
-+
-########
- at HiMom:7:1:3:1294
-TCACAATG
-+
-*37<<@5<
- at HiMom:7:1:3:131
-GTATAACA
-+
-48CCACAC
- at HiMom:7:1:3:1311
-GCACACGA
-+
-<?BAA at AB
- at HiMom:7:1:3:1319
-ACCAACTG
-+
-??8 at A>8:
- at HiMom:7:1:3:1328
-TCGGAATG
-+
-A@@2=?83
- at HiMom:7:1:3:1341
-AGATGCTT
-+
-B#######
- at HiMom:7:1:3:1348
-TGCTCGAC
-+
-B9??@7 at 5
- at HiMom:7:1:3:1358
-CTACAAGG
-+
-62BB####
- at HiMom:7:1:3:1406
-TCTGGCGA
-+
-AA=;5@=@
- at HiMom:7:1:3:1450
-AACTTGAC
-+
-BC1'<7A#
- at HiMom:7:1:3:1488
-GTATAACA
-+
-)7<9BBBB
- at HiMom:7:1:3:1513
-CATAGCGA
-+
-5 at B=37 at B
- at HiMom:7:1:3:1525
-CATGCTTA
-+
-BBB;BBBB
- at HiMom:7:1:3:1544
-GCACACGA
-+
-((<.;;1;
- at HiMom:7:1:3:1574
-TACTTAGC
-+
- at ACBBC@A
- at HiMom:7:1:3:162
-AACTTGAC
-+
-BBBC at 5>?
- at HiMom:7:1:3:1677
-AACTTGAC
-+
-BCA>=4=B
- at HiMom:7:1:3:1688
-CCAGTTAG
-+
->@==;CA=
- at HiMom:7:1:3:1717
-TCTGGCGA
-+
-AB=11;A@
- at HiMom:7:1:3:176
-CTACCAGG
-+
-ABBB?ABB
- at HiMom:7:1:3:1760
-AACTTGAC
-+
-BABBABAA
- at HiMom:7:1:3:1764
-AAGGATGT
-+
-BB?BB@:A
- at HiMom:7:1:3:1861
-AGTTGCTT
-+
-B9@><A<C
- at HiMom:7:1:3:1867
-ATTATGTT
-+
-BBA at 79>B
- at HiMom:7:1:3:1927
-CAGGAGCC
-+
-B@<@@=@?
- at HiMom:7:1:3:1973
-GTATAACA
-+
-7;CACCBC
- at HiMom:7:1:3:198
-CTACCAGG
-+
-ABBBAA?@
- at HiMom:7:1:3:1981
-TGCTCGAC
-+
-=*@1;@BB
- at HiMom:7:1:3:2027
-AAGGATGT
-+
-B>7-<::#
- at HiMom:7:1:3:2037
-TCGGAATG
-+
-?<):=@=@
- at HiMom:7:1:3:273
-AAGGATGT
-+
-38=5+AC7
- at HiMom:7:1:3:277
-CATAGCGA
-+
-BA?;3>B=
- at HiMom:7:1:3:289
-GTATAACA
-+
->BCCCCB>
- at HiMom:7:1:3:301
-GCACACGA
-+
-########
- at HiMom:7:1:3:33
-GGTCCAGA
-+
-17=;,'@@
- at HiMom:7:1:3:347
-ATTATGTT
-+
-4A>?@)6<
- at HiMom:7:1:3:389
-GCACATCT
-+
-<:@@@56;
- at HiMom:7:1:3:405
-ACACAAGA
-+
-0(><=###
- at HiMom:7:1:3:471
-GGTCCAGA
-+
-<A=@B=?@
- at HiMom:7:1:3:579
-AATCATGT
-+
-73######
- at HiMom:7:1:3:583
-CCAGTTAG
-+
-=>93;CA>
- at HiMom:7:1:3:608
-AAGGATGT
-+
-AA5B?BB@
- at HiMom:7:1:3:673
-TGCCCAAA
-+
-(<######
- at HiMom:7:1:3:676
-GATCCAGA
-+
-:(.<((:@
- at HiMom:7:1:3:683
-CACATCCT
-+
-B at 8@B?CB
- at HiMom:7:1:3:695
-TCGGAATG
-+
-B?;BBB=?
- at HiMom:7:1:3:699
-AGTTGCTT
-+
-98?>8>##
- at HiMom:7:1:3:751
-CACATCCT
-+
-9 at CACCCC
- at HiMom:7:1:3:795
-ACCAACTG
-+
->88 at A>##
- at HiMom:7:1:3:880
-TTCGCTGA
-+
->@62;A==
- at HiMom:7:1:3:890
-GTCACCAT
-+
-########
- at HiMom:7:1:3:900
-CTCCCAGG
-+
-(((.A at 85
- at HiMom:7:1:3:905
-ACATCCTA
-+
-AA78/<:#
- at HiMom:7:1:3:918
-ACTACCTT
-+
-)?4B>###
- at HiMom:7:1:3:959
-GCACACGA
-+
-3?;AB?=<
- at HiMom:7:1:3:985
-AACTTGAC
-+
-BBBB@>@B
- at HiMom:7:1:3:996
-CCAGTTAG
-+
-A at 5=>C<#
- at HiMom:7:2:0:1073
-NNNNNCAN
-+
-########
- at HiMom:7:2:0:1135
-NNNNNAGN
-+
-########
- at HiMom:7:2:0:1198
-NNNNNCCN
-+
-########
- at HiMom:7:2:0:1278
-NNNNNTAN
-+
-########
- at HiMom:7:2:0:135
-NNNNNCGN
-+
-########
- at HiMom:7:2:0:1547
-NNNNNCAN
-+
-########
- at HiMom:7:2:0:1598
-NNNNNAGN
-+
-########
- at HiMom:7:2:0:1620
-NNNNNTGN
-+
-########
- at HiMom:7:2:0:1668
-NNNNNCTN
-+
-########
- at HiMom:7:2:0:186
-NNNNNCCN
-+
-########
- at HiMom:7:2:0:205
-NNNNNAGN
-+
-########
- at HiMom:7:2:0:287
-NNNNNGAN
-+
-########
- at HiMom:7:2:0:382
-NNNNNTAN
-+
-########
- at HiMom:7:2:0:441
-NNNNNAGN
-+
-########
- at HiMom:7:2:0:50
-NNNNNGAN
-+
-########
- at HiMom:7:2:0:501
-NNNNNTAN
-+
-########
- at HiMom:7:2:0:73
-NNNNNCGN
-+
-########
- at HiMom:7:2:0:740
-NNNNNGGN
-+
-########
- at HiMom:7:2:0:766
-NNNNNCCN
-+
-########
- at HiMom:7:2:0:87
-NNNNNCGN
-+
-########
- at HiMom:7:2:1:1004
-NNNGCCGA
-+
-########
- at HiMom:7:2:1:1034
-NNNAGCCT
-+
-########
- at HiMom:7:2:1:1159
-NNNTNGAC
-+
-########
- at HiMom:7:2:1:1168
-NNNGNTAG
-+
-########
- at HiMom:7:2:1:1180
-NNNTNAGC
-+
-########
- at HiMom:7:2:1:1214
-NNNCATGA
-+
-########
- at HiMom:7:2:1:1221
-NNGGATGT
-+
-########
- at HiMom:7:2:1:1306
-NNNANCTG
-+
-########
- at HiMom:7:2:1:1351
-NNNNNTTN
-+
-########
- at HiMom:7:2:1:1424
-NNNCNTCT
-+
-########
- at HiMom:7:2:1:1452
-NNAGATCC
-+
-########
- at HiMom:7:2:1:1515
-NNNGNATG
-+
-########
- at HiMom:7:2:1:1521
-NNNCNAGG
-+
-########
- at HiMom:7:2:1:1536
-NNACATCT
-+
-########
- at HiMom:7:2:1:1543
-NNNANTTC
-+
-########
- at HiMom:7:2:1:1617
-NNNCNAGG
-+
-########
- at HiMom:7:2:1:1627
-NNNANCTG
-+
-########
- at HiMom:7:2:1:1646
-NNNTNGAC
-+
-########
- at HiMom:7:2:1:1653
-NNNGNTGT
-+
-########
- at HiMom:7:2:1:1682
-NNNGNGCC
-+
-########
- at HiMom:7:2:1:170
-NNGAGCCT
-+
-########
- at HiMom:7:2:1:1731
-NNNTNAGC
-+
-########
- at HiMom:7:2:1:1755
-NNNNNCAN
-+
-########
- at HiMom:7:2:1:1812
-NNNCNTAT
-+
-########
- at HiMom:7:2:1:1853
-NNNCNCGA
-+
-########
- at HiMom:7:2:1:1919
-NNNANCTG
-+
-########
- at HiMom:7:2:1:1924
-NNNAACTG
-+
-########
- at HiMom:7:2:1:1933
-NNNTTAGC
-+
-########
- at HiMom:7:2:1:1938
-NNCTCGAC
-+
-########
- at HiMom:7:2:1:1950
-NNNNNGTN
-+
-########
- at HiMom:7:2:1:1959
-NNTGCTTA
-+
-########
- at HiMom:7:2:1:1987
-NNNNNTAN
-+
-########
- at HiMom:7:2:1:2006
-NNNGNGCC
-+
-########
- at HiMom:7:2:1:211
-NNNGNTGT
-+
-########
- at HiMom:7:2:1:234
-NNNGCTTA
-+
-########
- at HiMom:7:2:1:242
-NNNCNCGC
-+
-########
- at HiMom:7:2:1:262
-NNNCNAGG
-+
-########
- at HiMom:7:2:1:298
-NNNGNTAG
-+
-########
- at HiMom:7:2:1:312
-NNNANGTT
-+
-########
- at HiMom:7:2:1:363
-NNTATGTT
-+
-%%.99999
- at HiMom:7:2:1:37
-NNNGNCGA
-+
-########
- at HiMom:7:2:1:370
-NNNANCAT
-+
-########
- at HiMom:7:2:1:377
-NNNCNTCT
-+
-########
- at HiMom:7:2:1:414
-NNNGNTTA
-+
-########
- at HiMom:7:2:1:421
-NNNANCCT
-+
-########
- at HiMom:7:2:1:428
-NNNATGTT
-+
-########
- at HiMom:7:2:1:44
-NNNAGCGA
-+
-########
- at HiMom:7:2:1:466
-NNNTNACA
-+
-########
- at HiMom:7:2:1:555
-NNNCNGAT
-+
-########
- at HiMom:7:2:1:558
-NNNANCGA
-+
-########
- at HiMom:7:2:1:56
-NNNTNAGC
-+
-########
- at HiMom:7:2:1:569
-NNNANCTG
-+
-########
- at HiMom:7:2:1:604
-NNCAACTG
-+
-########
- at HiMom:7:2:1:628
-NNNTAACA
-+
-########
- at HiMom:7:2:1:64
-NNNANGTT
-+
-########
- at HiMom:7:2:1:684
-NNAAACGA
-+
-########
- at HiMom:7:2:1:699
-NNNCNCGA
-+
-########
- at HiMom:7:2:1:714
-NNNAGCGA
-+
-########
- at HiMom:7:2:1:722
-NNNCNAGG
-+
-########
- at HiMom:7:2:1:749
-NNNTNGAC
-+
-########
- at HiMom:7:2:1:760
-NNACAACA
-+
-########
- at HiMom:7:2:1:8
-NNNANNNN
-+
-########
- at HiMom:7:2:1:833
-NNNANCCT
-+
-########
- at HiMom:7:2:1:848
-NNNANCGA
-+
-########
- at HiMom:7:2:1:893
-NNCAATTC
-+
-########
- at HiMom:7:2:1:998
-NNNANGTT
-+
-########
- at HiMom:7:2:2:0
-NNNNNNNN
-+
-########
- at HiMom:7:2:2:101
-TACTTAGC
-+
-BB=CCCC?
- at HiMom:7:2:2:1012
-CACATCCT
-+
-BB?BABBB
- at HiMom:7:2:2:1038
-GGTCCAGA
-+
-=7=??B@@
- at HiMom:7:2:2:115
-TGCTCGAC
-+
-BA=>=@@=
- at HiMom:7:2:2:12
-TACTTAGC
-+
-A8%9<=##
- at HiMom:7:2:2:1298
-ACCAACTG
-+
-A7><<%;<
- at HiMom:7:2:2:131
-CACAATCC
-+
-AACCBCA@
- at HiMom:7:2:2:1365
-AACTTGAC
-+
-BCAB>>AB
- at HiMom:7:2:2:1402
-CACATCCT
-+
-=@@BABCB
- at HiMom:7:2:2:1559
-TTGAGCCT
-+
-A at 5@@4BC
- at HiMom:7:2:2:1567
-GCACATCT
-+
- at B=;@B?@
- at HiMom:7:2:2:1636
-ATCAACCC
-+
-368?####
- at HiMom:7:2:2:1662
-GTATAACA
-+
-82BA at AAB
- at HiMom:7:2:2:1671
-CCAGTTAG
-+
-@>>B;BA9
- at HiMom:7:2:2:1723
-CCAATTAG
-+
- at A######
- at HiMom:7:2:2:1745
-ACCAACTG
-+
-BA>BBABB
- at HiMom:7:2:2:184
-GCACACGA
-+
->;<@A@@3
- at HiMom:7:2:2:1842
-AAGGATGT
-+
-@:1;39B>
- at HiMom:7:2:2:1874
-ACCAACTG
-+
-B>>>?8@=
- at HiMom:7:2:2:1944
-AAGGATGT
-+
-BB9BBA:#
- at HiMom:7:2:2:1974
-AGCAATCT
-+
->#######
- at HiMom:7:2:2:1985
-AAGGATGT
-+
-BC?7>2<8
- at HiMom:7:2:2:220
-TCGGAATG
-+
-BA==@@?;
- at HiMom:7:2:2:255
-CCAGTTAG
-+
-A<?CAA@;
- at HiMom:7:2:2:303
-CAGGAGCC
-+
-A>*@@9##
- at HiMom:7:2:2:351
-TGATAGAA
-+
-########
- at HiMom:7:2:2:463
-CNTAGCGA
-+
-:%98.(>9
- at HiMom:7:2:2:488
-TTGAGCCT
-+
-@>=@@;@A
- at HiMom:7:2:2:599
-AGCAATTC
-+
-:-8BABB?
- at HiMom:7:2:2:61
-GTATAACA
-+
-<ABCBB9B
- at HiMom:7:2:2:611
-CATAGCGA
-+
-8 at CCB=;@
- at HiMom:7:2:2:646
-ATCAATTA
-+
-((>4/406
- at HiMom:7:2:2:669
-TTCGCTGA
-+
-B>BB at BB9
- at HiMom:7:2:2:679
-CATGCTTA
-+
-5?@??8<@
- at HiMom:7:2:2:775
-TTCGCTGA
-+
-BCC6ABBC
- at HiMom:7:2:2:828
-TATATCGA
-+
-########
- at HiMom:7:2:2:904
-ACCAACTG
-+
-A?ABB?;7
- at HiMom:7:2:2:953
-CAGGAACC
-+
-5(:9;';;
- at HiMom:7:2:3:1016
-CATAGCGA
-+
->@C@@1 at C
- at HiMom:7:2:3:1025
-GCACACGA
-+
-@=ABA@@@
- at HiMom:7:2:3:1053
-GCACATCT
-+
-6<?B?C at 4
- at HiMom:7:2:3:1094
-CACATCCT
-+
-ABCBC>:B
- at HiMom:7:2:3:1101
-TTGAGCCT
-+
-7 at 57<*5=
- at HiMom:7:2:3:112
-CCAGTTAG
-+
-B@<CAC at 6
- at HiMom:7:2:3:1123
-TTGAGCCT
-+
-B at 67(.AA
- at HiMom:7:2:3:1133
-AGCAATTC
-+
-??9 at 5AB;
- at HiMom:7:2:3:1179
-CCAGTTAG
-+
-);;9@@;#
- at HiMom:7:2:3:1209
-AACTTGAC
-+
-3?@?92;B
- at HiMom:7:2:3:1290
-GCACACGA
-+
-)5;=@<(;
- at HiMom:7:2:3:1326
-AACTTGAC
-+
-BCBBB3BB
- at HiMom:7:2:3:1352
-GGTCCAGA
-+
-0)<0;@@@
- at HiMom:7:2:3:1387
-CCAGTTAG
-+
-;+B,232A
- at HiMom:7:2:3:1389
-TGTCGGAT
-+
-?2ACA at B<
- at HiMom:7:2:3:143
-TGTCGGAT
-+
-A>AB??=B
- at HiMom:7:2:3:1484
-CCAGTTAG
-+
->BAAAC@<
- at HiMom:7:2:3:151
-CAGGAGCC
-+
- at A8/;A==
- at HiMom:7:2:3:1529
-TAGAACCT
-+
-9)@73?B=
- at HiMom:7:2:3:157
-AGCAATTC
-+
-BBB??CBA
- at HiMom:7:2:3:1576
-CCAGTTAG
-+
-:B?=CACA
- at HiMom:7:2:3:1581
-GTATAACA
-+
-:4<BAAAC
- at HiMom:7:2:3:16
-CACATCCT
-+
-<<4@@='@
- at HiMom:7:2:3:1602
-AGCAATTC
-+
-?6<A at B>8
- at HiMom:7:2:3:1712
-CACATCCT
-+
-BB>@@?=>
- at HiMom:7:2:3:1733
-GGTCCAGA
-+
-/>BBBAA=
- at HiMom:7:2:3:1775
-CATGCTTA
-+
-;<39<;@@
- at HiMom:7:2:3:179
-GTTTATTA
-+
-########
- at HiMom:7:2:3:1807
-AACTTGAC
-+
-B?4=B@><
- at HiMom:7:2:3:1844
-TACTTAGC
-+
-B?BC>:@@
- at HiMom:7:2:3:1898
-CATAGCGA
-+
-BBCB@=B@
- at HiMom:7:2:3:1917
-GCACACGA
-+
-/5;@=;B9
- at HiMom:7:2:3:1941
-AACTTGAC
-+
-BCBBBBBB
- at HiMom:7:2:3:1952
-AAGGATGT
-+
-BB?BB at B<
- at HiMom:7:2:3:1962
-AGTTGCTT
-+
-A76 at 8=0=
- at HiMom:7:2:3:1970
-CTACCAGG
-+
-BABBBAB@
- at HiMom:7:2:3:198
-CAGGATCT
-+
-5)0*@782
- at HiMom:7:2:3:2004
-TCTGGCGA
-+
-@?>/>BBB
- at HiMom:7:2:3:2013
-CATAGCGA
-+
-7BCB<@?<
- at HiMom:7:2:3:2030
-GATCAAGA
-+
-(((>(<@<
- at HiMom:7:2:3:2038
-AACTTGAC
-+
-BA@;(1>B
- at HiMom:7:2:3:207
-ACCAACTG
-+
-BA;6@??@
- at HiMom:7:2:3:247
-CGGTAGCT
-+
-########
- at HiMom:7:2:3:274
-AGTTGCTT
-+
-@@??<?BC
- at HiMom:7:2:3:317
-TGCTCGAC
-+
-BAABBA<=
- at HiMom:7:2:3:328
-CAAATCCT
-+
-3<)):<(<
- at HiMom:7:2:3:386
-GGTCCAGA
-+
-9@@99@@9
- at HiMom:7:2:3:399
-CATAGCGA
-+
-=BB@==A@
- at HiMom:7:2:3:4
-NNNNNNNN
-+
-########
- at HiMom:7:2:3:470
-AAGGATGT
-+
-B at 6::=B:
- at HiMom:7:2:3:490
-AAGGATGT
-+
-?#######
- at HiMom:7:2:3:495
-GCACACGA
-+
-5;5<A@=;
- at HiMom:7:2:3:567
-TCGGAATG
-+
-@?@?AB@<
- at HiMom:7:2:3:577
-ACCAACTG
-+
-B?:4<A??
- at HiMom:7:2:3:584
-CATGCTTA
-+
->A??<CCC
- at HiMom:7:2:3:589
-AAGGATGT
-+
-?BB9BB at 9
- at HiMom:7:2:3:640
-AGTTGCTT
-+
-A=BBB;<A
- at HiMom:7:2:3:663
-TCGGAATG
-+
-=<23<C=8
- at HiMom:7:2:3:691
-AGTTGCTT
-+
-@=8@>@?A
- at HiMom:7:2:3:695
-TCTGGCGA
-+
-AA?>9=@A
- at HiMom:7:2:3:72
-AGTTGCTT
-+
-BCBCA>BB
- at HiMom:7:2:3:728
-TACTTAGC
-+
-BBCA>B7#
- at HiMom:7:2:3:782
-TTGAGCCT
-+
-BAAA<;B?
- at HiMom:7:2:3:80
-TACTTAGC
-+
-B at 9ABA@8
- at HiMom:7:2:3:808
-AGCAATTC
-+
->25:9?##
- at HiMom:7:2:3:862
-TAACAAGA
-+
-4)=69)=@
- at HiMom:7:2:3:875
-CCTACCAT
-+
-;=@@@8 at B
- at HiMom:7:2:3:889
-ATTATGTT
-+
-0A6=A<+A
- at HiMom:7:2:3:898
-TGTCGGAT
-+
->8>A@=<@
- at HiMom:7:2:3:922
-TCGGAATG
-+
-BA<ABC?;
- at HiMom:7:2:3:932
-CATGCTTA
-+
-=C at AACCB
- at HiMom:7:2:3:983
-CATAGCGA
-+
-ACCC@?A?
- at HiMom:7:2:3:987
-TCTCGCGA
-+
-0<(.(;1@
- at HiMom:7:2:3:99
-CAGGAGCG
-+
-(1;A;###
- at HiMom:7:2:3:991
-AGCAATTC
-+
-BBAB at BB<
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC.sam
deleted file mode 100644
index 908618e..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC.sam
+++ /dev/null
@@ -1,15 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.AACTTGAC LB:LN_AACTTGAC PI:10001 DS:DESC1 SM:SA_AACTTGAC CN:BI
-HiMom:7:1:2:358 516 * 0 0 * * 0 0 .TCTGTTGTTATTTCCCTGTTACTTTTGGT ############################## RG:Z:HiMom.7
-HiMom:7:1:3:1222 4 * 0 0 * * 0 0 TGGCATCCAGCTTTGTACTCATGAAAATTG A?=@CBA@=7A@>@9 at BBA?>B=;<=@?B@ RG:Z:HiMom.7
-HiMom:7:1:3:1450 516 * 0 0 * * 0 0 .GATTCGATTAGAATCATCGAATGGACTCG ############################## RG:Z:HiMom.7
-HiMom:7:1:3:162 4 * 0 0 * * 0 0 AATGAAGGCCACAGAGTGGTCCAAATAGCC ?@@5@@@>>A<0?;=0839:2<AAABA=## RG:Z:HiMom.7
-HiMom:7:1:3:1677 4 * 0 0 * * 0 0 AGTGCAGTGGCGTGATCTTGGCTCACTGCA A?7BBB@?9969A7B7;@;1>9:'=7;7 at B RG:Z:HiMom.7
-HiMom:7:1:3:1760 4 * 0 0 * * 0 0 ACAAGAGACCCTAACATTAGGTAGGAATAT A:@@5A<B<48 at B@=>?A?:;:?5>AB?@@ RG:Z:HiMom.7
-HiMom:7:1:3:985 4 * 0 0 * * 0 0 AGGTTTAATTGGTTCCAGGAGGTCACACTG ?898 at BBB?@6<;@>;B::>:-79BA at A@: RG:Z:HiMom.7
-HiMom:7:2:2:1365 516 * 0 0 * * 0 0 .ATAAAGATTATCCGTGAATGGCGCCTCCA ############################## RG:Z:HiMom.7
-HiMom:7:2:3:1209 4 * 0 0 * * 0 0 .TTGAGGATGTTACTACATTATTATACAAA %/3370/010.55################# RG:Z:HiMom.7
-HiMom:7:2:3:1326 516 * 0 0 * * 0 0 AGGAGGGAATGATGAACCAGTAGGTTAAGG B>=<28+<B5%9:/;A78>+/=A####### RG:Z:HiMom.7
-HiMom:7:2:3:1807 516 * 0 0 * * 0 0 .GCATACTTCTTTCTTTCTTATTTTTCTTT ############################## RG:Z:HiMom.7
-HiMom:7:2:3:1941 4 * 0 0 * * 0 0 TGTACTCGTGTAGCCTTTCACAGGCACAGC B<.ACBBB2;9C>@5ABBBCBCBABCCC5B RG:Z:HiMom.7
-HiMom:7:2:3:2038 516 * 0 0 * * 0 0 .A.AGATAGATAGATAGATAGATAGATAGA ############################## RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGACTTGAGCCT.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGACTTGAGCCT.sam
deleted file mode 100644
index d9499b3..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGACTTGAGCCT.sam
+++ /dev/null
@@ -1,15 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.AACTTGAC-TTGAGCCT LB:LN_AACTTGACTTGAGCCT PI:10001 DS:DESC01 SM:SA_AACTTGACTTGAGCCT CN:BI
-HiMom:9:1:2:358 516 * 0 0 * * 0 0 .TCTGTTGTTATTTCCCTGTTACTTTTGGT ############################## RG:Z:HiMom.9
-HiMom:9:1:3:1222 4 * 0 0 * * 0 0 TGGCATCCAGCTTTGTACTCATGAAAATTG A?=@CBA@=7A@>@9 at BBA?>B=;<=@?B@ RG:Z:HiMom.9
-HiMom:9:1:3:1450 516 * 0 0 * * 0 0 .GATTCGATTAGAATCATCGAATGGACTCG ############################## RG:Z:HiMom.9
-HiMom:9:1:3:162 4 * 0 0 * * 0 0 AATGAAGGCCACAGAGTGGTCCAAATAGCC ?@@5@@@>>A<0?;=0839:2<AAABA=## RG:Z:HiMom.9
-HiMom:9:1:3:1677 4 * 0 0 * * 0 0 AGTGCAGTGGCGTGATCTTGGCTCACTGCA A?7BBB@?9969A7B7;@;1>9:'=7;7 at B RG:Z:HiMom.9
-HiMom:9:1:3:1760 4 * 0 0 * * 0 0 ACAAGAGACCCTAACATTAGGTAGGAATAT A:@@5A<B<48 at B@=>?A?:;:?5>AB?@@ RG:Z:HiMom.9
-HiMom:9:1:3:985 4 * 0 0 * * 0 0 AGGTTTAATTGGTTCCAGGAGGTCACACTG ?898 at BBB?@6<;@>;B::>:-79BA at A@: RG:Z:HiMom.9
-HiMom:9:2:2:1365 516 * 0 0 * * 0 0 .ATAAAGATTATCCGTGAATGGCGCCTCCA ############################## RG:Z:HiMom.9
-HiMom:9:2:3:1209 4 * 0 0 * * 0 0 .TTGAGGATGTTACTACATTATTATACAAA %/3370/010.55################# RG:Z:HiMom.9
-HiMom:9:2:3:1326 516 * 0 0 * * 0 0 AGGAGGGAATGATGAACCAGTAGGTTAAGG B>=<28+<B5%9:/;A78>+/=A####### RG:Z:HiMom.9
-HiMom:9:2:3:1807 516 * 0 0 * * 0 0 .GCATACTTCTTTCTTTCTTATTTTTCTTT ############################## RG:Z:HiMom.9
-HiMom:9:2:3:1941 4 * 0 0 * * 0 0 TGTACTCGTGTAGCCTTTCACAGGCACAGC B<.ACBBB2;9C>@5ABBBCBCBABCCC5B RG:Z:HiMom.9
-HiMom:9:2:3:2038 516 * 0 0 * * 0 0 .A.AGATAGATAGATAGATAGATAGATAGA ############################## RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AAGGATGT.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AAGGATGT.sam
deleted file mode 100644
index 1efa900..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AAGGATGT.sam
+++ /dev/null
@@ -1,15 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.AAGGATGT LB:LN_AAGGATGT PI:10002 DS:DESC2 SM:SA_AAGGATGT CN:BI
-HiMom:7:1:2:1417 4 * 0 0 * * 0 0 .ATTCCATTCGATGATTCCATTCGAGTCCA %-::567;93-510788014:8538122## RG:Z:HiMom.7
-HiMom:7:1:2:1889 4 * 0 0 * * 0 0 .GAAATGTATCAAGGTTTGTATAATTGCTG %-7<<:::<2:::8:4<<:07547765978 RG:Z:HiMom.7
-HiMom:7:1:3:1764 516 * 0 0 * * 0 0 .TCTATGGGGTGTGTATCTGTTTCTGGACT %09::845(4586/6666884;8851.314 RG:Z:HiMom.7
-HiMom:7:1:3:2027 4 * 0 0 * * 0 0 AATGTATTATGTTTCATAAGAAAACAAAAG BA7/- at 8=@4,*1=>?:A@:>B at BBCB@8# RG:Z:HiMom.7
-HiMom:7:1:3:273 516 * 0 0 * * 0 0 .AATTGACATAAATCAATATTGTTAAAATG ############################## RG:Z:HiMom.7
-HiMom:7:1:3:608 4 * 0 0 * * 0 0 .TGTGCTTCAATGATGCTATCAGGTGTGTT %.9675:747:766553::9:7119::8:: RG:Z:HiMom.7
-HiMom:7:2:2:1842 516 * 0 0 * * 0 0 .GGTGGATCCCCTGAGGTCAGGAGTTCAAG ############################## RG:Z:HiMom.7
-HiMom:7:2:2:1944 4 * 0 0 * * 0 0 .ATTAAATATATATTTTATTCTGAACATAA %09::<<<<<;:<<<:99<<9<<;<;<:<< RG:Z:HiMom.7
-HiMom:7:2:2:1985 516 * 0 0 * * 0 0 .GACTATCACTCTAGGGCCTCCACCCTTGC %%2266466667186(66############ RG:Z:HiMom.7
-HiMom:7:2:3:1952 4 * 0 0 * * 0 0 .ATAGATGATAAAAACATTTGACAGTGAAA %.8737868:::<;<;9;9979::9858;; RG:Z:HiMom.7
-HiMom:7:2:3:470 4 * 0 0 * * 0 0 TGTGGATTCCATTCGAATTCATTCGATTAT BBCBBACC at CCCC>)@CBA>@CB?BCCCCC RG:Z:HiMom.7
-HiMom:7:2:3:490 516 * 0 0 * * 0 0 .CTAATTGATGGGTAAGAGGCAAAGCATGA ############################## RG:Z:HiMom.7
-HiMom:7:2:3:589 4 * 0 0 * * 0 0 TGAATGCAGGTGCCAGGGAGACGTGACTTC =8ACBB??>@=?<ACB9<;?A>??;A<>?3 RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AAGGATGTTTCGCTGA.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AAGGATGTTTCGCTGA.sam
deleted file mode 100644
index b981cae..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AAGGATGTTTCGCTGA.sam
+++ /dev/null
@@ -1,15 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.AAGGATGT-TTCGCTGA LB:LN_AAGGATGTTTCGCTGA PI:10002 DS:DESC02 SM:SA_AAGGATGTTTCGCTGA CN:BI
-HiMom:9:1:2:1417 4 * 0 0 * * 0 0 .ATTCCATTCGATGATTCCATTCGAGTCCA %-::567;93-510788014:8538122## RG:Z:HiMom.9
-HiMom:9:1:2:1889 4 * 0 0 * * 0 0 .GAAATGTATCAAGGTTTGTATAATTGCTG %-7<<:::<2:::8:4<<:07547765978 RG:Z:HiMom.9
-HiMom:9:1:3:1764 516 * 0 0 * * 0 0 .TCTATGGGGTGTGTATCTGTTTCTGGACT %09::845(4586/6666884;8851.314 RG:Z:HiMom.9
-HiMom:9:1:3:2027 4 * 0 0 * * 0 0 AATGTATTATGTTTCATAAGAAAACAAAAG BA7/- at 8=@4,*1=>?:A@:>B at BBCB@8# RG:Z:HiMom.9
-HiMom:9:1:3:273 516 * 0 0 * * 0 0 .AATTGACATAAATCAATATTGTTAAAATG ############################## RG:Z:HiMom.9
-HiMom:9:1:3:608 4 * 0 0 * * 0 0 .TGTGCTTCAATGATGCTATCAGGTGTGTT %.9675:747:766553::9:7119::8:: RG:Z:HiMom.9
-HiMom:9:2:2:1842 516 * 0 0 * * 0 0 .GGTGGATCCCCTGAGGTCAGGAGTTCAAG ############################## RG:Z:HiMom.9
-HiMom:9:2:2:1944 4 * 0 0 * * 0 0 .ATTAAATATATATTTTATTCTGAACATAA %09::<<<<<;:<<<:99<<9<<;<;<:<< RG:Z:HiMom.9
-HiMom:9:2:2:1985 516 * 0 0 * * 0 0 .GACTATCACTCTAGGGCCTCCACCCTTGC %%2266466667186(66############ RG:Z:HiMom.9
-HiMom:9:2:3:1952 4 * 0 0 * * 0 0 .ATAGATGATAAAAACATTTGACAGTGAAA %.8737868:::<;<;9;9979::9858;; RG:Z:HiMom.9
-HiMom:9:2:3:470 4 * 0 0 * * 0 0 TGTGGATTCCATTCGAATTCATTCGATTAT BBCBBACC at CCCC>)@CBA>@CB?BCCCCC RG:Z:HiMom.9
-HiMom:9:2:3:490 516 * 0 0 * * 0 0 .CTAATTGATGGGTAAGAGGCAAAGCATGA ############################## RG:Z:HiMom.9
-HiMom:9:2:3:589 4 * 0 0 * * 0 0 TGAATGCAGGTGCCAGGGAGACGTGACTTC =8ACBB??>@=?<ACB9<;?A>??;A<>?3 RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ACCAACTG.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ACCAACTG.sam
deleted file mode 100644
index 5aa632c..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ACCAACTG.sam
+++ /dev/null
@@ -1,11 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.ACCAACTG LB:LN_ACCAACTG PI:10003 SM:SA_ACCAACTG CN:BI
-HiMom:7:1:3:1219 4 * 0 0 * * 0 0 AGTTACTTATAGTGAATGGTTATTACTCCA BA>BBBBBBA@?:?AA;;<8 at B9=97>9>A RG:Z:HiMom.7
-HiMom:7:1:3:1319 516 * 0 0 * * 0 0 TAAATGATTGCCTTCCACAGTATACATGTG BAAA<::=B at 7:89)>=>B+)B at B@=#### RG:Z:HiMom.7
-HiMom:7:1:3:795 516 * 0 0 * * 0 0 .GTAATGGAAGTCCTAGTACTAAAAATTAG ############################## RG:Z:HiMom.7
-HiMom:7:2:2:1298 516 * 0 0 * * 0 0 .GATTCCATTCAATGAATCCATTCGATTCC %.235+22976################### RG:Z:HiMom.7
-HiMom:7:2:2:1745 4 * 0 0 * * 0 0 .GGGAGCTAAGTAACTGGAACAAGTTTTTG %-5237789999:8886689:9:9569887 RG:Z:HiMom.7
-HiMom:7:2:2:1874 4 * 0 0 * * 0 0 .GGCATATATCCTTTTACATACCCAACACA %,0137:949699;9;88798789717996 RG:Z:HiMom.7
-HiMom:7:2:2:904 516 * 0 0 * * 0 0 .TTAGACACCATGAAGGTAACTTCCTACTC %0:62667999/&.6058::5978489366 RG:Z:HiMom.7
-HiMom:7:2:3:207 4 * 0 0 * * 0 0 AGTTAGAAACAGAATACGGGTAATAATGTA BBCCCA at BA@AAABC at CC@AACBCBBBCBC RG:Z:HiMom.7
-HiMom:7:2:3:577 516 * 0 0 * * 0 0 .TTCAACTCTGGGAGTTGAATGCAAACATC ############################## RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ACCAACTGTGTCGGAT.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ACCAACTGTGTCGGAT.sam
deleted file mode 100644
index 1683816..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ACCAACTGTGTCGGAT.sam
+++ /dev/null
@@ -1,11 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.ACCAACTG-TGTCGGAT LB:LN_ACCAACTGTGTCGGAT PI:10003 DS:DESC03 SM:SA_ACCAACTGTGTCGGAT CN:BI
-HiMom:9:1:3:1219 4 * 0 0 * * 0 0 AGTTACTTATAGTGAATGGTTATTACTCCA BA>BBBBBBA@?:?AA;;<8 at B9=97>9>A RG:Z:HiMom.9
-HiMom:9:1:3:1319 516 * 0 0 * * 0 0 TAAATGATTGCCTTCCACAGTATACATGTG BAAA<::=B at 7:89)>=>B+)B at B@=#### RG:Z:HiMom.9
-HiMom:9:1:3:795 516 * 0 0 * * 0 0 .GTAATGGAAGTCCTAGTACTAAAAATTAG ############################## RG:Z:HiMom.9
-HiMom:9:2:2:1298 516 * 0 0 * * 0 0 .GATTCCATTCAATGAATCCATTCGATTCC %.235+22976################### RG:Z:HiMom.9
-HiMom:9:2:2:1745 4 * 0 0 * * 0 0 .GGGAGCTAAGTAACTGGAACAAGTTTTTG %-5237789999:8886689:9:9569887 RG:Z:HiMom.9
-HiMom:9:2:2:1874 4 * 0 0 * * 0 0 .GGCATATATCCTTTTACATACCCAACACA %,0137:949699;9;88798789717996 RG:Z:HiMom.9
-HiMom:9:2:2:904 516 * 0 0 * * 0 0 .TTAGACACCATGAAGGTAACTTCCTACTC %0:62667999/&.6058::5978489366 RG:Z:HiMom.9
-HiMom:9:2:3:207 4 * 0 0 * * 0 0 AGTTAGAAACAGAATACGGGTAATAATGTA BBCCCA at BA@AAABC at CC@AACBCBBBCBC RG:Z:HiMom.9
-HiMom:9:2:3:577 516 * 0 0 * * 0 0 .TTCAACTCTGGGAGTTGAATGCAAACATC ############################## RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGCAATTC.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGCAATTC.sam
deleted file mode 100644
index c63d293..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGCAATTC.sam
+++ /dev/null
@@ -1,10 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.AGCAATTC LB:LN_AGCAATTC PI:10004 DS:DESC4 SM:SA_AGCAATTC CN:BI
-HiMom:7:1:2:1507 4 * 0 0 * * 0 0 .GGCTTGGAAAGTGTAGGAGGGAGAGTCAC ############################## RG:Z:HiMom.7
-HiMom:7:1:2:658 4 * 0 0 * * 0 0 .GATGCTTCTGTCCTAAGAAGCTTGAGACA %%2632887412107753560555542255 RG:Z:HiMom.7
-HiMom:7:2:2:599 516 * 0 0 * * 0 0 .AAACAAAAAAGCTGATGGCCTGGCGGGGT %.836844751583,38-)/8638###### RG:Z:HiMom.7
-HiMom:7:2:3:1133 4 * 0 0 * * 0 0 AGAAGCTTTCTATTCTGATCCCCAAGGAGT BACBA>BB=1;?BA??5A>:@25<=.43;? RG:Z:HiMom.7
-HiMom:7:2:3:157 4 * 0 0 * * 0 0 TGGGTGGTTCAAACTAAGCAGTCCAACTGC BACC at BBABBBBCBBCBBBBBB?AAB?B?A RG:Z:HiMom.7
-HiMom:7:2:3:1602 4 * 0 0 * * 0 0 AATTCATGAATACTTTTCAGTCTTTAAAAA BCBAAABBBBB?<@BAB?AA=?BBBBBBBB RG:Z:HiMom.7
-HiMom:7:2:3:808 516 * 0 0 * * 0 0 .GAGTGTAATACAATGGTATGGATTTTAAC ############################## RG:Z:HiMom.7
-HiMom:7:2:3:991 4 * 0 0 * * 0 0 TGGAAGCCAGCCAAAGATACACTCTTGGCA BABC>6BBCBBBBCAAA at BACB<<?BABBB RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGCAATTCTGCTCGAC.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGCAATTCTGCTCGAC.sam
deleted file mode 100644
index b990376..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGCAATTCTGCTCGAC.sam
+++ /dev/null
@@ -1,10 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.AGCAATTC-TGCTCGAC LB:LN_AGCAATTCTGCTCGAC PI:10004 DS:DESC04 SM:SA_AGCAATTCTGCTCGAC CN:BI
-HiMom:9:1:2:1507 4 * 0 0 * * 0 0 .GGCTTGGAAAGTGTAGGAGGGAGAGTCAC ############################## RG:Z:HiMom.9
-HiMom:9:1:2:658 4 * 0 0 * * 0 0 .GATGCTTCTGTCCTAAGAAGCTTGAGACA %%2632887412107753560555542255 RG:Z:HiMom.9
-HiMom:9:2:2:599 516 * 0 0 * * 0 0 .AAACAAAAAAGCTGATGGCCTGGCGGGGT %.836844751583,38-)/8638###### RG:Z:HiMom.9
-HiMom:9:2:3:1133 4 * 0 0 * * 0 0 AGAAGCTTTCTATTCTGATCCCCAAGGAGT BACBA>BB=1;?BA??5A>:@25<=.43;? RG:Z:HiMom.9
-HiMom:9:2:3:157 4 * 0 0 * * 0 0 TGGGTGGTTCAAACTAAGCAGTCCAACTGC BACC at BBABBBBCBBCBBBBBB?AAB?B?A RG:Z:HiMom.9
-HiMom:9:2:3:1602 4 * 0 0 * * 0 0 AATTCATGAATACTTTTCAGTCTTTAAAAA BCBAAABBBBB?<@BAB?AA=?BBBBBBBB RG:Z:HiMom.9
-HiMom:9:2:3:808 516 * 0 0 * * 0 0 .GAGTGTAATACAATGGTATGGATTTTAAC ############################## RG:Z:HiMom.9
-HiMom:9:2:3:991 4 * 0 0 * * 0 0 TGGAAGCCAGCCAAAGATACACTCTTGGCA BABC>6BBCBBBBCAAA at BACB<<?BABBB RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGTTGCTT.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGTTGCTT.sam
deleted file mode 100644
index 0bc0f35..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGTTGCTT.sam
+++ /dev/null
@@ -1,10 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.AGTTGCTT LB:LN_AGTTGCTT PI:10005 DS:DESC5 SM:SA_AGTTGCTT CN:BI
-HiMom:7:1:3:1341 4 * 0 0 * * 0 0 TGAAGAGTTTCTGGCACATAGGCACTCAAC B7AACB;>C7A??4AB<B>B:':@CAAAAB RG:Z:HiMom.7
-HiMom:7:1:3:1861 4 * 0 0 * * 0 0 .GATTAATGAATAGAGTGAATAGTGTCTGA %-07:::5.3<<7788529:<<530:9646 RG:Z:HiMom.7
-HiMom:7:1:3:699 516 * 0 0 * * 0 0 .TGTCTTCTTACACTATTTTTTTTAAAATC ############################## RG:Z:HiMom.7
-HiMom:7:2:3:1962 4 * 0 0 * * 0 0 ACTAAATCCAAGAGCACATCAAAATGTTAA B5;BBB@@8 at BAB9>BBBABACB@@B;@BB RG:Z:HiMom.7
-HiMom:7:2:3:274 4 * 0 0 * * 0 0 AGTGAAGTGCTTAGCACCTGGGCCAGCAGC :57.:@@>96=@97>@=;=>;@;@=@9=9; RG:Z:HiMom.7
-HiMom:7:2:3:640 4 * 0 0 * * 0 0 AGATTAAAAAAAAATGACGTGACAAATTAA =6CBC at CABCBBCBC@>@=@ABBCCBBBCC RG:Z:HiMom.7
-HiMom:7:2:3:691 4 * 0 0 * * 0 0 ATTTTCAAATCATAAATATGGATTGCTGTG BBBABACBBA at ABBBBBBB727AB8+;B55 RG:Z:HiMom.7
-HiMom:7:2:3:72 4 * 0 0 * * 0 0 CTAGTCTTTGACTTATATCAATTCAGTATT BBC?ACCCCCB at CCCCCCCBCCCCCA@BCC RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGTTGCTTTCTGGCGA.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGTTGCTTTCTGGCGA.sam
deleted file mode 100644
index c90a907..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AGTTGCTTTCTGGCGA.sam
+++ /dev/null
@@ -1,10 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.AGTTGCTT-TCTGGCGA LB:LN_AGTTGCTTTCTGGCGA PI:10005 DS:DESC05 SM:SA_AGTTGCTTTCTGGCGA CN:BI
-HiMom:9:1:3:1341 4 * 0 0 * * 0 0 TGAAGAGTTTCTGGCACATAGGCACTCAAC B7AACB;>C7A??4AB<B>B:':@CAAAAB RG:Z:HiMom.9
-HiMom:9:1:3:1861 4 * 0 0 * * 0 0 .GATTAATGAATAGAGTGAATAGTGTCTGA %-07:::5.3<<7788529:<<530:9646 RG:Z:HiMom.9
-HiMom:9:1:3:699 516 * 0 0 * * 0 0 .TGTCTTCTTACACTATTTTTTTTAAAATC ############################## RG:Z:HiMom.9
-HiMom:9:2:3:1962 4 * 0 0 * * 0 0 ACTAAATCCAAGAGCACATCAAAATGTTAA B5;BBB@@8 at BAB9>BBBABACB@@B;@BB RG:Z:HiMom.9
-HiMom:9:2:3:274 4 * 0 0 * * 0 0 AGTGAAGTGCTTAGCACCTGGGCCAGCAGC :57.:@@>96=@97>@=;=>;@;@=@9=9; RG:Z:HiMom.9
-HiMom:9:2:3:640 4 * 0 0 * * 0 0 AGATTAAAAAAAAATGACGTGACAAATTAA =6CBC at CABCBBCBC@>@=@ABBCCBBBCC RG:Z:HiMom.9
-HiMom:9:2:3:691 4 * 0 0 * * 0 0 ATTTTCAAATCATAAATATGGATTGCTGTG BBBABACBBA at ABBBBBBB727AB8+;B55 RG:Z:HiMom.9
-HiMom:9:2:3:72 4 * 0 0 * * 0 0 CTAGTCTTTGACTTATATCAATTCAGTATT BBC?ACCCCCB at CCCCCCCBCCCCCA@BCC RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ATTATGTT.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ATTATGTT.sam
deleted file mode 100644
index 5ab460c..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ATTATGTT.sam
+++ /dev/null
@@ -1,5 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.ATTATGTT LB:LN_ATTATGTT PI:10006 DS:DESC6 SM:SA_ATTATGTT CN:BI
-HiMom:7:1:3:1867 4 * 0 0 * * 0 0 AGAAGCATTCTCAGAAACTTATTTGTGATG BB>81>BB?->?;07>4;B at BABB?:<@=: RG:Z:HiMom.7
-HiMom:7:1:3:347 516 * 0 0 * * 0 0 .GTGGTGTGAGGTGTATCTGGGTCAGCAGG ############################## RG:Z:HiMom.7
-HiMom:7:2:3:889 516 * 0 0 * * 0 0 .TTTTTATAACACCTCAGGCATCGTCAAAC ############################## RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ATTATGTTTCGGAATG.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ATTATGTTTCGGAATG.sam
deleted file mode 100644
index bdc7a66..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/ATTATGTTTCGGAATG.sam
+++ /dev/null
@@ -1,5 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.ATTATGTT-TCGGAATG LB:LN_ATTATGTTTCGGAATG PI:10006 DS:DESC06 SM:SA_ATTATGTTTCGGAATG CN:BI
-HiMom:9:1:3:1867 4 * 0 0 * * 0 0 AGAAGCATTCTCAGAAACTTATTTGTGATG BB>81>BB?->?;07>4;B at BABB?:<@=: RG:Z:HiMom.9
-HiMom:9:1:3:347 516 * 0 0 * * 0 0 .GTGGTGTGAGGTGTATCTGGGTCAGCAGG ############################## RG:Z:HiMom.9
-HiMom:9:2:3:889 516 * 0 0 * * 0 0 .TTTTTATAACACCTCAGGCATCGTCAAAC ############################## RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CACATCCT.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CACATCCT.sam
deleted file mode 100644
index c0d5292..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CACATCCT.sam
+++ /dev/null
@@ -1,11 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.CACATCCT LB:LN_CACATCCT DS:DESC7 SM:SA_CACATCCT CN:BI
-HiMom:7:1:2:1465 516 * 0 0 * * 0 0 .TTGTATTTCTGAAACCCCGAAGGGCATGG ############################## RG:Z:HiMom.7
-HiMom:7:1:3:683 4 * 0 0 * * 0 0 .AAGTTTTTATTTATACGTAGAATTTATAC %.611<<:;<98;<<<93993789<;<;9: RG:Z:HiMom.7
-HiMom:7:1:3:751 4 * 0 0 * * 0 0 CACTTTTATTCTTAAGTACCACCTTCTGGA 6A=CCCCBCCCAAA??@CC8@@CCBC:>)@ RG:Z:HiMom.7
-HiMom:7:2:2:1012 4 * 0 0 * * 0 0 .AGAAATACCATTTGACCCACCAATCCCAT %066:::9636963567778::88895-58 RG:Z:HiMom.7
-HiMom:7:2:2:1402 516 * 0 0 * * 0 0 .GGATGGCTTCCAGTATGGGAACCTTTTCA %.5484-/858865/78/(/62'/886555 RG:Z:HiMom.7
-HiMom:7:2:3:1094 4 * 0 0 * * 0 0 CATATGGTATCACCACTCAGATACATAAAG AABB<:=1CBBCBC@?AA@)>CCBBCCB?= RG:Z:HiMom.7
-HiMom:7:2:3:16 4 * 0 0 * * 0 0 AGCTGGGCATGGTGATGCGCCCCTGTAATC A;?;<<?@9?@@@@4=3)1 at 59??9<5.<2 RG:Z:HiMom.7
-HiMom:7:2:3:1712 4 * 0 0 * * 0 0 AGTGCTGTGGCCTGGATGGATGTCAGGATT >91:?5:=5:77>305>/;=>1:<B9694; RG:Z:HiMom.7
-HiMom:7:2:3:328 516 * 0 0 * * 0 0 AGCTTAATATAGCATAGCAGATAAGATTTG (:*8>=,3:))<)?A<(8>########### RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CACATCCTTACTTAGC.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CACATCCTTACTTAGC.sam
deleted file mode 100644
index 16bb0b0..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CACATCCTTACTTAGC.sam
+++ /dev/null
@@ -1,11 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.CACATCCT-TACTTAGC LB:LN_CACATCCTTACTTAGC PI:10007 DS:DESC07 SM:SA_CACATCCTTACTTAGC CN:BI
-HiMom:9:1:2:1465 516 * 0 0 * * 0 0 .TTGTATTTCTGAAACCCCGAAGGGCATGG ############################## RG:Z:HiMom.9
-HiMom:9:1:3:683 4 * 0 0 * * 0 0 .AAGTTTTTATTTATACGTAGAATTTATAC %.611<<:;<98;<<<93993789<;<;9: RG:Z:HiMom.9
-HiMom:9:1:3:751 4 * 0 0 * * 0 0 CACTTTTATTCTTAAGTACCACCTTCTGGA 6A=CCCCBCCCAAA??@CC8@@CCBC:>)@ RG:Z:HiMom.9
-HiMom:9:2:2:1012 4 * 0 0 * * 0 0 .AGAAATACCATTTGACCCACCAATCCCAT %066:::9636963567778::88895-58 RG:Z:HiMom.9
-HiMom:9:2:2:1402 516 * 0 0 * * 0 0 .GGATGGCTTCCAGTATGGGAACCTTTTCA %.5484-/858865/78/(/62'/886555 RG:Z:HiMom.9
-HiMom:9:2:3:1094 4 * 0 0 * * 0 0 CATATGGTATCACCACTCAGATACATAAAG AABB<:=1CBBCBC@?AA@)>CCBBCCB?= RG:Z:HiMom.9
-HiMom:9:2:3:16 4 * 0 0 * * 0 0 AGCTGGGCATGGTGATGCGCCCCTGTAATC A;?;<<?@9?@@@@4=3)1 at 59??9<5.<2 RG:Z:HiMom.9
-HiMom:9:2:3:1712 4 * 0 0 * * 0 0 AGTGCTGTGGCCTGGATGGATGTCAGGATT >91:?5:=5:77>305>/;=>1:<B9694; RG:Z:HiMom.9
-HiMom:9:2:3:328 516 * 0 0 * * 0 0 AGCTTAATATAGCATAGCAGATAAGATTTG (:*8>=,3:))<)?A<(8>########### RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CAGGAGCC.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CAGGAGCC.sam
deleted file mode 100644
index f247663..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CAGGAGCC.sam
+++ /dev/null
@@ -1,11 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.CAGGAGCC LB:LN_CAGGAGCC PI:10008 DS:DESC8 SM:SA_CAGGAGCC CN:BI
-HiMom:7:1:2:1336 4 * 0 0 * * 0 0 .AAGTCTAAAATTATCTTGAAGTAAAAAGT %.75795:89<<<<4-7::58579<<<8.7 RG:Z:HiMom.7
-HiMom:7:1:2:1878 4 * 0 0 * * 0 0 .AATACTGAGATGTATTTAAGGCTGACACT %.9:957/3767079:::7:5/57::9999 RG:Z:HiMom.7
-HiMom:7:1:2:425 4 * 0 0 * * 0 0 .AATATATGCAAGACTCCTGTTATTAGAAA %099:99055:726<<9<9977::9:::<< RG:Z:HiMom.7
-HiMom:7:1:2:802 4 * 0 0 * * 0 0 .AAGTTAATTGTGTATTATTAACATCATTC %/627<<<<444358<<::::989957972 RG:Z:HiMom.7
-HiMom:7:1:3:1927 516 * 0 0 * * 0 0 CACATCACCTTCTACTACATTTGAAATTCT BCACA8B>C=BA?C8BC:'8=-5@)@=0=B RG:Z:HiMom.7
-HiMom:7:2:2:303 516 * 0 0 * * 0 0 .AGATCTTGTCTTTCAATCTTTTTAAATTC ############################## RG:Z:HiMom.7
-HiMom:7:2:2:953 516 * 0 0 * * 0 0 .GTTTAGTACATACTAGGTTTCACCAAATT ############################## RG:Z:HiMom.7
-HiMom:7:2:3:151 4 * 0 0 * * 0 0 AGAGAACAGATAGGTCTGTCAGGGCTGACC ?>=99B>BA?B>)?;5AB;89;=6??<73> RG:Z:HiMom.7
-HiMom:7:2:3:99 516 * 0 0 * * 0 0 CATATCTGTGTTATTTTAGCATAAATTTGA 1 at +@31?('4(A;73>)?73))@))@C?## RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CAGGAGCCGTATAACA.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CAGGAGCCGTATAACA.sam
deleted file mode 100644
index f5835f7..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CAGGAGCCGTATAACA.sam
+++ /dev/null
@@ -1,11 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.CAGGAGCC-GTATAACA LB:LN_CAGGAGCCGTATAACA PI:10008 DS:DESC08 SM:SA_CAGGAGCCGTATAACA CN:BI
-HiMom:9:1:2:1336 4 * 0 0 * * 0 0 .AAGTCTAAAATTATCTTGAAGTAAAAAGT %.75795:89<<<<4-7::58579<<<8.7 RG:Z:HiMom.9
-HiMom:9:1:2:1878 4 * 0 0 * * 0 0 .AATACTGAGATGTATTTAAGGCTGACACT %.9:957/3767079:::7:5/57::9999 RG:Z:HiMom.9
-HiMom:9:1:2:425 4 * 0 0 * * 0 0 .AATATATGCAAGACTCCTGTTATTAGAAA %099:99055:726<<9<9977::9:::<< RG:Z:HiMom.9
-HiMom:9:1:2:802 4 * 0 0 * * 0 0 .AAGTTAATTGTGTATTATTAACATCATTC %/627<<<<444358<<::::989957972 RG:Z:HiMom.9
-HiMom:9:1:3:1927 516 * 0 0 * * 0 0 CACATCACCTTCTACTACATTTGAAATTCT BCACA8B>C=BA?C8BC:'8=-5@)@=0=B RG:Z:HiMom.9
-HiMom:9:2:2:303 516 * 0 0 * * 0 0 .AGATCTTGTCTTTCAATCTTTTTAAATTC ############################## RG:Z:HiMom.9
-HiMom:9:2:2:953 516 * 0 0 * * 0 0 .GTTTAGTACATACTAGGTTTCACCAAATT ############################## RG:Z:HiMom.9
-HiMom:9:2:3:151 4 * 0 0 * * 0 0 AGAGAACAGATAGGTCTGTCAGGGCTGACC ?>=99B>BA?B>)?;5AB;89;=6??<73> RG:Z:HiMom.9
-HiMom:9:2:3:99 516 * 0 0 * * 0 0 CATATCTGTGTTATTTTAGCATAAATTTGA 1 at +@31?('4(A;73>)?73))@))@C?## RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATAGCGA.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATAGCGA.sam
deleted file mode 100644
index 62f27b7..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATAGCGA.sam
+++ /dev/null
@@ -1,14 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.CATAGCGA LB:LN_CATAGCGA PI:10009 DS:DESC9 SM:SA_CATAGCGA CN:BI
-HiMom:7:1:2:119 4 * 0 0 * * 0 0 .GATTGGAATCAACCCGAGTGGAATGGAAT %06:75577786742-6-66///288517# RG:Z:HiMom.7
-HiMom:7:1:2:1895 4 * 0 0 * * 0 0 .AAAACTTCTAAGTAATCATGAAGCTCTGC %.7;9:::::<84:99989:<678<:6776 RG:Z:HiMom.7
-HiMom:7:1:2:190 4 * 0 0 * * 0 0 .ATAAGTGTATATTTATTTGTACCATGACA %-;8694777:8;;9<:<<<<99998:996 RG:Z:HiMom.7
-HiMom:7:1:3:1513 4 * 0 0 * * 0 0 CACGCCACTGCGCCTGCAGCCTGGGCAATA B=55 at AA6@=;>;>/;@@9@<>52<?@ABA RG:Z:HiMom.7
-HiMom:7:1:3:277 516 * 0 0 * * 0 0 .GATGGGAAGGCCCCGGCCTGGGGAGGTGG ############################## RG:Z:HiMom.7
-HiMom:7:2:2:463 516 * 0 0 * * 0 0 .GTGCTTGGGGGCGTCTGTGTTGATGCGTG ############################## RG:Z:HiMom.7
-HiMom:7:2:2:611 516 * 0 0 * * 0 0 .GGAACCAGGCAGGGCCACACACAGGTAGC ############################## RG:Z:HiMom.7
-HiMom:7:2:3:1016 4 * 0 0 * * 0 0 TGGCTCTGTCCTAATATCTTATTCTTACAA <3=@BBA?@<=BBCC@>6>BBBBB at B?@AC RG:Z:HiMom.7
-HiMom:7:2:3:1898 516 * 0 0 * * 0 0 .TTGAATTGCTGGACTTCAATGTGTGTGGG %08868:64680+0-5:8765255647522 RG:Z:HiMom.7
-HiMom:7:2:3:2013 516 * 0 0 * * 0 0 AGCAGAAGCCTGCTGTGGGAACACTCAGTC B?B########################### RG:Z:HiMom.7
-HiMom:7:2:3:399 4 * 0 0 * * 0 0 AGGGTATGTAAACCGAGTTTTGCGGGGGAT A@@@>BBBBBAA>@;?B?BBAA>@:@:?AB RG:Z:HiMom.7
-HiMom:7:2:3:983 4 * 0 0 * * 0 0 TGTTTTTTATTTTAACAGATGAAGTACCAA B=BCCCCCCCCCCCA>AACCBCC at AC@>BC RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATAGCGAGGTCCAGA.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATAGCGAGGTCCAGA.sam
deleted file mode 100644
index d454804..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATAGCGAGGTCCAGA.sam
+++ /dev/null
@@ -1,14 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.CATAGCGA-GGTCCAGA LB:LN_CATAGCGAGGTCCAGA PI:10009 DS:DESC09 SM:SA_CATAGCGAGGTCCAGA CN:BI
-HiMom:9:1:2:119 4 * 0 0 * * 0 0 .GATTGGAATCAACCCGAGTGGAATGGAAT %06:75577786742-6-66///288517# RG:Z:HiMom.9
-HiMom:9:1:2:1895 4 * 0 0 * * 0 0 .AAAACTTCTAAGTAATCATGAAGCTCTGC %.7;9:::::<84:99989:<678<:6776 RG:Z:HiMom.9
-HiMom:9:1:2:190 4 * 0 0 * * 0 0 .ATAAGTGTATATTTATTTGTACCATGACA %-;8694777:8;;9<:<<<<99998:996 RG:Z:HiMom.9
-HiMom:9:1:3:1513 4 * 0 0 * * 0 0 CACGCCACTGCGCCTGCAGCCTGGGCAATA B=55 at AA6@=;>;>/;@@9@<>52<?@ABA RG:Z:HiMom.9
-HiMom:9:1:3:277 516 * 0 0 * * 0 0 .GATGGGAAGGCCCCGGCCTGGGGAGGTGG ############################## RG:Z:HiMom.9
-HiMom:9:2:2:463 516 * 0 0 * * 0 0 .GTGCTTGGGGGCGTCTGTGTTGATGCGTG ############################## RG:Z:HiMom.9
-HiMom:9:2:2:611 516 * 0 0 * * 0 0 .GGAACCAGGCAGGGCCACACACAGGTAGC ############################## RG:Z:HiMom.9
-HiMom:9:2:3:1016 4 * 0 0 * * 0 0 TGGCTCTGTCCTAATATCTTATTCTTACAA <3=@BBA?@<=BBCC@>6>BBBBB at B?@AC RG:Z:HiMom.9
-HiMom:9:2:3:1898 516 * 0 0 * * 0 0 .TTGAATTGCTGGACTTCAATGTGTGTGGG %08868:64680+0-5:8765255647522 RG:Z:HiMom.9
-HiMom:9:2:3:2013 516 * 0 0 * * 0 0 AGCAGAAGCCTGCTGTGGGAACACTCAGTC B?B########################### RG:Z:HiMom.9
-HiMom:9:2:3:399 4 * 0 0 * * 0 0 AGGGTATGTAAACCGAGTTTTGCGGGGGAT A@@@>BBBBBAA>@;?B?BBAA>@:@:?AB RG:Z:HiMom.9
-HiMom:9:2:3:983 4 * 0 0 * * 0 0 TGTTTTTTATTTTAACAGATGAAGTACCAA B=BCCCCCCCCCCCA>AACCBCC at AC@>BC RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATGCTTA.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATGCTTA.sam
deleted file mode 100644
index b99e401..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATGCTTA.sam
+++ /dev/null
@@ -1,7 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.CATGCTTA LB:LN_CATGCTTA PI:10010 DS:DESC10 SM:SA_CATGCTTA CN:BI
-HiMom:7:1:3:1525 4 * 0 0 * * 0 0 AGAAAATATCTGCATAGATGTGTTGAAGTC BBBBBBAA@@?<3<:B=?B@@A at BAAA@=A RG:Z:HiMom.7
-HiMom:7:2:2:679 516 * 0 0 * * 0 0 .CTCTGTCTCAAAAAATAAAAATAAAAATA ############################## RG:Z:HiMom.7
-HiMom:7:2:3:1775 4 * 0 0 * * 0 0 .AATCCGACAATTATGTGTCTTGGAGTTGC %.22301499988866456250*.424955 RG:Z:HiMom.7
-HiMom:7:2:3:584 4 * 0 0 * * 0 0 AAAGTCCTGGGATTACAGGCATGAGCCACT ABC2<@=>8;6=>?>3>-3<>B9@/=9A;< RG:Z:HiMom.7
-HiMom:7:2:3:932 4 * 0 0 * * 0 0 AGAAAGACAGACAGACAAACTGACTCTCAG @>@C at 4A=?2 at B@.>ABABBBB>=A:;>@# RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATGCTTAGCACATCT.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATGCTTAGCACATCT.sam
deleted file mode 100644
index eb22906..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CATGCTTAGCACATCT.sam
+++ /dev/null
@@ -1,7 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.CATGCTTA-GCACATCT LB:LN_CATGCTTAGCACATCT PI:10010 DS:DESC10 SM:SA_CATGCTTAGCACATCT CN:BI
-HiMom:9:1:3:1525 4 * 0 0 * * 0 0 AGAAAATATCTGCATAGATGTGTTGAAGTC BBBBBBAA@@?<3<:B=?B@@A at BAAA@=A RG:Z:HiMom.9
-HiMom:9:2:2:679 516 * 0 0 * * 0 0 .CTCTGTCTCAAAAAATAAAAATAAAAATA ############################## RG:Z:HiMom.9
-HiMom:9:2:3:1775 4 * 0 0 * * 0 0 .AATCCGACAATTATGTGTCTTGGAGTTGC %.22301499988866456250*.424955 RG:Z:HiMom.9
-HiMom:9:2:3:584 4 * 0 0 * * 0 0 AAAGTCCTGGGATTACAGGCATGAGCCACT ABC2<@=>8;6=>?>3>-3<>B9@/=9A;< RG:Z:HiMom.9
-HiMom:9:2:3:932 4 * 0 0 * * 0 0 AGAAAGACAGACAGACAAACTGACTCTCAG @>@C at 4A=?2 at B@.>ABABBBB>=A:;>@# RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCAGTTAG.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCAGTTAG.sam
deleted file mode 100644
index 3379e12..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCAGTTAG.sam
+++ /dev/null
@@ -1,13 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.CCAGTTAG LB:LN_CCAGTTAG SM:SA_CCAGTTAG CN:BI
-HiMom:7:1:3:1688 4 * 0 0 * * 0 0 .CCTTCTTTACACACTGAGGAACTTAACCT %..99999:9:7753564-357708:9777 RG:Z:HiMom.7
-HiMom:7:1:3:583 4 * 0 0 * * 0 0 GGCTTACACAGTCAAACTGGAGAGAAGTAG (56=CCCC=B8BABBBC@:=BBAAA?, at A< RG:Z:HiMom.7
-HiMom:7:1:3:996 4 * 0 0 * * 0 0 AAGGGAATTCTTGGACTTGATTAAATTGGT =C9?6?BBB?6;6>;>A?BA?@2<@BB:## RG:Z:HiMom.7
-HiMom:7:2:2:1671 516 * 0 0 * * 0 0 .GGGAATTACATGGAAAATGATCAAAGGAA ############################## RG:Z:HiMom.7
-HiMom:7:2:2:1723 516 * 0 0 * * 0 0 .GAAGCTGACATTACAGGTTTCAGACACCA ############################## RG:Z:HiMom.7
-HiMom:7:2:2:255 4 * 0 0 * * 0 0 .GGGTCCAAATAAGAGAAGGAGAAAAACAG %00412036893057554167465;98977 RG:Z:HiMom.7
-HiMom:7:2:3:112 4 * 0 0 * * 0 0 .ATGGAGTCTTGCTCTATTGCCCAGGCTGG ############################## RG:Z:HiMom.7
-HiMom:7:2:3:1179 516 * 0 0 * * 0 0 ATTTAATAAATAAAGCAACCTGACAACTGA @15;'88?A at 1/3='106/9A7.*:/08## RG:Z:HiMom.7
-HiMom:7:2:3:1387 516 * 0 0 * * 0 0 .CGATTATGACTCTGAGAGAAAGTAGGGCA ############################## RG:Z:HiMom.7
-HiMom:7:2:3:1484 4 * 0 0 * * 0 0 CATCAACCTGTCACAAAATGACAAAACCTA =A at 5@CB?B5@?B@@BBBB?ABCCBC at ABB RG:Z:HiMom.7
-HiMom:7:2:3:1576 516 * 0 0 * * 0 0 .GAAACCACGTGCCCATTTTCAGTTCTGGT %*/%.55663117868788787/765#### RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCAGTTAGGCACACGA.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCAGTTAGGCACACGA.sam
deleted file mode 100644
index 946721c..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCAGTTAGGCACACGA.sam
+++ /dev/null
@@ -1,13 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.CCAGTTAG-GCACACGA LB:LN_CCAGTTAGGCACACGA PI:10011 DS:DESC11 SM:SA_CCAGTTAGGCACACGA CN:BI
-HiMom:9:1:3:1688 4 * 0 0 * * 0 0 .CCTTCTTTACACACTGAGGAACTTAACCT %..99999:9:7753564-357708:9777 RG:Z:HiMom.9
-HiMom:9:1:3:583 4 * 0 0 * * 0 0 GGCTTACACAGTCAAACTGGAGAGAAGTAG (56=CCCC=B8BABBBC@:=BBAAA?, at A< RG:Z:HiMom.9
-HiMom:9:1:3:996 4 * 0 0 * * 0 0 AAGGGAATTCTTGGACTTGATTAAATTGGT =C9?6?BBB?6;6>;>A?BA?@2<@BB:## RG:Z:HiMom.9
-HiMom:9:2:2:1671 516 * 0 0 * * 0 0 .GGGAATTACATGGAAAATGATCAAAGGAA ############################## RG:Z:HiMom.9
-HiMom:9:2:2:1723 516 * 0 0 * * 0 0 .GAAGCTGACATTACAGGTTTCAGACACCA ############################## RG:Z:HiMom.9
-HiMom:9:2:2:255 4 * 0 0 * * 0 0 .GGGTCCAAATAAGAGAAGGAGAAAAACAG %00412036893057554167465;98977 RG:Z:HiMom.9
-HiMom:9:2:3:112 4 * 0 0 * * 0 0 .ATGGAGTCTTGCTCTATTGCCCAGGCTGG ############################## RG:Z:HiMom.9
-HiMom:9:2:3:1179 516 * 0 0 * * 0 0 ATTTAATAAATAAAGCAACCTGACAACTGA @15;'88?A at 1/3='106/9A7.*:/08## RG:Z:HiMom.9
-HiMom:9:2:3:1387 516 * 0 0 * * 0 0 .CGATTATGACTCTGAGAGAAAGTAGGGCA ############################## RG:Z:HiMom.9
-HiMom:9:2:3:1484 4 * 0 0 * * 0 0 CATCAACCTGTCACAAAATGACAAAACCTA =A at 5@CB?B5@?B@@BBBB?ABCCBC at ABB RG:Z:HiMom.9
-HiMom:9:2:3:1576 516 * 0 0 * * 0 0 .GAAACCACGTGCCCATTTTCAGTTCTGGT %*/%.55663117868788787/765#### RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCTACCAT.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCTACCAT.sam
deleted file mode 100644
index 33ad327..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCTACCAT.sam
+++ /dev/null
@@ -1,4 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.CCTACCAT LB:LN_CCTACCAT PI:10012 DS:DESC12 SM:SA_CCTACCAT CN:BI
-HiMom:7:1:2:636 516 * 0 0 * * 0 0 .GATCATTTACTGTTGTCAACTACCAAAAT %/72'+769621513-1-563202356557 RG:Z:HiMom.7
-HiMom:7:2:3:875 516 * 0 0 * * 0 0 AGGCAGTAGTCTAATCCCGAGGATCCCAAG :,73=@?<.=@;??@::3?8)5<=9%:?>7 RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCTACCATCTACCAGG.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCTACCATCTACCAGG.sam
deleted file mode 100644
index 81639cc..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CCTACCATCTACCAGG.sam
+++ /dev/null
@@ -1,4 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.CCTACCAT-CTACCAGG LB:LN_CCTACCATCTACCAGG PI:10012 DS:DESC12 SM:SA_CCTACCATCTACCAGG CN:BI
-HiMom:9:1:2:636 516 * 0 0 * * 0 0 .GATCATTTACTGTTGTCAACTACCAAAAT %/72'+769621513-1-563202356557 RG:Z:HiMom.9
-HiMom:9:2:3:875 516 * 0 0 * * 0 0 AGGCAGTAGTCTAATCCCGAGGATCCCAAG :,73=@?<.=@;??@::3?8)5<=9%:?>7 RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CTACCAGG.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CTACCAGG.sam
deleted file mode 100644
index 67c769d..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CTACCAGG.sam
+++ /dev/null
@@ -1,8 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.CTACCAGG LB:LN_CTACCAGG PI:10013 DS:DESC13 SM:SA_CTACCAGG CN:BI
-HiMom:7:1:2:1995 4 * 0 0 * * 0 0 .ATTTCCTGAACACAGCACAGGGAAGAGGA %/78777738777:8877786776858225 RG:Z:HiMom.7
-HiMom:7:1:3:1358 516 * 0 0 * * 0 0 .TCCTTCCTCAAGGGGACCCCGCCTCCCCT ############################## RG:Z:HiMom.7
-HiMom:7:1:3:176 4 * 0 0 * * 0 0 ATATTTCATGAAAGACATAAATTTACAGTT BBBCCB at BBBABBBB?ABBBBBBBBABB at B RG:Z:HiMom.7
-HiMom:7:1:3:198 4 * 0 0 * * 0 0 TATAATTTAATGGTTTTTATATATTCAGAG BBC=BBCCA=@=8<BCBCBBABBCB=BB<9 RG:Z:HiMom.7
-HiMom:7:1:3:900 516 * 0 0 * * 0 0 TGAATCTTTGTTCAACACAGATTATTCCAG )>@+5*<B1':(5,23A>5)@:)(/>:=## RG:Z:HiMom.7
-HiMom:7:2:3:1970 4 * 0 0 * * 0 0 .TAATACTCTTTGAGAAAGGACTGAGGGAA %.:77558:68862.3;8455:0057535; RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CTACCAGGCCTACCAT.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CTACCAGGCCTACCAT.sam
deleted file mode 100644
index 82e4c9c..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/CTACCAGGCCTACCAT.sam
+++ /dev/null
@@ -1,8 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.CTACCAGG-CCTACCAT LB:LN_CTACCAGGCCTACCAT PI:10013 DS:DESC13 SM:SA_CTACCAGGCCTACCAT CN:BI
-HiMom:9:1:2:1995 4 * 0 0 * * 0 0 .ATTTCCTGAACACAGCACAGGGAAGAGGA %/78777738777:8877786776858225 RG:Z:HiMom.9
-HiMom:9:1:3:1358 516 * 0 0 * * 0 0 .TCCTTCCTCAAGGGGACCCCGCCTCCCCT ############################## RG:Z:HiMom.9
-HiMom:9:1:3:176 4 * 0 0 * * 0 0 ATATTTCATGAAAGACATAAATTTACAGTT BBBCCB at BBBABBBB?ABBBBBBBBABB at B RG:Z:HiMom.9
-HiMom:9:1:3:198 4 * 0 0 * * 0 0 TATAATTTAATGGTTTTTATATATTCAGAG BBC=BBCCA=@=8<BCBCBBABBCB=BB<9 RG:Z:HiMom.9
-HiMom:9:1:3:900 516 * 0 0 * * 0 0 TGAATCTTTGTTCAACACAGATTATTCCAG )>@+5*<B1':(5,23A>5)@:)(/>:=## RG:Z:HiMom.9
-HiMom:9:2:3:1970 4 * 0 0 * * 0 0 .TAATACTCTTTGAGAAAGGACTGAGGGAA %.:77558:68862.3;8455:0057535; RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACACGA.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACACGA.sam
deleted file mode 100644
index 74dcf49..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACACGA.sam
+++ /dev/null
@@ -1,11 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.GCACACGA LB:LN_GCACACGA PI:10014 DS:DESC14 SM:SA_GCACACGA CN:BI
-HiMom:7:1:3:1311 4 * 0 0 * * 0 0 AGACATAAAACCAGAGAGAAGATAGTGGGT @@@BBBBCBA;>B>ABBBBBBBBA?;9:3> RG:Z:HiMom.7
-HiMom:7:1:3:1544 516 * 0 0 * * 0 0 CGTGGATGGTTTTGATGAGTCCCACTGCAC =@=<)*@22375A9@?36(768@:'897<# RG:Z:HiMom.7
-HiMom:7:1:3:301 516 * 0 0 * * 0 0 .TACGTGTGTGGCTGGATAGTCTGGACCAT ############################## RG:Z:HiMom.7
-HiMom:7:1:3:959 4 * 0 0 * * 0 0 .AAAGTTTCCTGTGAGAAGGCGCATGGCAT %.52-487848866757############# RG:Z:HiMom.7
-HiMom:7:2:2:184 516 * 0 0 * * 0 0 .GAAACGTTTTTCGGTTGAGGAAACTTTTT ############################## RG:Z:HiMom.7
-HiMom:7:2:3:1025 4 * 0 0 * * 0 0 .AATGGAAAGGAGTCCAATGGAAGGGAATC %/4626885-+3-3777:532570313837 RG:Z:HiMom.7
-HiMom:7:2:3:1290 516 * 0 0 * * 0 0 .TCACCTGAATCCACGTTAGCTGGGGAAGA ############################## RG:Z:HiMom.7
-HiMom:7:2:3:1917 516 * 0 0 * * 0 0 .TCCACAAAAAAAAAAAAAATTAGTTGGGT %*6<737<4756################## RG:Z:HiMom.7
-HiMom:7:2:3:495 516 * 0 0 * * 0 0 .TCCGTTTTTATAACTGTAAATTTATCACT ############################## RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACACGACCAGTTAG.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACACGACCAGTTAG.sam
deleted file mode 100644
index bea26c2..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACACGACCAGTTAG.sam
+++ /dev/null
@@ -1,11 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.GCACACGA-CCAGTTAG LB:LN_GCACACGACCAGTTAG PI:10014 DS:DESC14 SM:SA_GCACACGACCAGTTAG CN:BI
-HiMom:9:1:3:1311 4 * 0 0 * * 0 0 AGACATAAAACCAGAGAGAAGATAGTGGGT @@@BBBBCBA;>B>ABBBBBBBBA?;9:3> RG:Z:HiMom.9
-HiMom:9:1:3:1544 516 * 0 0 * * 0 0 CGTGGATGGTTTTGATGAGTCCCACTGCAC =@=<)*@22375A9@?36(768@:'897<# RG:Z:HiMom.9
-HiMom:9:1:3:301 516 * 0 0 * * 0 0 .TACGTGTGTGGCTGGATAGTCTGGACCAT ############################## RG:Z:HiMom.9
-HiMom:9:1:3:959 4 * 0 0 * * 0 0 .AAAGTTTCCTGTGAGAAGGCGCATGGCAT %.52-487848866757############# RG:Z:HiMom.9
-HiMom:9:2:2:184 516 * 0 0 * * 0 0 .GAAACGTTTTTCGGTTGAGGAAACTTTTT ############################## RG:Z:HiMom.9
-HiMom:9:2:3:1025 4 * 0 0 * * 0 0 .AATGGAAAGGAGTCCAATGGAAGGGAATC %/4626885-+3-3777:532570313837 RG:Z:HiMom.9
-HiMom:9:2:3:1290 516 * 0 0 * * 0 0 .TCACCTGAATCCACGTTAGCTGGGGAAGA ############################## RG:Z:HiMom.9
-HiMom:9:2:3:1917 516 * 0 0 * * 0 0 .TCCACAAAAAAAAAAAAAATTAGTTGGGT %*6<737<4756################## RG:Z:HiMom.9
-HiMom:9:2:3:495 516 * 0 0 * * 0 0 .TCCGTTTTTATAACTGTAAATTTATCACT ############################## RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACATCT.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACATCT.sam
deleted file mode 100644
index 7650df4..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACATCT.sam
+++ /dev/null
@@ -1,5 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.GCACATCT LB:LN_GCACATCT DS:DESC15 SM:SA_GCACATCT CN:BI
-HiMom:7:1:3:389 516 * 0 0 * * 0 0 .GATGTTCAAACATGCATAACTCTAAGTAT ############################## RG:Z:HiMom.7
-HiMom:7:2:2:1567 4 * 0 0 * * 0 0 .AGACAGCAGTAACCTCTGCAGACTTAAAC %,67:720544;4667:62-5667::6877 RG:Z:HiMom.7
-HiMom:7:2:3:1053 516 * 0 0 * * 0 0 .TTTGATCATGATTCCATTCGAGACCATTC %.;;########################## RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACATCTCATGCTTA.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACATCTCATGCTTA.sam
deleted file mode 100644
index 500823b..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GCACATCTCATGCTTA.sam
+++ /dev/null
@@ -1,5 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.GCACATCT-CATGCTTA LB:LN_GCACATCTCATGCTTA PI:10015 DS:DESC15 SM:SA_GCACATCTCATGCTTA CN:BI
-HiMom:9:1:3:389 516 * 0 0 * * 0 0 .GATGTTCAAACATGCATAACTCTAAGTAT ############################## RG:Z:HiMom.9
-HiMom:9:2:2:1567 4 * 0 0 * * 0 0 .AGACAGCAGTAACCTCTGCAGACTTAAAC %,67:720544;4667:62-5667::6877 RG:Z:HiMom.9
-HiMom:9:2:3:1053 516 * 0 0 * * 0 0 .TTTGATCATGATTCCATTCGAGACCATTC %.;;########################## RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GGTCCAGA.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GGTCCAGA.sam
deleted file mode 100644
index 8341974..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GGTCCAGA.sam
+++ /dev/null
@@ -1,9 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.GGTCCAGA LB:LN_GGTCCAGA PI:10016 DS:DESC16 SM:SA_GGTCCAGA CN:BI
-HiMom:7:1:3:33 516 * 0 0 * * 0 0 CGGGCGCGGTGGATTCCGCCTTTAATCCTA 71@=>3?BA##################### RG:Z:HiMom.7
-HiMom:7:1:3:471 4 * 0 0 * * 0 0 AGAAAAAGACAAGCAGGCCTCTCACAGAGC @=B>CB@?8BBBA<B<@ABBAAA=<@>>3< RG:Z:HiMom.7
-HiMom:7:1:3:676 516 * 0 0 * * 0 0 ATAAGAAAATGCCAACCCATTTACAGTTTT ?':7%68>?<(.9A7(=:68>A=2>(9@?? RG:Z:HiMom.7
-HiMom:7:2:2:1038 516 * 0 0 * * 0 0 .ATGGAATCAACCTGAGTGGAATGAAATGG ############################## RG:Z:HiMom.7
-HiMom:7:2:3:1352 4 * 0 0 * * 0 0 AAAGTGGCCCTTTCTGCATAATTCTTCTTG @B@>2:@@:>B at AAA:AA>?B?>:=<1=<# RG:Z:HiMom.7
-HiMom:7:2:3:1733 4 * 0 0 * * 0 0 .TTAAATGAGTGTAAATATTCAATTATGCA %,:6::2/5;393<<9:<;919<97##### RG:Z:HiMom.7
-HiMom:7:2:3:386 516 * 0 0 * * 0 0 .TGAATAAATAAATATCTGTATTATTCCTA %156;99:999:5773,4-57973851.48 RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GGTCCAGACATAGCGA.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GGTCCAGACATAGCGA.sam
deleted file mode 100644
index cdc7e7b..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GGTCCAGACATAGCGA.sam
+++ /dev/null
@@ -1,9 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.GGTCCAGA-CATAGCGA LB:LN_GGTCCAGACATAGCGA PI:10016 DS:DESC16 SM:SA_GGTCCAGACATAGCGA CN:BI
-HiMom:9:1:3:33 516 * 0 0 * * 0 0 CGGGCGCGGTGGATTCCGCCTTTAATCCTA 71@=>3?BA##################### RG:Z:HiMom.9
-HiMom:9:1:3:471 4 * 0 0 * * 0 0 AGAAAAAGACAAGCAGGCCTCTCACAGAGC @=B>CB@?8BBBA<B<@ABBAAA=<@>>3< RG:Z:HiMom.9
-HiMom:9:1:3:676 516 * 0 0 * * 0 0 ATAAGAAAATGCCAACCCATTTACAGTTTT ?':7%68>?<(.9A7(=:68>A=2>(9@?? RG:Z:HiMom.9
-HiMom:9:2:2:1038 516 * 0 0 * * 0 0 .ATGGAATCAACCTGAGTGGAATGAAATGG ############################## RG:Z:HiMom.9
-HiMom:9:2:3:1352 4 * 0 0 * * 0 0 AAAGTGGCCCTTTCTGCATAATTCTTCTTG @B@>2:@@:>B at AAA:AA>?B?>:=<1=<# RG:Z:HiMom.9
-HiMom:9:2:3:1733 4 * 0 0 * * 0 0 .TTAAATGAGTGTAAATATTCAATTATGCA %,:6::2/5;393<<9:<;919<97##### RG:Z:HiMom.9
-HiMom:9:2:3:386 516 * 0 0 * * 0 0 .TGAATAAATAAATATCTGTATTATTCCTA %156;99:999:5773,4-57973851.48 RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GTATAACA.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GTATAACA.sam
deleted file mode 100644
index 73fb2a5..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GTATAACA.sam
+++ /dev/null
@@ -1,12 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.GTATAACA LB:LN_GTATAACA PI:10017 DS:DESC17 SM:SA_GTATAACA CN:BI
-HiMom:7:1:2:11 516 * 0 0 * * 0 0 .AAATGAAAAAAGAAATGCATTGTCAGGTG ############################## RG:Z:HiMom.7
-HiMom:7:1:2:455 516 * 0 0 * * 0 0 .GCTTGAACTCAGGATTCACAATTTCAACC ############################## RG:Z:HiMom.7
-HiMom:7:1:3:1188 4 * 0 0 * * 0 0 GCGAATGCCATTATTTCATTCCTTTTCATG =@CACA?AABCCCCCCCCAB??CBCBCCBB RG:Z:HiMom.7
-HiMom:7:1:3:131 4 * 0 0 * * 0 0 TAAAATAAAGTAAAAAGAAAGCAAGGTCCT BBBBCCCBBA<CCCCA<<CBC>BBC=AC=C RG:Z:HiMom.7
-HiMom:7:1:3:1488 4 * 0 0 * * 0 0 .ATTCTGAGTAGCATGCTGGATCCCACCCC %-445014,42/1666423########### RG:Z:HiMom.7
-HiMom:7:1:3:1973 4 * 0 0 * * 0 0 .CTTTTATTGAATTAGCTTCTGTGGAAACC %.<774<<145;105<<:6<7<:88;#### RG:Z:HiMom.7
-HiMom:7:1:3:289 4 * 0 0 * * 0 0 ATAGTGCTACAATAAACATGGGAGTGCAGA BB=;>AABB at BBBBBB@ACBA>>BA;9@?A RG:Z:HiMom.7
-HiMom:7:2:2:1662 516 * 0 0 * * 0 0 .ACTAAAGACCTTATTCATGTAGCCAAATA %.2556331)%079799::9:71855<88: RG:Z:HiMom.7
-HiMom:7:2:2:61 4 * 0 0 * * 0 0 .TTTCGATGGTGTTTCCATTTGATTCATTC %0;:9:;799:8:97779:<679<977;:: RG:Z:HiMom.7
-HiMom:7:2:3:1581 516 * 0 0 * * 0 0 .ATAGGCAGGGAGCAAACCTCAATAAAAAG ############################## RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GTATAACACAGGAGCC.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GTATAACACAGGAGCC.sam
deleted file mode 100644
index a9ed0e2..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/GTATAACACAGGAGCC.sam
+++ /dev/null
@@ -1,12 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.GTATAACA-CAGGAGCC LB:LN_GTATAACACAGGAGCC PI:10017 DS:DESC17 SM:SA_GTATAACACAGGAGCC CN:BI
-HiMom:9:1:2:11 516 * 0 0 * * 0 0 .AAATGAAAAAAGAAATGCATTGTCAGGTG ############################## RG:Z:HiMom.9
-HiMom:9:1:2:455 516 * 0 0 * * 0 0 .GCTTGAACTCAGGATTCACAATTTCAACC ############################## RG:Z:HiMom.9
-HiMom:9:1:3:1188 4 * 0 0 * * 0 0 GCGAATGCCATTATTTCATTCCTTTTCATG =@CACA?AABCCCCCCCCAB??CBCBCCBB RG:Z:HiMom.9
-HiMom:9:1:3:131 4 * 0 0 * * 0 0 TAAAATAAAGTAAAAAGAAAGCAAGGTCCT BBBBCCCBBA<CCCCA<<CBC>BBC=AC=C RG:Z:HiMom.9
-HiMom:9:1:3:1488 4 * 0 0 * * 0 0 .ATTCTGAGTAGCATGCTGGATCCCACCCC %-445014,42/1666423########### RG:Z:HiMom.9
-HiMom:9:1:3:1973 4 * 0 0 * * 0 0 .CTTTTATTGAATTAGCTTCTGTGGAAACC %.<774<<145;105<<:6<7<:88;#### RG:Z:HiMom.9
-HiMom:9:1:3:289 4 * 0 0 * * 0 0 ATAGTGCTACAATAAACATGGGAGTGCAGA BB=;>AABB at BBBBBB@ACBA>>BA;9@?A RG:Z:HiMom.9
-HiMom:9:2:2:1662 516 * 0 0 * * 0 0 .ACTAAAGACCTTATTCATGTAGCCAAATA %.2556331)%079799::9:71855<88: RG:Z:HiMom.9
-HiMom:9:2:2:61 4 * 0 0 * * 0 0 .TTTCGATGGTGTTTCCATTTGATTCATTC %0;:9:;799:8:97779:<679<977;:: RG:Z:HiMom.9
-HiMom:9:2:3:1581 516 * 0 0 * * 0 0 .ATAGGCAGGGAGCAAACCTCAATAAAAAG ############################## RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/N.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/N.sam
deleted file mode 100644
index 1c8169a..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/N.sam
+++ /dev/null
@@ -1,225 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.N LB:LN_N PI:10025 DS:DESC25 SM:SA_N CN:BI
-HiMom:7:1:0:1038 516 * 0 0 * * 0 0 .....C..CA...C...C.CC...C..... ############################## BC:Z:NNNNNGTN RG:Z:HiMom.7
-HiMom:7:1:0:1093 516 * 0 0 * * 0 0 .....C..GT...A...G.AA...A..... ############################## BC:Z:NNNNNTGN RG:Z:HiMom.7
-HiMom:7:1:0:113 516 * 0 0 * * 0 0 ........G...........A......... ############################## BC:Z:NNNNNNNN RG:Z:HiMom.7
-HiMom:7:1:0:1193 516 * 0 0 * * 0 0 ........T....T...T..T...C..... ############################## BC:Z:NNNNNGTN RG:Z:HiMom.7
-HiMom:7:1:0:1291 516 * 0 0 * * 0 0 ........A........A..T......... ############################## BC:Z:NNNNNGNN RG:Z:HiMom.7
-HiMom:7:1:0:1307 516 * 0 0 * * 0 0 ........C....A...T..T...C..... ############################## BC:Z:NNNNNTAN RG:Z:HiMom.7
-HiMom:7:1:0:1434 516 * 0 0 * * 0 0 .............................. ############################## BC:Z:NNNNNNNN RG:Z:HiMom.7 XN:i:1
-HiMom:7:1:0:1475 516 * 0 0 * * 0 0 .....G..A....A...A..A...A..... ############################## BC:Z:NNNNNCCN RG:Z:HiMom.7
-HiMom:7:1:0:1690 516 * 0 0 * * 0 0 ........A........G..C...C..... ############################## BC:Z:NNNNNANN RG:Z:HiMom.7
-HiMom:7:1:0:1703 516 * 0 0 * * 0 0 ........A...........A......... ############################## BC:Z:NNNNNNNN RG:Z:HiMom.7 XN:i:1
-HiMom:7:1:0:1940 516 * 0 0 * * 0 0 ........C........T..T......... ############################## BC:Z:NNNNNCNN RG:Z:HiMom.7
-HiMom:7:1:0:2001 516 * 0 0 * * 0 0 .....A..TG...G...A.GC...A..... ############################## BC:Z:NNNNNGAN RG:Z:HiMom.7
-HiMom:7:1:0:205 516 * 0 0 * * 0 0 ........A........A..T...A..... ############################## BC:Z:NNNNNCGN RG:Z:HiMom.7
-HiMom:7:1:0:275 516 * 0 0 * * 0 0 .....A..CA...T...G.CC...A..... ############################## BC:Z:NNNNNATN RG:Z:HiMom.7
-HiMom:7:1:0:324 516 * 0 0 * * 0 0 ........T........T..A...A..... ############################## BC:Z:NNNNNGTN RG:Z:HiMom.7
-HiMom:7:1:0:37 516 * 0 0 * * 0 0 ........A........C..T...C..... ############################## BC:Z:NNNNNGNN RG:Z:HiMom.7
-HiMom:7:1:0:464 516 * 0 0 * * 0 0 .............................. ############################## BC:Z:NNNNNNNN RG:Z:HiMom.7 XN:i:1
-HiMom:7:1:0:586 516 * 0 0 * * 0 0 ........C........C..C...A..... ############################## BC:Z:NNNNNCNN RG:Z:HiMom.7
-HiMom:7:1:0:841 516 * 0 0 * * 0 0 ........C...........T......... ############################## BC:Z:NNNNNNNN RG:Z:HiMom.7
-HiMom:7:1:0:879 516 * 0 0 * * 0 0 ........T...........T......... ############################## BC:Z:NNNNNNNN RG:Z:HiMom.7
-HiMom:7:1:1:1013 516 * 0 0 * * 0 0 ..C..T.CAG...C...A.GT...G..... ############################## BC:Z:NNNNNGAN RG:Z:HiMom.7
-HiMom:7:1:1:111 516 * 0 0 * * 0 0 ..C..T.GCG...T...A.CT...T..... ############################## BC:Z:NNNNNCGN RG:Z:HiMom.7
-HiMom:7:1:1:1153 516 * 0 0 * * 0 0 ..T..T.TGG...T...C.TC...T..... ############################## BC:Z:NNNNNCTN RG:Z:HiMom.7
-HiMom:7:1:1:1184 516 * 0 0 * * 0 0 ..A..G.TCG...A...T.CA...T..... ############################## BC:Z:NNNNNAGN RG:Z:HiMom.7
-HiMom:7:1:1:1241 516 * 0 0 * * 0 0 ..A..G.TGG...T...C.TG...A..... ############################## BC:Z:NNNNNCTN RG:Z:HiMom.7
-HiMom:7:1:1:1243 516 * 0 0 * * 0 0 ..A..A.GGA...A...C.TA...T..... ############################## BC:Z:NNNNNTGN RG:Z:HiMom.7
-HiMom:7:1:1:1247 516 * 0 0 * * 0 0 .CCAGC.TTT...T...T.CT...G..... ############################## BC:Z:NNNNNACN RG:Z:HiMom.7
-HiMom:7:1:1:1282 516 * 0 0 * * 0 0 ..A..A.GGG...T...G.AG...C..... ############################## BC:Z:NNNNNCCN RG:Z:HiMom.7
-HiMom:7:1:1:132 516 * 0 0 * * 0 0 ..A..G.GGG...G...G.GG...G..... ############################## BC:Z:NNNNNTGN RG:Z:HiMom.7
-HiMom:7:1:1:1320 516 * 0 0 * * 0 0 ..A..T.AGT...G...G.TA...C..... ############################## BC:Z:NNNNNCGN RG:Z:HiMom.7
-HiMom:7:1:1:1372 516 * 0 0 * * 0 0 .ACATTTTTTAG.T.A.TTGTT.AC.A... ############################## BC:Z:NNNGNTTA RG:Z:HiMom.7
-HiMom:7:1:1:1379 516 * 0 0 * * 0 0 .AATATAATT...T...TTAGA.TT..... ############################## BC:Z:NNNCNGAT RG:Z:HiMom.7
-HiMom:7:1:1:1391 516 * 0 0 * * 0 0 ..G..T.TAA...A...T.AT...T..... ############################## BC:Z:NNNNNAGN RG:Z:HiMom.7
-HiMom:7:1:1:140 516 * 0 0 * * 0 0 ..A..T.TAA...G...C.TT...T..... ############################## BC:Z:NNNNNCAN RG:Z:HiMom.7
-HiMom:7:1:1:1513 516 * 0 0 * * 0 0 .....A..TT...A...A.AA...C..... ############################## BC:Z:NNNNNCTN RG:Z:HiMom.7
-HiMom:7:1:1:1521 516 * 0 0 * * 0 0 .AACAA.ATT...T...A.TA..TA..... ############################## BC:Z:NNNNNCCN RG:Z:HiMom.7
-HiMom:7:1:1:155 516 * 0 0 * * 0 0 ..G..C.AGT...C...A.TT...G..... ############################## BC:Z:NNNNNCAN RG:Z:HiMom.7
-HiMom:7:1:1:1555 516 * 0 0 * * 0 0 ..T..G.AGA...A...C.TA...A..... ############################## BC:Z:NNNNNCAN RG:Z:HiMom.7
-HiMom:7:1:1:164 516 * 0 0 * * 0 0 ..A..A.TAA...T...T.AT...T..... ############################## BC:Z:NNNNNTTN RG:Z:HiMom.7
-HiMom:7:1:1:1684 516 * 0 0 * * 0 0 ..G..A.GGT...G...T.TC...T..... ############################## BC:Z:NNNNNCGN RG:Z:HiMom.7
-HiMom:7:1:1:1696 516 * 0 0 * * 0 0 ..A..G..GC...G...A.AC...T..... ############################## BC:Z:NNNNNCTN RG:Z:HiMom.7
-HiMom:7:1:1:170 516 * 0 0 * * 0 0 ..T..C.CAC...G...G.TC...G..... ############################## BC:Z:NNNNNACN RG:Z:HiMom.7
-HiMom:7:1:1:173 516 * 0 0 * * 0 0 .....A..AT...T...C.TT...T..... ############################## BC:Z:NNNNNCCN RG:Z:HiMom.7
-HiMom:7:1:1:1733 516 * 0 0 * * 0 0 ..A..G.GTC...T...T.AG...A..... ############################## BC:Z:NNNNNGAN RG:Z:HiMom.7
-HiMom:7:1:1:1770 516 * 0 0 * * 0 0 ..C..T.CTG...G...G.CA...A..... ############################## BC:Z:NNNNNTCN RG:Z:HiMom.7
-HiMom:7:1:1:18 516 * 0 0 * * 0 0 .ATCAG.CTG...A...T.GT..AA..... ############################## BC:Z:NNNNNCGN RG:Z:HiMom.7
-HiMom:7:1:1:1815 516 * 0 0 * * 0 0 .ATGAAAATA...T...TAAAT.AT..... ############################## BC:Z:NNNTNGAC RG:Z:HiMom.7
-HiMom:7:1:1:1836 516 * 0 0 * * 0 0 .....G..TA...G...T.CT...C..... ############################## BC:Z:NNNNNGTN RG:Z:HiMom.7
-HiMom:7:1:1:184 516 * 0 0 * * 0 0 ..C..T.TAA...A...T.AT...G..... ############################## BC:Z:NNNNNGTN RG:Z:HiMom.7
-HiMom:7:1:1:1886 4 * 0 0 * * 0 0 .ACATATGCATACATATATAATAGATA... %.9:;<217;:999;<;;<<<;;####### BC:Z:NNNGNGCC RG:Z:HiMom.7
-HiMom:7:1:1:1906 516 * 0 0 * * 0 0 ..T..C.ATA...C...T.CT...G..... ############################## BC:Z:NNNNNCGN RG:Z:HiMom.7
-HiMom:7:1:1:1917 516 * 0 0 * * 0 0 .....T..GA...C...A.AA...A..... ############################## BC:Z:NNNNNACN RG:Z:HiMom.7
-HiMom:7:1:1:195 516 * 0 0 * * 0 0 ..A..G.GTG...G...C.AT...A..... ############################## BC:Z:NNNNNCGN RG:Z:HiMom.7
-HiMom:7:1:1:1954 516 * 0 0 * * 0 0 .AGA.T.CTT...G...G.AG...C..... ############################## BC:Z:NNNNNCCN RG:Z:HiMom.7
-HiMom:7:1:1:2 516 * 0 0 * * 0 0 ..A..G.GAA...C................ ############################## BC:Z:NNNNNNNN RG:Z:HiMom.7
-HiMom:7:1:1:2011 516 * 0 0 * * 0 0 .ACAGCTGGCA..T...AGAGC.AG.A... ############################## BC:Z:NNNGNTAG RG:Z:HiMom.7
-HiMom:7:1:1:240 516 * 0 0 * * 0 0 ..G..A.GTA...T...T.CC...C..... ############################## BC:Z:NNNNNGAN RG:Z:HiMom.7
-HiMom:7:1:1:262 516 * 0 0 * * 0 0 ..C..G.CAT...A...C.TG...C..... ############################## BC:Z:NNNNNCAN RG:Z:HiMom.7
-HiMom:7:1:1:264 516 * 0 0 * * 0 0 .AACTG.AAT...C...A.CA..CT..... ############################## BC:Z:NNNNNCGA RG:Z:HiMom.7
-HiMom:7:1:1:299 516 * 0 0 * * 0 0 ..C..T.GCA...A...C.AA...T..... ############################## BC:Z:NNNNNCGN RG:Z:HiMom.7
-HiMom:7:1:1:30 516 * 0 0 * * 0 0 ..A..A.TTT...T...G.TC...T..... ############################## BC:Z:NNNNNACN RG:Z:HiMom.7
-HiMom:7:1:1:353 516 * 0 0 * * 0 0 ..A..T.TAG...A...T.AT...A..... ############################## BC:Z:NNNNNCGN RG:Z:HiMom.7
-HiMom:7:1:1:367 516 * 0 0 * * 0 0 ..A..T.AGC...G...A.GT...C..... ############################## BC:Z:NNNNNAGN RG:Z:HiMom.7
-HiMom:7:1:1:41 516 * 0 0 * * 0 0 ..A..C.AAA...G...T.CA...C..... ############################## BC:Z:NNNNNGAN RG:Z:HiMom.7
-HiMom:7:1:1:416 516 * 0 0 * * 0 0 ..A..C.AAT...G...G.AC...C..... ############################## BC:Z:NNNNNGAN RG:Z:HiMom.7
-HiMom:7:1:1:483 516 * 0 0 * * 0 0 ..G..G.GGG...G...G.TT...T..... ############################## BC:Z:NNNNNTAN RG:Z:HiMom.7
-HiMom:7:1:1:486 516 * 0 0 * * 0 0 ..A..A.TTT...A...A.AG...T..... ############################## BC:Z:NNNNNTGN RG:Z:HiMom.7
-HiMom:7:1:1:495 516 * 0 0 * * 0 0 ..C..A.CGT...T...T.AA...C..... ############################## BC:Z:NNNNNGAN RG:Z:HiMom.7
-HiMom:7:1:1:508 516 * 0 0 * * 0 0 ..G..C.CAG...T...C.CT...C..... ############################## BC:Z:NNNNNCTN RG:Z:HiMom.7
-HiMom:7:1:1:517 516 * 0 0 * * 0 0 .TCATAAAACATCA.TATTGGAAAGGA... %.75:<999578################## BC:Z:NNNCNAGA RG:Z:HiMom.7
-HiMom:7:1:1:535 516 * 0 0 * * 0 0 .GCCCAAGTATTGA.TATGTGCTCTAA... %.599:7187:940%0::52599####### BC:Z:NNNCNCGA RG:Z:HiMom.7
-HiMom:7:1:1:55 516 * 0 0 * * 0 0 .TTTATGTCCTT.A.AACTTAG.AGTT... %/9<<83599#################### BC:Z:NNNGNTTA RG:Z:HiMom.7
-HiMom:7:1:1:554 516 * 0 0 * * 0 0 ..A..G.AGA...G...T.TC...A..... ############################## BC:Z:NNNNNTAN RG:Z:HiMom.7
-HiMom:7:1:1:567 516 * 0 0 * * 0 0 ..C..C.GTT...C...G.AC...C..... ############################## BC:Z:NNNNNCCN RG:Z:HiMom.7
-HiMom:7:1:1:59 516 * 0 0 * * 0 0 ..A..G.TGC...T...T.AC...A..... ############################## BC:Z:NNNNNACN RG:Z:HiMom.7
-HiMom:7:1:1:613 516 * 0 0 * * 0 0 ..G..A.TAT...C...G.AT...A..... ############################## BC:Z:NNNNNAGN RG:Z:HiMom.7
-HiMom:7:1:1:622 516 * 0 0 * * 0 0 ..T..C.AGT...C...A.CT...T..... ############################## BC:Z:NNNNNAGN RG:Z:HiMom.7
-HiMom:7:1:1:627 516 * 0 0 * * 0 0 ..A..T.GAC...T...A.GC...C..... ############################## BC:Z:NNNNNGAN RG:Z:HiMom.7
-HiMom:7:1:1:684 516 * 0 0 * * 0 0 ..T..T.AGA...C...A.AG...A..... ############################## BC:Z:NNNNNGAN RG:Z:HiMom.7
-HiMom:7:1:1:72 516 * 0 0 * * 0 0 .ACACACATATCAC.CACATCATACAC... %..48696;5:6;.%)49;;;9######## BC:Z:NNNTNGAC RG:Z:HiMom.7
-HiMom:7:1:1:812 516 * 0 0 * * 0 0 ..A..C.AAG...T...A.TC...A..... ############################## BC:Z:NNNNNGAN RG:Z:HiMom.7
-HiMom:7:1:1:874 516 * 0 0 * * 0 0 ..A..A.GCC...G...T.TA...T..... ############################## BC:Z:NNNNNGTN RG:Z:HiMom.7
-HiMom:7:1:1:931 516 * 0 0 * * 0 0 ..T..G.GAT...G...C.TT...C..... ############################## BC:Z:NNNNNCAN RG:Z:HiMom.7
-HiMom:7:1:1:965 516 * 0 0 * * 0 0 .ACTAATCTTCCGC.CATATCCCCAAA... ############################## BC:Z:NNNTNTAA RG:Z:HiMom.7
-HiMom:7:1:1:994 516 * 0 0 * * 0 0 ..A..T.GAT...T...G.TT...C..... ############################## BC:Z:NNNNNCGN RG:Z:HiMom.7
-HiMom:7:1:2:1158 4 * 0 0 * * 0 0 .GGGTCCTTCATAGTTTTTTTCTACTTTCC %0777646;099:::95;;;688::99### BC:Z:NNCTTAGC RG:Z:HiMom.7
-HiMom:7:1:2:1238 516 * 0 0 * * 0 0 .TCCTTATATTCAATTATTAATATTTTTAC ############################## BC:Z:NNCTAAGC RG:Z:HiMom.7
-HiMom:7:1:2:1275 4 * 0 0 * * 0 0 .AGTGAAATAAGCCAGACACAGAAAGACA. %/5204:99971773,44755-39717### BC:Z:NNNANCTG RG:Z:HiMom.7
-HiMom:7:1:2:1301 516 * 0 0 * * 0 0 .AGTAGACTGCATTAATTAATTGGAAGAG. %0370)024263144:48;;########## BC:Z:NNNTAACA RG:Z:HiMom.7
-HiMom:7:1:2:1453 4 * 0 0 * * 0 0 .ATATCTTATTTTCTTTTCTTTCAGGCTCT %.:7,,395255################## BC:Z:NNACCAGG RG:Z:HiMom.7
-HiMom:7:1:2:150 516 * 0 0 * * 0 0 .AAGACTTGATTATATCCCTTGTATGA... ############################## BC:Z:NNNANCCT RG:Z:HiMom.7
-HiMom:7:1:2:1592 4 * 0 0 * * 0 0 .GAAAACTGGCACAAGACAAGGATGCCCTC %,67786861,3466(8485868648583# BC:Z:NNNGAGCC RG:Z:HiMom.7
-HiMom:7:1:2:1706 4 * 0 0 * * 0 0 .GATATGTGGATACAGCTCACAAAGAG... %,99:6/566999/7############### BC:Z:NNNCNGAT RG:Z:HiMom.7
-HiMom:7:1:2:1722 516 * 0 0 * * 0 0 .AAAGAAAATTAAAGAAAAATATACACGT. ############################## BC:Z:NNNTCGAC RG:Z:HiMom.7
-HiMom:7:1:2:1727 516 * 0 0 * * 0 0 .TATTGAAGGACTTTTGTATCCTCCTTAT. ############################## BC:Z:NNNTNCTT RG:Z:HiMom.7
-HiMom:7:1:2:1753 516 * 0 0 * * 0 0 .GTTCACACAAGGATAATATTTTTGATTAT ############################## BC:Z:NNTGCTTA RG:Z:HiMom.7
-HiMom:7:1:2:1782 4 * 0 0 * * 0 0 .ACCAAGTGTTTGGAGTATGCTGCCTA... %0:::668885-5335/85########### BC:Z:NNNTNAGC RG:Z:HiMom.7
-HiMom:7:1:2:1827 4 * 0 0 * * 0 0 .AACCGAGGATGTACACTGTCCCTGTGAAA ############################## BC:Z:NNCAACTG RG:Z:HiMom.7
-HiMom:7:1:2:1932 4 * 0 0 * * 0 0 .AGCGATCCTCCCGCCTCTGCCTCCCA... %,1545541455################## BC:Z:NNNCNAGA RG:Z:HiMom.7
-HiMom:7:1:2:1946 516 * 0 0 * * 0 0 .ATCTTCTGGAATTTCTAACAGCTTGGAA. %0515.,.35<997################ BC:Z:NNNTNGAC RG:Z:HiMom.7
-HiMom:7:1:2:209 516 * 0 0 * * 0 0 .GACTCAACTCCTGGGCTCCCTACGACCAT ############################## BC:Z:NNCATTTC RG:Z:HiMom.7
-HiMom:7:1:2:246 516 * 0 0 * * 0 0 .GGAGGTTTCATTTAGCCGATATTGTG... ############################## BC:Z:NNNANTTC RG:Z:HiMom.7
-HiMom:7:1:2:25 516 * 0 0 * * 0 0 .GCTTTGGCAAGACAAATCTCCCGTCTGG. ############################## BC:Z:NNNGATGA RG:Z:HiMom.7
-HiMom:7:1:2:307 516 * 0 0 * * 0 0 .GGATGAACAGAAACTAAAATAACACA... ############################## BC:Z:NNNTNGAC RG:Z:HiMom.7
-HiMom:7:1:2:363 516 * 0 0 * * 0 0 .ATATTCTTTTTTTTTATTTATCAGAT... ############################## BC:Z:NNNTNCTT RG:Z:HiMom.7
-HiMom:7:1:2:449 516 * 0 0 * * 0 0 .ATTCTAATTCTAGGAAATTAACAATC... %.9315<936970%0############### BC:Z:NNNGNTGT RG:Z:HiMom.7
-HiMom:7:1:2:546 516 * 0 0 * * 0 0 .GGTTGTGTCTCTCTCAGCCTTTGGGATC. %,46888444685-35############## BC:Z:NNNANGTT RG:Z:HiMom.7
-HiMom:7:1:2:605 4 * 0 0 * * 0 0 .GCATTGAGCAGACGTGGCATCCAGAT... %)085222/55453################ BC:Z:NNNTNGAC RG:Z:HiMom.7
-HiMom:7:1:2:69 516 * 0 0 * * 0 0 .TCAGTCTGCTGTTTTAAAAAAATACTGTG ############################## BC:Z:NNGGAGCC RG:Z:HiMom.7
-HiMom:7:1:2:747 516 * 0 0 * * 0 0 .AACAACAGCGGAAAATAATAAAAAAAAA. ############################## BC:Z:NNNCCAGG RG:Z:HiMom.7
-HiMom:7:1:2:786 4 * 0 0 * * 0 0 .TAAACAATAATCTGATGATTTATAATCC. %09<<<<;<;<8<9;<9<;<::<<::#### BC:Z:NNNGATGT RG:Z:HiMom.7
-HiMom:7:1:2:858 4 * 0 0 * * 0 0 .AAACGTTGCTGATCTTCTGTTTTAAACTA %/;7-222265366-6977035:::;626; BC:Z:NNACATCT RG:Z:HiMom.7
-HiMom:7:1:2:943 4 * 0 0 * * 0 0 .AATACCAATAAACCTAGAATGTCTCATAC %08<9646<6378744774:1005799<4# BC:Z:NNACCAGG RG:Z:HiMom.7
-HiMom:7:1:2:974 4 * 0 0 * * 0 0 .GATCAATGATCACATCTTTGGATATGTAT %/9979<99:999::9;;:7511<<<77<< BC:Z:NNTATGTT RG:Z:HiMom.7
-HiMom:7:1:2:988 4 * 0 0 * * 0 0 .AAAGGAATGTTCAGCTCTGTGAGTTGAAC %/92/04:2-2785-3875/404362-162 BC:Z:NNTGGCGA RG:Z:HiMom.7
-HiMom:7:1:3:1233 516 * 0 0 * * 0 0 .AACCAATTTCTTTACATACCAAATACGCC ############################## BC:Z:CCAACAGG RG:Z:HiMom.7
-HiMom:7:1:3:1294 516 * 0 0 * * 0 0 TGTAACTTTACTTTAGTTGCTTATTTGTAG BA############################ BC:Z:TCACAATG RG:Z:HiMom.7
-HiMom:7:1:3:405 516 * 0 0 * * 0 0 AAAAAACATAGAACGGGGTCAATATTTTAT (?A>8(7B?<(:')?@)8(:(*:<8:0>'> BC:Z:ACACAAGA RG:Z:HiMom.7
-HiMom:7:1:3:579 516 * 0 0 * * 0 0 .GAAAAATGACCACACTTGCCTCCTGAGAA ############################## BC:Z:AATCATGT RG:Z:HiMom.7
-HiMom:7:1:3:673 516 * 0 0 * * 0 0 TCCTCAAAAACAAGATAAAACGGTTGAAAT >()>)''85BBC?################# BC:Z:TGCCCAAA RG:Z:HiMom.7
-HiMom:7:1:3:890 516 * 0 0 * * 0 0 TGCTTCTGTTTCCGTTAGCTAGATAAAGTT ############################## BC:Z:GTCACCAT RG:Z:HiMom.7
-HiMom:7:1:3:905 516 * 0 0 * * 0 0 TGTTATGTTTAATTTTCTTTAGCACCCTTC >7>?A:-<BA at 0>@:@8=A;5%7;9?=:9@ BC:Z:ACATCCTA RG:Z:HiMom.7
-HiMom:7:1:3:918 516 * 0 0 * * 0 0 TTTTCATTCCTAGTCATCCACCCCATCAGA 0()@A=:2>3:>(/((<22A>:0(20:@)@ BC:Z:ACTACCTT RG:Z:HiMom.7
-HiMom:7:2:0:1073 516 * 0 0 * * 0 0 .....A.CAC...C...C.CA...C..... ############################## BC:Z:NNNNNCAN RG:Z:HiMom.7
-HiMom:7:2:0:1135 516 * 0 0 * * 0 0 .....G..GT...A...T.TA...G..... ############################## BC:Z:NNNNNAGN RG:Z:HiMom.7
-HiMom:7:2:0:1198 516 * 0 0 * * 0 0 .....T.CTA...T...C.CA...A..... ############################## BC:Z:NNNNNCCN RG:Z:HiMom.7
-HiMom:7:2:0:1278 516 * 0 0 * * 0 0 ........TA...T...C..A...G..... ############################## BC:Z:NNNNNTAN RG:Z:HiMom.7
-HiMom:7:2:0:135 516 * 0 0 * * 0 0 ........A...........G......... ############################## BC:Z:NNNNNCGN RG:Z:HiMom.7
-HiMom:7:2:0:1547 516 * 0 0 * * 0 0 ........C...........G...A..... ############################## BC:Z:NNNNNCAN RG:Z:HiMom.7
-HiMom:7:2:0:1598 516 * 0 0 * * 0 0 ........AT...T...A..G...C..... ############################## BC:Z:NNNNNAGN RG:Z:HiMom.7
-HiMom:7:2:0:1620 516 * 0 0 * * 0 0 ........CA.......A..C...C..... ############################## BC:Z:NNNNNTGN RG:Z:HiMom.7
-HiMom:7:2:0:1668 516 * 0 0 * * 0 0 .....A.ATA...A...G.TG...T..... ############################## BC:Z:NNNNNCTN RG:Z:HiMom.7
-HiMom:7:2:0:186 516 * 0 0 * * 0 0 ........CC...A...T..T...T..... ############################## BC:Z:NNNNNCCN RG:Z:HiMom.7
-HiMom:7:2:0:205 516 * 0 0 * * 0 0 ........A........T..C...T..... ############################## BC:Z:NNNNNAGN RG:Z:HiMom.7
-HiMom:7:2:0:287 516 * 0 0 * * 0 0 ........CC...C...T..A...A..... ############################## BC:Z:NNNNNGAN RG:Z:HiMom.7
-HiMom:7:2:0:382 516 * 0 0 * * 0 0 ........CA...T...T..A...A..... ############################## BC:Z:NNNNNTAN RG:Z:HiMom.7
-HiMom:7:2:0:441 516 * 0 0 * * 0 0 ........TT...A...A..T...T..... ############################## BC:Z:NNNNNAGN RG:Z:HiMom.7
-HiMom:7:2:0:50 516 * 0 0 * * 0 0 ........T........T..G...G..... ############################## BC:Z:NNNNNGAN RG:Z:HiMom.7
-HiMom:7:2:0:501 516 * 0 0 * * 0 0 .....G..AG...A...C.CT...C..... ############################## BC:Z:NNNNNTAN RG:Z:HiMom.7
-HiMom:7:2:0:73 516 * 0 0 * * 0 0 .....A.CAT...G...A.AC...G..... ############################## BC:Z:NNNNNCGN RG:Z:HiMom.7
-HiMom:7:2:0:740 516 * 0 0 * * 0 0 ........TT...A...T..A...A..... ############################## BC:Z:NNNNNGGN RG:Z:HiMom.7
-HiMom:7:2:0:766 516 * 0 0 * * 0 0 ........TG...A...A..T...T..... ############################## BC:Z:NNNNNCCN RG:Z:HiMom.7
-HiMom:7:2:0:87 516 * 0 0 * * 0 0 ........G........A..T...T..... ############################## BC:Z:NNNNNCGN RG:Z:HiMom.7
-HiMom:7:2:1:1004 516 * 0 0 * * 0 0 .ATTTATCACTA.A.ATCCGCAAACCCTCC ############################## BC:Z:NNNGCCGA RG:Z:HiMom.7
-HiMom:7:2:1:1034 516 * 0 0 * * 0 0 .ATCATTTTCAT.C.TTTCACTGATACATT %.737:887471%-%1:8555545;696:: BC:Z:NNNAGCCT RG:Z:HiMom.7
-HiMom:7:2:1:1159 516 * 0 0 * * 0 0 ..ACTT.TAG...G...AAAT..CC.A... ############################## BC:Z:NNNTNGAC RG:Z:HiMom.7
-HiMom:7:2:1:1168 516 * 0 0 * * 0 0 ..TCTA.CTT...T...ATTG..TT.T... ############################## BC:Z:NNNGNTAG RG:Z:HiMom.7
-HiMom:7:2:1:1180 516 * 0 0 * * 0 0 ..ATGG.CTT...C...AGAA..TC.A... ############################## BC:Z:NNNTNAGC RG:Z:HiMom.7
-HiMom:7:2:1:1214 516 * 0 0 * * 0 0 .AAAAAAAAAAA.A.TATAAGAAAGAATCA %035:######################### BC:Z:NNNCATGA RG:Z:HiMom.7
-HiMom:7:2:1:1221 516 * 0 0 * * 0 0 .GGTCACACTCACATAGTGTTCAGAGCACT ############################## BC:Z:NNGGATGT RG:Z:HiMom.7
-HiMom:7:2:1:1306 516 * 0 0 * * 0 0 ..ACAT.AAA...T...AACA..GT.A... ############################## BC:Z:NNNANCTG RG:Z:HiMom.7
-HiMom:7:2:1:1351 516 * 0 0 * * 0 0 .....C.ATA...T...A.AA...T..... ############################## BC:Z:NNNNNTTN RG:Z:HiMom.7
-HiMom:7:2:1:1424 516 * 0 0 * * 0 0 ..TCAT.TAG...C...ATGG..GT.C... ############################## BC:Z:NNNCNTCT RG:Z:HiMom.7
-HiMom:7:2:1:1452 516 * 0 0 * * 0 0 .GAAATTTGTAAAA.CACCTGCAGAATACT ############################## BC:Z:NNAGATCC RG:Z:HiMom.7
-HiMom:7:2:1:1515 516 * 0 0 * * 0 0 .ATTAAATAT.A.A..GTAATAATAATA.. %/9########################### BC:Z:NNNGNATG RG:Z:HiMom.7
-HiMom:7:2:1:1521 516 * 0 0 * * 0 0 ..ACAC.AAA...G...ATCT..TT.C... ############################## BC:Z:NNNCNAGG RG:Z:HiMom.7
-HiMom:7:2:1:1536 516 * 0 0 * * 0 0 .AGCAAAGACTT.G.ACCAACCCAAATGTT ############################## BC:Z:NNACATCT RG:Z:HiMom.7
-HiMom:7:2:1:1543 516 * 0 0 * * 0 0 ..TTGA.ATC...A...AATA..TA.C... ############################## BC:Z:NNNANTTC RG:Z:HiMom.7
-HiMom:7:2:1:1617 516 * 0 0 * * 0 0 ..CCAT.ATC...G...CCAG..GT.T... ############################## BC:Z:NNNCNAGG RG:Z:HiMom.7
-HiMom:7:2:1:1627 516 * 0 0 * * 0 0 ..TGGT.AGA...C...AAAA..CA.T... ############################## BC:Z:NNNANCTG RG:Z:HiMom.7
-HiMom:7:2:1:1646 516 * 0 0 * * 0 0 .TTAATTATA...A..TAAACATTCTAA.. ############################## BC:Z:NNNTNGAC RG:Z:HiMom.7
-HiMom:7:2:1:1653 516 * 0 0 * * 0 0 ..AATT.AAA...T...ATCT..AG.A... ############################## BC:Z:NNNGNTGT RG:Z:HiMom.7
-HiMom:7:2:1:1682 516 * 0 0 * * 0 0 ..TCTT.TTT...G...AAAA..AA.T... ############################## BC:Z:NNNGNGCC RG:Z:HiMom.7
-HiMom:7:2:1:170 4 * 0 0 * * 0 0 .AGAAGAAATGGGATCCTGCTGTGGCCAGT %/888865284168866767663(6874/5 BC:Z:NNGAGCCT RG:Z:HiMom.7
-HiMom:7:2:1:1731 516 * 0 0 * * 0 0 ..TATA.GAA...T...TGCT..AG.T... ############################## BC:Z:NNNTNAGC RG:Z:HiMom.7
-HiMom:7:2:1:1755 516 * 0 0 * * 0 0 ..GT.A.TCT...C...C.TG...G.A... ############################## BC:Z:NNNNNCAN RG:Z:HiMom.7
-HiMom:7:2:1:1812 516 * 0 0 * * 0 0 ..TTGC.CAC...C...CCAT..AA.G... ############################## BC:Z:NNNCNTAT RG:Z:HiMom.7
-HiMom:7:2:1:1853 516 * 0 0 * * 0 0 ..ATCT.TTC...A...AGTG..AT.C... ############################## BC:Z:NNNCNCGA RG:Z:HiMom.7
-HiMom:7:2:1:1919 516 * 0 0 * * 0 0 ..AATT.AAA...A...AGAA..AG.A... ############################## BC:Z:NNNANCTG RG:Z:HiMom.7
-HiMom:7:2:1:1924 516 * 0 0 * * 0 0 .ATATTCTGAAG.A..CCAATGAACCAAA. %116<9579<7################### BC:Z:NNNAACTG RG:Z:HiMom.7
-HiMom:7:2:1:1933 516 * 0 0 * * 0 0 .AGGGTACAT.T.C..AATGTGCGGGTT.. ############################## BC:Z:NNNTTAGC RG:Z:HiMom.7
-HiMom:7:2:1:1938 4 * 0 0 * * 0 0 .AGTCCAGTGTCTCTGCTTCCGCAGGGACA %/818865/058858644866457646668 BC:Z:NNCTCGAC RG:Z:HiMom.7
-HiMom:7:2:1:1950 516 * 0 0 * * 0 0 ..TT.A.AAA...C...T.CA...T.C... ############################## BC:Z:NNNNNGTN RG:Z:HiMom.7
-HiMom:7:2:1:1959 516 * 0 0 * * 0 0 .GACACATTCCTAC.ACAGAGAAAAATTTA %*77;;<;<<:<;,%.::;:6:9::<4488 BC:Z:NNTGCTTA RG:Z:HiMom.7
-HiMom:7:2:1:1987 516 * 0 0 * * 0 0 ..AT.G.ACA...C...T.GT...T..... ############################## BC:Z:NNNNNTAN RG:Z:HiMom.7
-HiMom:7:2:1:2006 516 * 0 0 * * 0 0 ..GTAT.TGA...G...CCTT..AG.A... ############################## BC:Z:NNNGNGCC RG:Z:HiMom.7
-HiMom:7:2:1:211 516 * 0 0 * * 0 0 ..CTGA.ACA...G...TGCA..AC.C... ############################## BC:Z:NNNGNTGT RG:Z:HiMom.7
-HiMom:7:2:1:234 516 * 0 0 * * 0 0 .AAGCCTGTGGG.A..CCCAGTGGGAGCG. ############################## BC:Z:NNNGCTTA RG:Z:HiMom.7
-HiMom:7:2:1:242 516 * 0 0 * * 0 0 ..GCTC.AGC...A...ATAT..TT.G... ############################## BC:Z:NNNCNCGC RG:Z:HiMom.7
-HiMom:7:2:1:262 516 * 0 0 * * 0 0 ..ATTG.AAT...C...TTCC..AT.T... ############################## BC:Z:NNNCNAGG RG:Z:HiMom.7
-HiMom:7:2:1:298 516 * 0 0 * * 0 0 ..TCAA.TTG...T...CTGC..TT.T... ############################## BC:Z:NNNGNTAG RG:Z:HiMom.7
-HiMom:7:2:1:312 516 * 0 0 * * 0 0 ..TTGC.AGA...A...AACT..TG.A... ############################## BC:Z:NNNANGTT RG:Z:HiMom.7
-HiMom:7:2:1:363 4 * 0 0 * * 0 0 .GAAAGGTTTTGCAGCATGTGCAAACTCAC %-5565678:8177656503512/377856 BC:Z:NNTATGTT RG:Z:HiMom.7
-HiMom:7:2:1:37 516 * 0 0 * * 0 0 .TGTAAACGA...C..TTCCTGTTCAGC.. ############################## BC:Z:NNNGNCGA RG:Z:HiMom.7
-HiMom:7:2:1:370 516 * 0 0 * * 0 0 ..CTGG.AGC...T...CATA..AA.C... ############################## BC:Z:NNNANCAT RG:Z:HiMom.7
-HiMom:7:2:1:377 516 * 0 0 * * 0 0 ..AGAA.GTG...T...AAAT..AA.A... ############################## BC:Z:NNNCNTCT RG:Z:HiMom.7
-HiMom:7:2:1:414 516 * 0 0 * * 0 0 ..TAGA.AGC...A...TCAG..AC.G... ############################## BC:Z:NNNGNTTA RG:Z:HiMom.7
-HiMom:7:2:1:421 516 * 0 0 * * 0 0 ..GTTA.TTC...A...CGTG..AT.C... ############################## BC:Z:NNNANCCT RG:Z:HiMom.7
-HiMom:7:2:1:428 516 * 0 0 * * 0 0 .ATGTGAATA.T.A..TAGTTGGGATTCA. ############################## BC:Z:NNNATGTT RG:Z:HiMom.7
-HiMom:7:2:1:44 516 * 0 0 * * 0 0 .ACTACCTCA.G.A..AAGCAGGTTCTAA. ############################## BC:Z:NNNAGCGA RG:Z:HiMom.7
-HiMom:7:2:1:466 516 * 0 0 * * 0 0 .ACACTCACA.C.A..TGTTTGGAATGA.. ############################## BC:Z:NNNTNACA RG:Z:HiMom.7
-HiMom:7:2:1:555 516 * 0 0 * * 0 0 ..CAAT.TCT...G...TACA..CT.C... ############################## BC:Z:NNNCNGAT RG:Z:HiMom.7
-HiMom:7:2:1:558 516 * 0 0 * * 0 0 .AAAATATCA.T.A..AATAAATAATCA.. ############################## BC:Z:NNNANCGA RG:Z:HiMom.7
-HiMom:7:2:1:56 516 * 0 0 * * 0 0 ..GCCA.GGT...A...TCAC..GG.C... ############################## BC:Z:NNNTNAGC RG:Z:HiMom.7
-HiMom:7:2:1:569 516 * 0 0 * * 0 0 ..AGGC.AGT...G...GTCC..GT.A... ############################## BC:Z:NNNANCTG RG:Z:HiMom.7
-HiMom:7:2:1:604 516 * 0 0 * * 0 0 .ATGATGAAACTCT.TCTCTACTAAAAATA ############################## BC:Z:NNCAACTG RG:Z:HiMom.7
-HiMom:7:2:1:628 516 * 0 0 * * 0 0 .AGTATGCCC.C.C..ACCACTCCTATT.. ############################## BC:Z:NNNTAACA RG:Z:HiMom.7
-HiMom:7:2:1:64 516 * 0 0 * * 0 0 .ATTAATCTT...T..GCACAATTCATT.. ############################## BC:Z:NNNANGTT RG:Z:HiMom.7
-HiMom:7:2:1:684 516 * 0 0 * * 0 0 .AAAAATCAAATGA.CATAATTTTATAAAA ############################## BC:Z:NNAAACGA RG:Z:HiMom.7
-HiMom:7:2:1:699 516 * 0 0 * * 0 0 ..AATT.TTG...T...ATTT..GA.T... ############################## BC:Z:NNNCNCGA RG:Z:HiMom.7
-HiMom:7:2:1:714 516 * 0 0 * * 0 0 .ATTAACTTA.A.T..ACCACAACCTAA.. %.:########################### BC:Z:NNNAGCGA RG:Z:HiMom.7
-HiMom:7:2:1:722 516 * 0 0 * * 0 0 ..CCTC.CTG...C...CTGT..TG.C... ############################## BC:Z:NNNCNAGG RG:Z:HiMom.7
-HiMom:7:2:1:749 516 * 0 0 * * 0 0 ..AGTG.TAC...T...CTTG..CT.T... ############################## BC:Z:NNNTNGAC RG:Z:HiMom.7
-HiMom:7:2:1:760 516 * 0 0 * * 0 0 .GTCTGTTTTATGT.AAATATTTTGTTTAA ############################## BC:Z:NNACAACA RG:Z:HiMom.7
-HiMom:7:2:1:8 516 * 0 0 * * 0 0 ..TGCG.TGG...C...AGGC..TT.T... ############################## BC:Z:NNNANNNN RG:Z:HiMom.7
-HiMom:7:2:1:833 516 * 0 0 * * 0 0 ..GAGC.CCT...A...CTCC..GA.G... ############################## BC:Z:NNNANCCT RG:Z:HiMom.7
-HiMom:7:2:1:848 516 * 0 0 * * 0 0 ..TACT.AGT...G...TGTT..GC.T... ############################## BC:Z:NNNANCGA RG:Z:HiMom.7
-HiMom:7:2:1:893 516 * 0 0 * * 0 0 .GAGACAGAGTCTC.CTCTGTTCCCTAGCC ############################## BC:Z:NNCAATTC RG:Z:HiMom.7
-HiMom:7:2:1:998 516 * 0 0 * * 0 0 ..ATGT.TGC...A...TATA..GG.A... ############################## BC:Z:NNNANGTT RG:Z:HiMom.7
-HiMom:7:2:2:0 516 * 0 0 * * 0 0 .ATTCCTT.A.................... ############################## BC:Z:NNNNNNNN RG:Z:HiMom.7
-HiMom:7:2:2:131 4 * 0 0 * * 0 0 .ATATATTGACAGCAGTCATGTTGTTGAAG %0<<<:<959874492:96999969:7784 BC:Z:CACAATCC RG:Z:HiMom.7
-HiMom:7:2:2:1636 516 * 0 0 * * 0 0 .GTGTAAAAGTAGGGAAATACTATAGCAAG ############################## BC:Z:ATCAACCC RG:Z:HiMom.7
-HiMom:7:2:2:1974 516 * 0 0 * * 0 0 .ACGCCAATACAAAAATGTTGAAGCTAGCT ############################## BC:Z:AGCAATCT RG:Z:HiMom.7
-HiMom:7:2:2:351 516 * 0 0 * * 0 0 .GGGGTTGAGGTGTAAATAGAACATTTGTA ############################## BC:Z:TGATAGAA RG:Z:HiMom.7
-HiMom:7:2:2:646 516 * 0 0 * * 0 0 .GAATCTAAGAAGACACAAAACTAAGGAAA ############################## BC:Z:ATCAATTA RG:Z:HiMom.7
-HiMom:7:2:2:828 516 * 0 0 * * 0 0 .TCAAGTCAATTTGGGACTTGAAACAGCTC ############################## BC:Z:TATATCGA RG:Z:HiMom.7
-HiMom:7:2:3:1529 516 * 0 0 * * 0 0 .TTATATGAATAGATAAATAAATAATCAAT ############################## BC:Z:TAGAACCT RG:Z:HiMom.7
-HiMom:7:2:3:179 516 * 0 0 * * 0 0 CATTATTGTTAGACTGATTTTTTATAATCT B@)104..*0-A(@@(<A9A<(+9)-=6(B BC:Z:GTTTATTA RG:Z:HiMom.7
-HiMom:7:2:3:198 516 * 0 0 * * 0 0 TGTCATTTTCTTTGCCTTAATTGTTCTTCT 5 at CBB7-*<=#################### BC:Z:CAGGATCT RG:Z:HiMom.7
-HiMom:7:2:3:2030 516 * 0 0 * * 0 0 CGAGATAATTTTTTAAAAAAAGTCCAAAAA ((@;()@==*7<(5A@<C>########### BC:Z:GATCAAGA RG:Z:HiMom.7
-HiMom:7:2:3:247 516 * 0 0 * * 0 0 TGTACATGACCAGGTAATTTGGTTATGTGA <@596353;)>@A7=:,A0'6>######## BC:Z:CGGTAGCT RG:Z:HiMom.7
-HiMom:7:2:3:4 516 * 0 0 * * 0 0 AGAGGCAATAAGTTTTAA............ A>BA at 9BAB3AA################## BC:Z:NNNNNNNN RG:Z:HiMom.7
-HiMom:7:2:3:862 516 * 0 0 * * 0 0 .CTTTAAGAAATCATTCATTCTGCAAACAC ############################## BC:Z:TAACAAGA RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/NN.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/NN.sam
deleted file mode 100644
index 64bdb0a..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/NN.sam
+++ /dev/null
@@ -1,225 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.N-N LB:LN_N PI:10025 DS:DESC25 SM:SA_N CN:BI
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-HiMom:9:1:0:1093 516 * 0 0 * * 0 0 .....C..GT...A...G.AA...A..... ############################## BC:Z:NNNNNTGN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:0:113 516 * 0 0 * * 0 0 ........G...........A......... ############################## BC:Z:NNNNNNNN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:0:1193 516 * 0 0 * * 0 0 ........T....T...T..T...C..... ############################## BC:Z:NNNNNGTN-NNNNNGTN RG:Z:HiMom.9
-HiMom:9:1:0:1291 516 * 0 0 * * 0 0 ........A........A..T......... ############################## BC:Z:NNNNNGNN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:0:1307 516 * 0 0 * * 0 0 ........C....A...T..T...C..... ############################## BC:Z:NNNNNTAN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:0:1434 516 * 0 0 * * 0 0 .............................. ############################## BC:Z:NNNNNNNN-NNNNNNNN RG:Z:HiMom.9 XN:i:1
-HiMom:9:1:0:1475 516 * 0 0 * * 0 0 .....G..A....A...A..A...A..... ############################## BC:Z:NNNNNCCN-NNNNNCNN RG:Z:HiMom.9
-HiMom:9:1:0:1690 516 * 0 0 * * 0 0 ........A........G..C...C..... ############################## BC:Z:NNNNNANN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:0:1703 516 * 0 0 * * 0 0 ........A...........A......... ############################## BC:Z:NNNNNNNN-NNNNNNNN RG:Z:HiMom.9 XN:i:1
-HiMom:9:1:0:1940 516 * 0 0 * * 0 0 ........C........T..T......... ############################## BC:Z:NNNNNCNN-NNNNNCNN RG:Z:HiMom.9
-HiMom:9:1:0:2001 516 * 0 0 * * 0 0 .....A..TG...G...A.GC...A..... ############################## BC:Z:NNNNNGAN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:0:205 516 * 0 0 * * 0 0 ........A........A..T...A..... ############################## BC:Z:NNNNNCGN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:0:275 516 * 0 0 * * 0 0 .....A..CA...T...G.CC...A..... ############################## BC:Z:NNNNNATN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:0:324 516 * 0 0 * * 0 0 ........T........T..A...A..... ############################## BC:Z:NNNNNGTN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:0:37 516 * 0 0 * * 0 0 ........A........C..T...C..... ############################## BC:Z:NNNNNGNN-NNNNNGNN RG:Z:HiMom.9
-HiMom:9:1:0:464 516 * 0 0 * * 0 0 .............................. ############################## BC:Z:NNNNNNNN-NNNNNNNN RG:Z:HiMom.9 XN:i:1
-HiMom:9:1:0:586 516 * 0 0 * * 0 0 ........C........C..C...A..... ############################## BC:Z:NNNNNCNN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:0:841 516 * 0 0 * * 0 0 ........C...........T......... ############################## BC:Z:NNNNNNNN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:0:879 516 * 0 0 * * 0 0 ........T...........T......... ############################## BC:Z:NNNNNNNN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:1:1013 516 * 0 0 * * 0 0 ..C..T.CAG...C...A.GT...G..... ############################## BC:Z:NNNNNGAN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:1:111 516 * 0 0 * * 0 0 ..C..T.GCG...T...A.CT...T..... ############################## BC:Z:NNNNNCGN-NNNNNNNN RG:Z:HiMom.9
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-HiMom:9:1:1:1320 516 * 0 0 * * 0 0 ..A..T.AGT...G...G.TA...C..... ############################## BC:Z:NNNNNCGN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:1:1372 516 * 0 0 * * 0 0 .ACATTTTTTAG.T.A.TTGTT.AC.A... ############################## BC:Z:NNNGNTTA-NNNGNNNN RG:Z:HiMom.9
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-HiMom:9:1:1:155 516 * 0 0 * * 0 0 ..G..C.AGT...C...A.TT...G..... ############################## BC:Z:NNNNNCAN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:1:1555 516 * 0 0 * * 0 0 ..T..G.AGA...A...C.TA...A..... ############################## BC:Z:NNNNNCAN-NNNNNCNN RG:Z:HiMom.9
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-HiMom:9:1:1:1684 516 * 0 0 * * 0 0 ..G..A.GGT...G...T.TC...T..... ############################## BC:Z:NNNNNCGN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:1:1696 516 * 0 0 * * 0 0 ..A..G..GC...G...A.AC...T..... ############################## BC:Z:NNNNNCTN-NNNNNCTN RG:Z:HiMom.9
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-HiMom:9:1:1:184 516 * 0 0 * * 0 0 ..C..T.TAA...A...T.AT...G..... ############################## BC:Z:NNNNNGTN-NNNNNGTN RG:Z:HiMom.9
-HiMom:9:1:1:1886 4 * 0 0 * * 0 0 .ACATATGCATACATATATAATAGATA... %.9:;<217;:999;<;;<<<;;####### BC:Z:NNNGNGCC-NNNGNNNN RG:Z:HiMom.9
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-HiMom:9:1:1:1954 516 * 0 0 * * 0 0 .AGA.T.CTT...G...G.AG...C..... ############################## BC:Z:NNNNNCCN-NNNNNCNN RG:Z:HiMom.9
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-HiMom:9:1:1:2011 516 * 0 0 * * 0 0 .ACAGCTGGCA..T...AGAGC.AG.A... ############################## BC:Z:NNNGNTAG-NNNNNNNN RG:Z:HiMom.9
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-HiMom:9:1:1:262 516 * 0 0 * * 0 0 ..C..G.CAT...A...C.TG...C..... ############################## BC:Z:NNNNNCAN-NNNNNCNN RG:Z:HiMom.9
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-HiMom:9:1:1:353 516 * 0 0 * * 0 0 ..A..T.TAG...A...T.AT...A..... ############################## BC:Z:NNNNNCGN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:1:367 516 * 0 0 * * 0 0 ..A..T.AGC...G...A.GT...C..... ############################## BC:Z:NNNNNAGN-NNNNNANN RG:Z:HiMom.9
-HiMom:9:1:1:41 516 * 0 0 * * 0 0 ..A..C.AAA...G...T.CA...C..... ############################## BC:Z:NNNNNGAN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:1:416 516 * 0 0 * * 0 0 ..A..C.AAT...G...G.AC...C..... ############################## BC:Z:NNNNNGAN-NNNNNNNN RG:Z:HiMom.9
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-HiMom:9:1:1:495 516 * 0 0 * * 0 0 ..C..A.CGT...T...T.AA...C..... ############################## BC:Z:NNNNNGAN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:1:508 516 * 0 0 * * 0 0 ..G..C.CAG...T...C.CT...C..... ############################## BC:Z:NNNNNCTN-NNNNNCNN RG:Z:HiMom.9
-HiMom:9:1:1:517 516 * 0 0 * * 0 0 .TCATAAAACATCA.TATTGGAAAGGA... %.75:<999578################## BC:Z:NNNCNAGA-NNNNNAGN RG:Z:HiMom.9
-HiMom:9:1:1:535 516 * 0 0 * * 0 0 .GCCCAAGTATTGA.TATGTGCTCTAA... %.599:7187:940%0::52599####### BC:Z:NNNCNCGA-NNNCNNNN RG:Z:HiMom.9
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-HiMom:9:1:1:554 516 * 0 0 * * 0 0 ..A..G.AGA...G...T.TC...A..... ############################## BC:Z:NNNNNTAN-NNNNNTAN RG:Z:HiMom.9
-HiMom:9:1:1:567 516 * 0 0 * * 0 0 ..C..C.GTT...C...G.AC...C..... ############################## BC:Z:NNNNNCCN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:1:59 516 * 0 0 * * 0 0 ..A..G.TGC...T...T.AC...A..... ############################## BC:Z:NNNNNACN-NNNNNANN RG:Z:HiMom.9
-HiMom:9:1:1:613 516 * 0 0 * * 0 0 ..G..A.TAT...C...G.AT...A..... ############################## BC:Z:NNNNNAGN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:1:622 516 * 0 0 * * 0 0 ..T..C.AGT...C...A.CT...T..... ############################## BC:Z:NNNNNAGN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:1:627 516 * 0 0 * * 0 0 ..A..T.GAC...T...A.GC...C..... ############################## BC:Z:NNNNNGAN-NNNNNGAN RG:Z:HiMom.9
-HiMom:9:1:1:684 516 * 0 0 * * 0 0 ..T..T.AGA...C...A.AG...A..... ############################## BC:Z:NNNNNGAN-NNNNNGAN RG:Z:HiMom.9
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-HiMom:9:1:1:931 516 * 0 0 * * 0 0 ..T..G.GAT...G...C.TT...C..... ############################## BC:Z:NNNNNCAN-NNNNNCNN RG:Z:HiMom.9
-HiMom:9:1:1:965 516 * 0 0 * * 0 0 .ACTAATCTTCCGC.CATATCCCCAAA... ############################## BC:Z:NNNTNTAA-NNNTNNNN RG:Z:HiMom.9
-HiMom:9:1:1:994 516 * 0 0 * * 0 0 ..A..T.GAT...T...G.TT...C..... ############################## BC:Z:NNNNNCGN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:2:1158 4 * 0 0 * * 0 0 .GGGTCCTTCATAGTTTTTTTCTACTTTCC %0777646;099:::95;;;688::99### BC:Z:NNCTTAGC-NNNNTANN RG:Z:HiMom.9
-HiMom:9:1:2:1238 516 * 0 0 * * 0 0 .TCCTTATATTCAATTATTAATATTTTTAC ############################## BC:Z:NNCTAAGC-NNNNNAGN RG:Z:HiMom.9
-HiMom:9:1:2:1275 4 * 0 0 * * 0 0 .AGTGAAATAAGCCAGACACAGAAAGACA. %/5204:99971773,44755-39717### BC:Z:NNNANCTG-NNNANNNN RG:Z:HiMom.9
-HiMom:9:1:2:1301 516 * 0 0 * * 0 0 .AGTAGACTGCATTAATTAATTGGAAGAG. %0370)024263144:48;;########## BC:Z:NNNTAACA-NNNTANNN RG:Z:HiMom.9
-HiMom:9:1:2:1453 4 * 0 0 * * 0 0 .ATATCTTATTTTCTTTTCTTTCAGGCTCT %.:7,,395255################## BC:Z:NNACCAGG-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:2:150 516 * 0 0 * * 0 0 .AAGACTTGATTATATCCCTTGTATGA... ############################## BC:Z:NNNANCCT-NNNANNNN RG:Z:HiMom.9
-HiMom:9:1:2:1592 4 * 0 0 * * 0 0 .GAAAACTGGCACAAGACAAGGATGCCCTC %,67786861,3466(8485868648583# BC:Z:NNNGAGCC-NNNGANNN RG:Z:HiMom.9
-HiMom:9:1:2:1706 4 * 0 0 * * 0 0 .GATATGTGGATACAGCTCACAAAGAG... %,99:6/566999/7############### BC:Z:NNNCNGAT-NNNCNNNN RG:Z:HiMom.9
-HiMom:9:1:2:1722 516 * 0 0 * * 0 0 .AAAGAAAATTAAAGAAAAATATACACGT. ############################## BC:Z:NNNTCGAC-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:2:1727 516 * 0 0 * * 0 0 .TATTGAAGGACTTTTGTATCCTCCTTAT. ############################## BC:Z:NNNTNCTT-NNNTNNNN RG:Z:HiMom.9
-HiMom:9:1:2:1753 516 * 0 0 * * 0 0 .GTTCACACAAGGATAATATTTTTGATTAT ############################## BC:Z:NNTGCTTA-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:2:1782 4 * 0 0 * * 0 0 .ACCAAGTGTTTGGAGTATGCTGCCTA... %0:::668885-5335/85########### BC:Z:NNNTNAGC-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:2:1827 4 * 0 0 * * 0 0 .AACCGAGGATGTACACTGTCCCTGTGAAA ############################## BC:Z:NNCAACTG-NNNNACNN RG:Z:HiMom.9
-HiMom:9:1:2:1932 4 * 0 0 * * 0 0 .AGCGATCCTCCCGCCTCTGCCTCCCA... %,1545541455################## BC:Z:NNNCNAGA-NNNCNNNN RG:Z:HiMom.9
-HiMom:9:1:2:1946 516 * 0 0 * * 0 0 .ATCTTCTGGAATTTCTAACAGCTTGGAA. %0515.,.35<997################ BC:Z:NNNTNGAC-NNNNNGNN RG:Z:HiMom.9
-HiMom:9:1:2:209 516 * 0 0 * * 0 0 .GACTCAACTCCTGGGCTCCCTACGACCAT ############################## BC:Z:NNCATTTC-NNNATNNN RG:Z:HiMom.9
-HiMom:9:1:2:246 516 * 0 0 * * 0 0 .GGAGGTTTCATTTAGCCGATATTGTG... ############################## BC:Z:NNNANTTC-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:2:25 516 * 0 0 * * 0 0 .GCTTTGGCAAGACAAATCTCCCGTCTGG. ############################## BC:Z:NNNGATGA-NNNGNNNN RG:Z:HiMom.9
-HiMom:9:1:2:307 516 * 0 0 * * 0 0 .GGATGAACAGAAACTAAAATAACACA... ############################## BC:Z:NNNTNGAC-NNNTNNNN RG:Z:HiMom.9
-HiMom:9:1:2:363 516 * 0 0 * * 0 0 .ATATTCTTTTTTTTTATTTATCAGAT... ############################## BC:Z:NNNTNCTT-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:2:449 516 * 0 0 * * 0 0 .ATTCTAATTCTAGGAAATTAACAATC... %.9315<936970%0############### BC:Z:NNNGNTGT-NNNGNNNN RG:Z:HiMom.9
-HiMom:9:1:2:546 516 * 0 0 * * 0 0 .GGTTGTGTCTCTCTCAGCCTTTGGGATC. %,46888444685-35############## BC:Z:NNNANGTT-NNNNNGNN RG:Z:HiMom.9
-HiMom:9:1:2:605 4 * 0 0 * * 0 0 .GCATTGAGCAGACGTGGCATCCAGAT... %)085222/55453################ BC:Z:NNNTNGAC-NNNTNNNN RG:Z:HiMom.9
-HiMom:9:1:2:69 516 * 0 0 * * 0 0 .TCAGTCTGCTGTTTTAAAAAAATACTGTG ############################## BC:Z:NNGGAGCC-NNNNAGNN RG:Z:HiMom.9
-HiMom:9:1:2:747 516 * 0 0 * * 0 0 .AACAACAGCGGAAAATAATAAAAAAAAA. ############################## BC:Z:NNNCCAGG-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:1:2:786 4 * 0 0 * * 0 0 .TAAACAATAATCTGATGATTTATAATCC. %09<<<<;<;<8<9;<9<;<::<<::#### BC:Z:NNNGATGT-NNNGNNNN RG:Z:HiMom.9
-HiMom:9:1:2:858 4 * 0 0 * * 0 0 .AAACGTTGCTGATCTTCTGTTTTAAACTA %/;7-222265366-6977035:::;626; BC:Z:NNACATCT-NNNNATNN RG:Z:HiMom.9
-HiMom:9:1:2:943 4 * 0 0 * * 0 0 .AATACCAATAAACCTAGAATGTCTCATAC %08<9646<6378744774:1005799<4# BC:Z:NNACCAGG-NNNCCNNN RG:Z:HiMom.9
-HiMom:9:1:2:974 4 * 0 0 * * 0 0 .GATCAATGATCACATCTTTGGATATGTAT %/9979<99:999::9;;:7511<<<77<< BC:Z:NNTATGTT-NNNATNNN RG:Z:HiMom.9
-HiMom:9:1:2:988 4 * 0 0 * * 0 0 .AAAGGAATGTTCAGCTCTGTGAGTTGAAC %/92/04:2-2785-3875/404362-162 BC:Z:NNTGGCGA-NNNGGNNN RG:Z:HiMom.9
-HiMom:9:1:3:1233 516 * 0 0 * * 0 0 .AACCAATTTCTTTACATACCAAATACGCC ############################## BC:Z:CCAACAGG-NNNACNNN RG:Z:HiMom.9
-HiMom:9:1:3:1294 516 * 0 0 * * 0 0 TGTAACTTTACTTTAGTTGCTTATTTGTAG BA############################ BC:Z:TCACAATG-TCNNNNNN RG:Z:HiMom.9
-HiMom:9:1:3:405 516 * 0 0 * * 0 0 AAAAAACATAGAACGGGGTCAATATTTTAT (?A>8(7B?<(:')?@)8(:(*:<8:0>'> BC:Z:ACACAAGA-NNNNNAGN RG:Z:HiMom.9
-HiMom:9:1:3:579 516 * 0 0 * * 0 0 .GAAAAATGACCACACTTGCCTCCTGAGAA ############################## BC:Z:AATCATGT-NNNNATNN RG:Z:HiMom.9
-HiMom:9:1:3:673 516 * 0 0 * * 0 0 TCCTCAAAAACAAGATAAAACGGTTGAAAT >()>)''85BBC?################# BC:Z:TGCCCAAA-NNNCCNNN RG:Z:HiMom.9
-HiMom:9:1:3:890 516 * 0 0 * * 0 0 TGCTTCTGTTTCCGTTAGCTAGATAAAGTT ############################## BC:Z:GTCACCAT-NNCANNNN RG:Z:HiMom.9
-HiMom:9:1:3:905 516 * 0 0 * * 0 0 TGTTATGTTTAATTTTCTTTAGCACCCTTC >7>?A:-<BA at 0>@:@8=A;5%7;9?=:9@ BC:Z:ACATCCTA-ACNNNNNN RG:Z:HiMom.9
-HiMom:9:1:3:918 516 * 0 0 * * 0 0 TTTTCATTCCTAGTCATCCACCCCATCAGA 0()@A=:2>3:>(/((<22A>:0(20:@)@ BC:Z:ACTACCTT-NNNNNCTN RG:Z:HiMom.9
-HiMom:9:2:0:1073 516 * 0 0 * * 0 0 .....A.CAC...C...C.CA...C..... ############################## BC:Z:NNNNNCAN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:0:1135 516 * 0 0 * * 0 0 .....G..GT...A...T.TA...G..... ############################## BC:Z:NNNNNAGN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:0:1198 516 * 0 0 * * 0 0 .....T.CTA...T...C.CA...A..... ############################## BC:Z:NNNNNCCN-NNNNNCCN RG:Z:HiMom.9
-HiMom:9:2:0:1278 516 * 0 0 * * 0 0 ........TA...T...C..A...G..... ############################## BC:Z:NNNNNTAN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:0:135 516 * 0 0 * * 0 0 ........A...........G......... ############################## BC:Z:NNNNNCGN-NNNNNCNN RG:Z:HiMom.9
-HiMom:9:2:0:1547 516 * 0 0 * * 0 0 ........C...........G...A..... ############################## BC:Z:NNNNNCAN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:0:1598 516 * 0 0 * * 0 0 ........AT...T...A..G...C..... ############################## BC:Z:NNNNNAGN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:0:1620 516 * 0 0 * * 0 0 ........CA.......A..C...C..... ############################## BC:Z:NNNNNTGN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:0:1668 516 * 0 0 * * 0 0 .....A.ATA...A...G.TG...T..... ############################## BC:Z:NNNNNCTN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:0:186 516 * 0 0 * * 0 0 ........CC...A...T..T...T..... ############################## BC:Z:NNNNNCCN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:0:205 516 * 0 0 * * 0 0 ........A........T..C...T..... ############################## BC:Z:NNNNNAGN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:0:287 516 * 0 0 * * 0 0 ........CC...C...T..A...A..... ############################## BC:Z:NNNNNGAN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:0:382 516 * 0 0 * * 0 0 ........CA...T...T..A...A..... ############################## BC:Z:NNNNNTAN-NNNNNTNN RG:Z:HiMom.9
-HiMom:9:2:0:441 516 * 0 0 * * 0 0 ........TT...A...A..T...T..... ############################## BC:Z:NNNNNAGN-NNNNNAGN RG:Z:HiMom.9
-HiMom:9:2:0:50 516 * 0 0 * * 0 0 ........T........T..G...G..... ############################## BC:Z:NNNNNGAN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:0:501 516 * 0 0 * * 0 0 .....G..AG...A...C.CT...C..... ############################## BC:Z:NNNNNTAN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:0:73 516 * 0 0 * * 0 0 .....A.CAT...G...A.AC...G..... ############################## BC:Z:NNNNNCGN-NNNNNCNN RG:Z:HiMom.9
-HiMom:9:2:0:740 516 * 0 0 * * 0 0 ........TT...A...T..A...A..... ############################## BC:Z:NNNNNGGN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:0:766 516 * 0 0 * * 0 0 ........TG...A...A..T...T..... ############################## BC:Z:NNNNNCCN-NNNNNCCN RG:Z:HiMom.9
-HiMom:9:2:0:87 516 * 0 0 * * 0 0 ........G........A..T...T..... ############################## BC:Z:NNNNNCGN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:1004 516 * 0 0 * * 0 0 .ATTTATCACTA.A.ATCCGCAAACCCTCC ############################## BC:Z:NNNGCCGA-NNNNNCGN RG:Z:HiMom.9
-HiMom:9:2:1:1034 516 * 0 0 * * 0 0 .ATCATTTTCAT.C.TTTCACTGATACATT %.737:887471%-%1:8555545;696:: BC:Z:NNNAGCCT-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:1159 516 * 0 0 * * 0 0 ..ACTT.TAG...G...AAAT..CC.A... ############################## BC:Z:NNNTNGAC-NNNTNNNN RG:Z:HiMom.9
-HiMom:9:2:1:1168 516 * 0 0 * * 0 0 ..TCTA.CTT...T...ATTG..TT.T... ############################## BC:Z:NNNGNTAG-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:1180 516 * 0 0 * * 0 0 ..ATGG.CTT...C...AGAA..TC.A... ############################## BC:Z:NNNTNAGC-NNNNNAGN RG:Z:HiMom.9
-HiMom:9:2:1:1214 516 * 0 0 * * 0 0 .AAAAAAAAAAA.A.TATAAGAAAGAATCA %035:######################### BC:Z:NNNCATGA-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:1221 516 * 0 0 * * 0 0 .GGTCACACTCACATAGTGTTCAGAGCACT ############################## BC:Z:NNGGATGT-NNNNNTGN RG:Z:HiMom.9
-HiMom:9:2:1:1306 516 * 0 0 * * 0 0 ..ACAT.AAA...T...AACA..GT.A... ############################## BC:Z:NNNANCTG-NNNNNCNN RG:Z:HiMom.9
-HiMom:9:2:1:1351 516 * 0 0 * * 0 0 .....C.ATA...T...A.AA...T..... ############################## BC:Z:NNNNNTTN-NNNNNTNN RG:Z:HiMom.9
-HiMom:9:2:1:1424 516 * 0 0 * * 0 0 ..TCAT.TAG...C...ATGG..GT.C... ############################## BC:Z:NNNCNTCT-NNNCNNNN RG:Z:HiMom.9
-HiMom:9:2:1:1452 516 * 0 0 * * 0 0 .GAAATTTGTAAAA.CACCTGCAGAATACT ############################## BC:Z:NNAGATCC-NNNNATNN RG:Z:HiMom.9
-HiMom:9:2:1:1515 516 * 0 0 * * 0 0 .ATTAAATAT.A.A..GTAATAATAATA.. %/9########################### BC:Z:NNNGNATG-NNNNNANN RG:Z:HiMom.9
-HiMom:9:2:1:1521 516 * 0 0 * * 0 0 ..ACAC.AAA...G...ATCT..TT.C... ############################## BC:Z:NNNCNAGG-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:1536 516 * 0 0 * * 0 0 .AGCAAAGACTT.G.ACCAACCCAAATGTT ############################## BC:Z:NNACATCT-NNANNNNN RG:Z:HiMom.9
-HiMom:9:2:1:1543 516 * 0 0 * * 0 0 ..TTGA.ATC...A...AATA..TA.C... ############################## BC:Z:NNNANTTC-NNNANNNN RG:Z:HiMom.9
-HiMom:9:2:1:1617 516 * 0 0 * * 0 0 ..CCAT.ATC...G...CCAG..GT.T... ############################## BC:Z:NNNCNAGG-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:1627 516 * 0 0 * * 0 0 ..TGGT.AGA...C...AAAA..CA.T... ############################## BC:Z:NNNANCTG-NNNANNNN RG:Z:HiMom.9
-HiMom:9:2:1:1646 516 * 0 0 * * 0 0 .TTAATTATA...A..TAAACATTCTAA.. ############################## BC:Z:NNNTNGAC-NNNTNNNN RG:Z:HiMom.9
-HiMom:9:2:1:1653 516 * 0 0 * * 0 0 ..AATT.AAA...T...ATCT..AG.A... ############################## BC:Z:NNNGNTGT-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:1682 516 * 0 0 * * 0 0 ..TCTT.TTT...G...AAAA..AA.T... ############################## BC:Z:NNNGNGCC-NNNNNGNN RG:Z:HiMom.9
-HiMom:9:2:1:170 4 * 0 0 * * 0 0 .AGAAGAAATGGGATCCTGCTGTGGCCAGT %/888865284168866767663(6874/5 BC:Z:NNGAGCCT-NNNAGNNN RG:Z:HiMom.9
-HiMom:9:2:1:1731 516 * 0 0 * * 0 0 ..TATA.GAA...T...TGCT..AG.T... ############################## BC:Z:NNNTNAGC-NNNNNAGN RG:Z:HiMom.9
-HiMom:9:2:1:1755 516 * 0 0 * * 0 0 ..GT.A.TCT...C...C.TG...G.A... ############################## BC:Z:NNNNNCAN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:1812 516 * 0 0 * * 0 0 ..TTGC.CAC...C...CCAT..AA.G... ############################## BC:Z:NNNCNTAT-NNNCNNNN RG:Z:HiMom.9
-HiMom:9:2:1:1853 516 * 0 0 * * 0 0 ..ATCT.TTC...A...AGTG..AT.C... ############################## BC:Z:NNNCNCGA-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:1919 516 * 0 0 * * 0 0 ..AATT.AAA...A...AGAA..AG.A... ############################## BC:Z:NNNANCTG-NNNANNNN RG:Z:HiMom.9
-HiMom:9:2:1:1924 516 * 0 0 * * 0 0 .ATATTCTGAAG.A..CCAATGAACCAAA. %116<9579<7################### BC:Z:NNNAACTG-NNNAANNN RG:Z:HiMom.9
-HiMom:9:2:1:1933 516 * 0 0 * * 0 0 .AGGGTACAT.T.C..AATGTGCGGGTT.. ############################## BC:Z:NNNTTAGC-NNNTNNNN RG:Z:HiMom.9
-HiMom:9:2:1:1938 4 * 0 0 * * 0 0 .AGTCCAGTGTCTCTGCTTCCGCAGGGACA %/818865/058858644866457646668 BC:Z:NNCTCGAC-NNCTNNNN RG:Z:HiMom.9
-HiMom:9:2:1:1950 516 * 0 0 * * 0 0 ..TT.A.AAA...C...T.CA...T.C... ############################## BC:Z:NNNNNGTN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:1959 516 * 0 0 * * 0 0 .GACACATTCCTAC.ACAGAGAAAAATTTA %*77;;<;<<:<;,%.::;:6:9::<4488 BC:Z:NNTGCTTA-NNNNCTNN RG:Z:HiMom.9
-HiMom:9:2:1:1987 516 * 0 0 * * 0 0 ..AT.G.ACA...C...T.GT...T..... ############################## BC:Z:NNNNNTAN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:2006 516 * 0 0 * * 0 0 ..GTAT.TGA...G...CCTT..AG.A... ############################## BC:Z:NNNGNGCC-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:211 516 * 0 0 * * 0 0 ..CTGA.ACA...G...TGCA..AC.C... ############################## BC:Z:NNNGNTGT-NNNNNTGN RG:Z:HiMom.9
-HiMom:9:2:1:234 516 * 0 0 * * 0 0 .AAGCCTGTGGG.A..CCCAGTGGGAGCG. ############################## BC:Z:NNNGCTTA-NNNNCTNN RG:Z:HiMom.9
-HiMom:9:2:1:242 516 * 0 0 * * 0 0 ..GCTC.AGC...A...ATAT..TT.G... ############################## BC:Z:NNNCNCGC-NNNCNNNN RG:Z:HiMom.9
-HiMom:9:2:1:262 516 * 0 0 * * 0 0 ..ATTG.AAT...C...TTCC..AT.T... ############################## BC:Z:NNNCNAGG-NNNCNNNN RG:Z:HiMom.9
-HiMom:9:2:1:298 516 * 0 0 * * 0 0 ..TCAA.TTG...T...CTGC..TT.T... ############################## BC:Z:NNNGNTAG-NNNGNNNN RG:Z:HiMom.9
-HiMom:9:2:1:312 516 * 0 0 * * 0 0 ..TTGC.AGA...A...AACT..TG.A... ############################## BC:Z:NNNANGTT-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:363 4 * 0 0 * * 0 0 .GAAAGGTTTTGCAGCATGTGCAAACTCAC %-5565678:8177656503512/377856 BC:Z:NNTATGTT-NNTNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:37 516 * 0 0 * * 0 0 .TGTAAACGA...C..TTCCTGTTCAGC.. ############################## BC:Z:NNNGNCGA-NNNGNNNN RG:Z:HiMom.9
-HiMom:9:2:1:370 516 * 0 0 * * 0 0 ..CTGG.AGC...T...CATA..AA.C... ############################## BC:Z:NNNANCAT-NNNANNNN RG:Z:HiMom.9
-HiMom:9:2:1:377 516 * 0 0 * * 0 0 ..AGAA.GTG...T...AAAT..AA.A... ############################## BC:Z:NNNCNTCT-NNNNNTNN RG:Z:HiMom.9
-HiMom:9:2:1:414 516 * 0 0 * * 0 0 ..TAGA.AGC...A...TCAG..AC.G... ############################## BC:Z:NNNGNTTA-NNNGNNNN RG:Z:HiMom.9
-HiMom:9:2:1:421 516 * 0 0 * * 0 0 ..GTTA.TTC...A...CGTG..AT.C... ############################## BC:Z:NNNANCCT-NNNANNNN RG:Z:HiMom.9
-HiMom:9:2:1:428 516 * 0 0 * * 0 0 .ATGTGAATA.T.A..TAGTTGGGATTCA. ############################## BC:Z:NNNATGTT-NNNANNNN RG:Z:HiMom.9
-HiMom:9:2:1:44 516 * 0 0 * * 0 0 .ACTACCTCA.G.A..AAGCAGGTTCTAA. ############################## BC:Z:NNNAGCGA-NNNAGNNN RG:Z:HiMom.9
-HiMom:9:2:1:466 516 * 0 0 * * 0 0 .ACACTCACA.C.A..TGTTTGGAATGA.. ############################## BC:Z:NNNTNACA-NNNTNNNN RG:Z:HiMom.9
-HiMom:9:2:1:555 516 * 0 0 * * 0 0 ..CAAT.TCT...G...TACA..CT.C... ############################## BC:Z:NNNCNGAT-NNNCNNNN RG:Z:HiMom.9
-HiMom:9:2:1:558 516 * 0 0 * * 0 0 .AAAATATCA.T.A..AATAAATAATCA.. ############################## BC:Z:NNNANCGA-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:56 516 * 0 0 * * 0 0 ..GCCA.GGT...A...TCAC..GG.C... ############################## BC:Z:NNNTNAGC-NNNNNANN RG:Z:HiMom.9
-HiMom:9:2:1:569 516 * 0 0 * * 0 0 ..AGGC.AGT...G...GTCC..GT.A... ############################## BC:Z:NNNANCTG-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:604 516 * 0 0 * * 0 0 .ATGATGAAACTCT.TCTCTACTAAAAATA ############################## BC:Z:NNCAACTG-NNCNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:628 516 * 0 0 * * 0 0 .AGTATGCCC.C.C..ACCACTCCTATT.. ############################## BC:Z:NNNTAACA-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:64 516 * 0 0 * * 0 0 .ATTAATCTT...T..GCACAATTCATT.. ############################## BC:Z:NNNANGTT-NNNNNGTN RG:Z:HiMom.9
-HiMom:9:2:1:684 516 * 0 0 * * 0 0 .AAAAATCAAATGA.CATAATTTTATAAAA ############################## BC:Z:NNAAACGA-NNAANNNN RG:Z:HiMom.9
-HiMom:9:2:1:699 516 * 0 0 * * 0 0 ..AATT.TTG...T...ATTT..GA.T... ############################## BC:Z:NNNCNCGA-NNNCNNNN RG:Z:HiMom.9
-HiMom:9:2:1:714 516 * 0 0 * * 0 0 .ATTAACTTA.A.T..ACCACAACCTAA.. %.:########################### BC:Z:NNNAGCGA-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:722 516 * 0 0 * * 0 0 ..CCTC.CTG...C...CTGT..TG.C... ############################## BC:Z:NNNCNAGG-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:749 516 * 0 0 * * 0 0 ..AGTG.TAC...T...CTTG..CT.T... ############################## BC:Z:NNNTNGAC-NNNNNGNN RG:Z:HiMom.9
-HiMom:9:2:1:760 516 * 0 0 * * 0 0 .GTCTGTTTTATGT.AAATATTTTGTTTAA ############################## BC:Z:NNACAACA-NNNNAANN RG:Z:HiMom.9
-HiMom:9:2:1:8 516 * 0 0 * * 0 0 ..TGCG.TGG...C...AGGC..TT.T... ############################## BC:Z:NNNANNNN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:1:833 516 * 0 0 * * 0 0 ..GAGC.CCT...A...CTCC..GA.G... ############################## BC:Z:NNNANCCT-NNNNNCCN RG:Z:HiMom.9
-HiMom:9:2:1:848 516 * 0 0 * * 0 0 ..TACT.AGT...G...TGTT..GC.T... ############################## BC:Z:NNNANCGA-NNNANNNN RG:Z:HiMom.9
-HiMom:9:2:1:893 516 * 0 0 * * 0 0 .GAGACAGAGTCTC.CTCTGTTCCCTAGCC ############################## BC:Z:NNCAATTC-NNNAANNN RG:Z:HiMom.9
-HiMom:9:2:1:998 516 * 0 0 * * 0 0 ..ATGT.TGC...A...TATA..GG.A... ############################## BC:Z:NNNANGTT-NNNNNGNN RG:Z:HiMom.9
-HiMom:9:2:2:0 516 * 0 0 * * 0 0 .ATTCCTT.A.................... ############################## BC:Z:NNNNNNNN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:2:131 4 * 0 0 * * 0 0 .ATATATTGACAGCAGTCATGTTGTTGAAG %0<<<:<959874492:96999969:7784 BC:Z:CACAATCC-NNNAANNN RG:Z:HiMom.9
-HiMom:9:2:2:1636 516 * 0 0 * * 0 0 .GTGTAAAAGTAGGGAAATACTATAGCAAG ############################## BC:Z:ATCAACCC-NNNAANNN RG:Z:HiMom.9
-HiMom:9:2:2:1974 516 * 0 0 * * 0 0 .ACGCCAATACAAAAATGTTGAAGCTAGCT ############################## BC:Z:AGCAATCT-NGCNNNNN RG:Z:HiMom.9
-HiMom:9:2:2:351 516 * 0 0 * * 0 0 .GGGGTTGAGGTGTAAATAGAACATTTGTA ############################## BC:Z:TGATAGAA-NNNNNGAN RG:Z:HiMom.9
-HiMom:9:2:2:646 516 * 0 0 * * 0 0 .GAATCTAAGAAGACACAAAACTAAGGAAA ############################## BC:Z:ATCAATTA-NTCNNNNN RG:Z:HiMom.9
-HiMom:9:2:2:828 516 * 0 0 * * 0 0 .TCAAGTCAATTTGGGACTTGAAACAGCTC ############################## BC:Z:TATATCGA-NNNNNCGN RG:Z:HiMom.9
-HiMom:9:2:3:1529 516 * 0 0 * * 0 0 .TTATATGAATAGATAAATAAATAATCAAT ############################## BC:Z:TAGAACCT-NAGNNNNN RG:Z:HiMom.9
-HiMom:9:2:3:179 516 * 0 0 * * 0 0 CATTATTGTTAGACTGATTTTTTATAATCT B@)104..*0-A(@@(<A9A<(+9)-=6(B BC:Z:GTTTATTA-NNNTANNN RG:Z:HiMom.9
-HiMom:9:2:3:198 516 * 0 0 * * 0 0 TGTCATTTTCTTTGCCTTAATTGTTCTTCT 5 at CBB7-*<=#################### BC:Z:CAGGATCT-NNNNNTCN RG:Z:HiMom.9
-HiMom:9:2:3:2030 516 * 0 0 * * 0 0 CGAGATAATTTTTTAAAAAAAGTCCAAAAA ((@;()@==*7<(5A@<C>########### BC:Z:GATCAAGA-NNNCANNN RG:Z:HiMom.9
-HiMom:9:2:3:247 516 * 0 0 * * 0 0 TGTACATGACCAGGTAATTTGGTTATGTGA <@596353;)>@A7=:,A0'6>######## BC:Z:CGGTAGCT-CGNNNNNN RG:Z:HiMom.9
-HiMom:9:2:3:4 516 * 0 0 * * 0 0 AGAGGCAATAAGTTTTAA............ A>BA at 9BAB3AA################## BC:Z:NNNNNNNN-NNNNNNNN RG:Z:HiMom.9
-HiMom:9:2:3:862 516 * 0 0 * * 0 0 .CTTTAAGAAATCATTCATTCTGCAAACAC ############################## BC:Z:TAACAAGA-TANNNNNN RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TACTTAGC.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TACTTAGC.sam
deleted file mode 100644
index 5668e11..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TACTTAGC.sam
+++ /dev/null
@@ -1,10 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.TACTTAGC LB:LN_TACTTAGC PI:10018 DS:DESC18 SM:SA_TACTTAGC CN:BI
-HiMom:7:1:2:737 516 * 0 0 * * 0 0 .AAAACAATTAAAATAAATGCTTAAAATCA ############################## RG:Z:HiMom.7
-HiMom:7:1:2:85 516 * 0 0 * * 0 0 .GATAAAGTACAATGCTAATCACTTAAGAT %.52353046874+'01999975;:9255; RG:Z:HiMom.7
-HiMom:7:1:3:1574 4 * 0 0 * * 0 0 .TTATTCCTTAGGAAATTTTAAATTCTGTA %0955357999999:99::99102::9:3: RG:Z:HiMom.7
-HiMom:7:2:2:101 4 * 0 0 * * 0 0 .GTTAATTTAGGGAAATTTGTTTGTATTTT %,3:969;<52718;<<<768;::9;999; RG:Z:HiMom.7
-HiMom:7:2:2:12 516 * 0 0 * * 0 0 .ATGCATTGTAATTTAATAGAGTGAAATGG ############################## RG:Z:HiMom.7
-HiMom:7:2:3:1844 516 * 0 0 * * 0 0 .GGACTACAAGCGCACGCCACATGCTCAGC ############################## RG:Z:HiMom.7
-HiMom:7:2:3:728 516 * 0 0 * * 0 0 TGCCTCCTTGGAGAGGGCCGCAAAGCCAGG =>=7?A?7'50>/996:;<+>AA at 7+8B67 RG:Z:HiMom.7
-HiMom:7:2:3:80 4 * 0 0 * * 0 0 AGGCAGGATGAAATTTTGTCTATTTATTCA @9:B at B@?B at ABABBBB??7AABBBBBB?A RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TACTTAGCCACATCCT.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TACTTAGCCACATCCT.sam
deleted file mode 100644
index 6190d39..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TACTTAGCCACATCCT.sam
+++ /dev/null
@@ -1,10 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.TACTTAGC-CACATCCT LB:LN_TACTTAGCCACATCCT PI:10018 DS:DESC18 SM:SA_TACTTAGCCACATCCT CN:BI
-HiMom:9:1:2:737 516 * 0 0 * * 0 0 .AAAACAATTAAAATAAATGCTTAAAATCA ############################## RG:Z:HiMom.9
-HiMom:9:1:2:85 516 * 0 0 * * 0 0 .GATAAAGTACAATGCTAATCACTTAAGAT %.52353046874+'01999975;:9255; RG:Z:HiMom.9
-HiMom:9:1:3:1574 4 * 0 0 * * 0 0 .TTATTCCTTAGGAAATTTTAAATTCTGTA %0955357999999:99::99102::9:3: RG:Z:HiMom.9
-HiMom:9:2:2:101 4 * 0 0 * * 0 0 .GTTAATTTAGGGAAATTTGTTTGTATTTT %,3:969;<52718;<<<768;::9;999; RG:Z:HiMom.9
-HiMom:9:2:2:12 516 * 0 0 * * 0 0 .ATGCATTGTAATTTAATAGAGTGAAATGG ############################## RG:Z:HiMom.9
-HiMom:9:2:3:1844 516 * 0 0 * * 0 0 .GGACTACAAGCGCACGCCACATGCTCAGC ############################## RG:Z:HiMom.9
-HiMom:9:2:3:728 516 * 0 0 * * 0 0 TGCCTCCTTGGAGAGGGCCGCAAAGCCAGG =>=7?A?7'50>/996:;<+>AA at 7+8B67 RG:Z:HiMom.9
-HiMom:9:2:3:80 4 * 0 0 * * 0 0 AGGCAGGATGAAATTTTGTCTATTTATTCA @9:B at B@?B at ABABBBB??7AABBBBBB?A RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TCGGAATG.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TCGGAATG.sam
deleted file mode 100644
index b6c3c3e..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TCGGAATG.sam
+++ /dev/null
@@ -1,9 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.TCGGAATG LB:LN_TCGGAATG PI:10019 DS:DESC19 SM:SA_TCGGAATG CN:BI
-HiMom:7:1:3:1328 516 * 0 0 * * 0 0 GCTACCAACCCCACTCCTAGATGAAAGACC 068,=@)=AA82 at C@8;;@3;8/<<##### RG:Z:HiMom.7
-HiMom:7:1:3:2037 516 * 0 0 * * 0 0 CATCCTGTAACAAAGTGTTTATAGTTTTCA :@9 at B6<?A>(>AB@<*)=<CBA:>51:7A RG:Z:HiMom.7
-HiMom:7:1:3:695 4 * 0 0 * * 0 0 TGATACTGCCTTTGCAAAAATTATAACAGT ;>ABBCC<?ACCBBBCCCCBBACBAABB<A RG:Z:HiMom.7
-HiMom:7:2:2:220 4 * 0 0 * * 0 0 .AATAAACCTCTTTCTTTGATAAATTACCC %.5:78335567:525<736:9868;8### RG:Z:HiMom.7
-HiMom:7:2:3:567 4 * 0 0 * * 0 0 TATCTTCACATAAAAACTACACAAAGCATT BCB<ACBB at BCCBBCB<BB<@;?BB>=BBB RG:Z:HiMom.7
-HiMom:7:2:3:663 516 * 0 0 * * 0 0 AAAAGCATGTTGCTCAGTAAAAGCAAATAG ############################## RG:Z:HiMom.7
-HiMom:7:2:3:922 4 * 0 0 * * 0 0 ATTTCTGTCTGACTTTTCCAAATGTGCTAT AABB@>>>@>9@>AAAA>;@BB@@53;BBB RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TCGGAATGATTATGTT.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TCGGAATGATTATGTT.sam
deleted file mode 100644
index e90d4c6..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TCGGAATGATTATGTT.sam
+++ /dev/null
@@ -1,9 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.TCGGAATG-ATTATGTT LB:LN_TCGGAATGATTATGTT PI:10019 DS:DESC19 SM:SA_TCGGAATGATTATGTT CN:BI
-HiMom:9:1:3:1328 516 * 0 0 * * 0 0 GCTACCAACCCCACTCCTAGATGAAAGACC 068,=@)=AA82 at C@8;;@3;8/<<##### RG:Z:HiMom.9
-HiMom:9:1:3:2037 516 * 0 0 * * 0 0 CATCCTGTAACAAAGTGTTTATAGTTTTCA :@9 at B6<?A>(>AB@<*)=<CBA:>51:7A RG:Z:HiMom.9
-HiMom:9:1:3:695 4 * 0 0 * * 0 0 TGATACTGCCTTTGCAAAAATTATAACAGT ;>ABBCC<?ACCBBBCCCCBBACBAABB<A RG:Z:HiMom.9
-HiMom:9:2:2:220 4 * 0 0 * * 0 0 .AATAAACCTCTTTCTTTGATAAATTACCC %.5:78335567:525<736:9868;8### RG:Z:HiMom.9
-HiMom:9:2:3:567 4 * 0 0 * * 0 0 TATCTTCACATAAAAACTACACAAAGCATT BCB<ACBB at BCCBBCB<BB<@;?BB>=BBB RG:Z:HiMom.9
-HiMom:9:2:3:663 516 * 0 0 * * 0 0 AAAAGCATGTTGCTCAGTAAAAGCAAATAG ############################## RG:Z:HiMom.9
-HiMom:9:2:3:922 4 * 0 0 * * 0 0 ATTTCTGTCTGACTTTTCCAAATGTGCTAT AABB@>>>@>9@>AAAA>;@BB@@53;BBB RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TCTGGCGA.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TCTGGCGA.sam
deleted file mode 100644
index f937247..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TCTGGCGA.sam
+++ /dev/null
@@ -1,7 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.TCTGGCGA LB:LN_TCTGGCGA PI:10020 DS:DESC20 SM:SA_TCTGGCGA CN:BI
-HiMom:7:1:3:1406 516 * 0 0 * * 0 0 .AAAATGCCAGATAAATTTTATGTAAAACC %1<<97227467::77(7;;;503<9:972 RG:Z:HiMom.7
-HiMom:7:1:3:1717 4 * 0 0 * * 0 0 .AAACAGACTTGTTTCTTGTAATAATTATG %/;;89689:999<76:8399:9:::::## RG:Z:HiMom.7
-HiMom:7:2:3:2004 516 * 0 0 * * 0 0 .AAGACTACCTTGCTGAAATAGGGCATTTA %.:875459;4-743(29;;5139266### RG:Z:HiMom.7
-HiMom:7:2:3:695 4 * 0 0 * * 0 0 .CAACTCCAAGACACATAATTGTCAGATTC %/:::95578589969:::;6559748;82 RG:Z:HiMom.7
-HiMom:7:2:3:987 516 * 0 0 * * 0 0 AAGAGCAATATTTTCTTTCACTATATTATT *@<@@?A at 0)7448)?C@)@4)9:@##### RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TCTGGCGAAGTTGCTT.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TCTGGCGAAGTTGCTT.sam
deleted file mode 100644
index 43e745b..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TCTGGCGAAGTTGCTT.sam
+++ /dev/null
@@ -1,7 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.TCTGGCGA-AGTTGCTT LB:LN_TCTGGCGAAGTTGCTT PI:10020 DS:DESC20 SM:SA_TCTGGCGAAGTTGCTT CN:BI
-HiMom:9:1:3:1406 516 * 0 0 * * 0 0 .AAAATGCCAGATAAATTTTATGTAAAACC %1<<97227467::77(7;;;503<9:972 RG:Z:HiMom.9
-HiMom:9:1:3:1717 4 * 0 0 * * 0 0 .AAACAGACTTGTTTCTTGTAATAATTATG %/;;89689:999<76:8399:9:::::## RG:Z:HiMom.9
-HiMom:9:2:3:2004 516 * 0 0 * * 0 0 .AAGACTACCTTGCTGAAATAGGGCATTTA %.:875459;4-743(29;;5139266### RG:Z:HiMom.9
-HiMom:9:2:3:695 4 * 0 0 * * 0 0 .CAACTCCAAGACACATAATTGTCAGATTC %/:::95578589969:::;6559748;82 RG:Z:HiMom.9
-HiMom:9:2:3:987 516 * 0 0 * * 0 0 AAGAGCAATATTTTCTTTCACTATATTATT *@<@@?A at 0)7448)?C@)@4)9:@##### RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TGCTCGAC.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TGCTCGAC.sam
deleted file mode 100644
index 8d00425..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TGCTCGAC.sam
+++ /dev/null
@@ -1,7 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.TGCTCGAC LB:LN_TGCTCGAC PI:10021 DS:DESC21 SM:SA_TGCTCGAC CN:BI
-HiMom:7:1:2:52 516 * 0 0 * * 0 0 .AAGTATAATGTAGAGACGCTTGTATTGTC ############################## RG:Z:HiMom.7
-HiMom:7:1:3:1348 4 * 0 0 * * 0 0 .ATATTGATTCTTCCTACCCATGAGTATGG %1;;78.+389999888;;89118;7;8## RG:Z:HiMom.7
-HiMom:7:1:3:1981 4 * 0 0 * * 0 0 AGCCTGTCTGTAGAAAAAATACAAAAATTA @3;=;8/@=:8B8=BBBBB:B?BBABB?:B RG:Z:HiMom.7
-HiMom:7:2:2:115 516 * 0 0 * * 0 0 .GATGTGCTACACACTTTCAAACAAACAGA %0:500&/99;69727::995313374484 RG:Z:HiMom.7
-HiMom:7:2:3:317 4 * 0 0 * * 0 0 AGAGAGAAATGTGGCATATGAGTATCACCT @4>BBB?ABCAB@>>ACBB?B<AABBCBBB RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TGCTCGACAGCAATTC.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TGCTCGACAGCAATTC.sam
deleted file mode 100644
index 17e1873..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TGCTCGACAGCAATTC.sam
+++ /dev/null
@@ -1,7 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.TGCTCGAC-AGCAATTC LB:LN_TGCTCGACAGCAATTC PI:10021 DS:DESC21 SM:SA_TGCTCGACAGCAATTC CN:BI
-HiMom:9:1:2:52 516 * 0 0 * * 0 0 .AAGTATAATGTAGAGACGCTTGTATTGTC ############################## RG:Z:HiMom.9
-HiMom:9:1:3:1348 4 * 0 0 * * 0 0 .ATATTGATTCTTCCTACCCATGAGTATGG %1;;78.+389999888;;89118;7;8## RG:Z:HiMom.9
-HiMom:9:1:3:1981 4 * 0 0 * * 0 0 AGCCTGTCTGTAGAAAAAATACAAAAATTA @3;=;8/@=:8B8=BBBBB:B?BBABB?:B RG:Z:HiMom.9
-HiMom:9:2:2:115 516 * 0 0 * * 0 0 .GATGTGCTACACACTTTCAAACAAACAGA %0:500&/99;69727::995313374484 RG:Z:HiMom.9
-HiMom:9:2:3:317 4 * 0 0 * * 0 0 AGAGAGAAATGTGGCATATGAGTATCACCT @4>BBB?ABCAB@>>ACBB?B<AABBCBBB RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TGTCGGAT.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TGTCGGAT.sam
deleted file mode 100644
index 7912603..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TGTCGGAT.sam
+++ /dev/null
@@ -1,6 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.TGTCGGAT LB:LN_TGTCGGAT PI:10022 DS:DESC22 SM:SA_TGTCGGAT CN:BI
-HiMom:7:1:2:950 4 * 0 0 * * 0 0 .GTGTGTGTTTTTAGAGATGCCTTTTAGAA %-7463817999<999998876999;6579 RG:Z:HiMom.7
-HiMom:7:2:3:1389 4 * 0 0 * * 0 0 TATCGATCTCCTGACCTCGTGATCCACCCA ACBCBCB?CBB at 6ABCB@)B>CBBCC at 4;5 RG:Z:HiMom.7
-HiMom:7:2:3:143 4 * 0 0 * * 0 0 AAAATCAATTCTGAAATGATTACATATTTT BBBACBBACB=B?BBBBCBBCBBBBBBCBB RG:Z:HiMom.7
-HiMom:7:2:3:898 4 * 0 0 * * 0 0 TAACATTCCCACAGTGCTTGCCACAGAGCC ACCCCCC at C@@B@);>;BBCC=@BC?B@;> RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TGTCGGATACCAACTG.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TGTCGGATACCAACTG.sam
deleted file mode 100644
index be209a0..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TGTCGGATACCAACTG.sam
+++ /dev/null
@@ -1,6 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.TGTCGGAT-ACCAACTG LB:LN_TGTCGGATACCAACTG PI:10022 DS:DESC22 SM:SA_TGTCGGATACCAACTG CN:BI
-HiMom:9:1:2:950 4 * 0 0 * * 0 0 .GTGTGTGTTTTTAGAGATGCCTTTTAGAA %-7463817999<999998876999;6579 RG:Z:HiMom.9
-HiMom:9:2:3:1389 4 * 0 0 * * 0 0 TATCGATCTCCTGACCTCGTGATCCACCCA ACBCBCB?CBB at 6ABCB@)B>CBBCC at 4;5 RG:Z:HiMom.9
-HiMom:9:2:3:143 4 * 0 0 * * 0 0 AAAATCAATTCTGAAATGATTACATATTTT BBBACBBACB=B?BBBBCBBCBBBBBBCBB RG:Z:HiMom.9
-HiMom:9:2:3:898 4 * 0 0 * * 0 0 TAACATTCCCACAGTGCTTGCCACAGAGCC ACCCCCC at C@@B@);>;BBCC=@BC?B@;> RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TTCGCTGA.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TTCGCTGA.sam
deleted file mode 100644
index 2a50b4b..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TTCGCTGA.sam
+++ /dev/null
@@ -1,7 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.TTCGCTGA LB:LN_TTCGCTGA PI:10023 DS:DESC23 SM:SA_TTCGCTGA CN:BI
-HiMom:7:1:2:309 4 * 0 0 * * 0 0 .AATGGCCATGCTGCCCAAAGTATTTTATA %.705699:5-227759996717:::9:9: RG:Z:HiMom.7
-HiMom:7:1:2:63 4 * 0 0 * * 0 0 .GAGTGGAATGGAATGGAGTGGAATGGCTT %,/66818682811553536525875686# RG:Z:HiMom.7
-HiMom:7:1:3:880 516 * 0 0 * * 0 0 ATGAGTGAGAAATAGAAGTCCTAAGTAGAT B@=;/75>)>?B@=3>@=<.2=B at 2@>49B RG:Z:HiMom.7
-HiMom:7:2:2:669 516 * 0 0 * * 0 0 .GGCTGAAGCAGGAGGGTCACTTGAGCCAA ############################## RG:Z:HiMom.7
-HiMom:7:2:2:775 4 * 0 0 * * 0 0 .GTTTATAATTGTGAGTTAAAAATCTAAAA %,-78:8:968:45524<<636;<:<<<<< RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TTCGCTGAAAGGATGT.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TTCGCTGAAAGGATGT.sam
deleted file mode 100644
index 53fe889..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TTCGCTGAAAGGATGT.sam
+++ /dev/null
@@ -1,7 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.TTCGCTGA-AAGGATGT LB:LN_TTCGCTGAAAGGATGT PI:10023 DS:DESC23 SM:SA_TTCGCTGAAAGGATGT CN:BI
-HiMom:9:1:2:309 4 * 0 0 * * 0 0 .AATGGCCATGCTGCCCAAAGTATTTTATA %.705699:5-227759996717:::9:9: RG:Z:HiMom.9
-HiMom:9:1:2:63 4 * 0 0 * * 0 0 .GAGTGGAATGGAATGGAGTGGAATGGCTT %,/66818682811553536525875686# RG:Z:HiMom.9
-HiMom:9:1:3:880 516 * 0 0 * * 0 0 ATGAGTGAGAAATAGAAGTCCTAAGTAGAT B@=;/75>)>?B@=3>@=<.2=B at 2@>49B RG:Z:HiMom.9
-HiMom:9:2:2:669 516 * 0 0 * * 0 0 .GGCTGAAGCAGGAGGGTCACTTGAGCCAA ############################## RG:Z:HiMom.9
-HiMom:9:2:2:775 4 * 0 0 * * 0 0 .GTTTATAATTGTGAGTTAAAAATCTAAAA %,-78:8:968:45524<<636;<:<<<<< RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TTGAGCCT.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TTGAGCCT.sam
deleted file mode 100644
index d56372d..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TTGAGCCT.sam
+++ /dev/null
@@ -1,8 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7.TTGAGCCT LB:LN_TTGAGCCT PI:10024 DS:DESC24 SM:SA_TTGAGCCT CN:BI
-HiMom:7:1:3:1155 516 * 0 0 * * 0 0 .CAGCGAAAGAAGTACCAGGGTATGGGAAG ############################## RG:Z:HiMom.7
-HiMom:7:2:2:1559 4 * 0 0 * * 0 0 .ACAGAAGGGAAAAGGTCACAGACTAAAGA %//6;;;8849;:91,35::757:4:;:9: RG:Z:HiMom.7
-HiMom:7:2:2:488 4 * 0 0 * * 0 0 .TGGGAAACTAAACCCCATGAGGGCAGAGC %/2/156666785445255551/12545/4 RG:Z:HiMom.7
-HiMom:7:2:3:1101 4 * 0 0 * * 0 0 AAGATTATATGAGTATAATGGAGCTATTTG B<38>B=>>B==30ABBA886;?;AAA@@> RG:Z:HiMom.7
-HiMom:7:2:3:1123 516 * 0 0 * * 0 0 .CCTCTTCCACAACTTCCTTCTTCTCCTTT %.23)7475776876486:;67348867:8 RG:Z:HiMom.7
-HiMom:7:2:3:782 4 * 0 0 * * 0 0 AGCCATGGGCATATAGAATCACTGTAAACA B at BBBB>7;BCBCBB at BBB?BB>:=BAB at B RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TTGAGCCTAACTTGAC.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TTGAGCCTAACTTGAC.sam
deleted file mode 100644
index 7029f65..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/TTGAGCCTAACTTGAC.sam
+++ /dev/null
@@ -1,8 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.9 PL:illumina PU:HiMom.9.TTGAGCCT-AACTTGAC LB:LN_TTGAGCCTAACTTGAC PI:10024 DS:DESC24 SM:SA_TTGAGCCTAACTTGAC CN:BI
-HiMom:9:1:3:1155 516 * 0 0 * * 0 0 .CAGCGAAAGAAGTACCAGGGTATGGGAAG ############################## RG:Z:HiMom.9
-HiMom:9:2:2:1559 4 * 0 0 * * 0 0 .ACAGAAGGGAAAAGGTCACAGACTAAAGA %//6;;;8849;:91,35::757:4:;:9: RG:Z:HiMom.9
-HiMom:9:2:2:488 4 * 0 0 * * 0 0 .TGGGAAACTAAACCCCATGAGGGCAGAGC %/2/156666785445255551/12545/4 RG:Z:HiMom.9
-HiMom:9:2:3:1101 4 * 0 0 * * 0 0 AAGATTATATGAGTATAATGGAGCTATTTG B<38>B=>>B==30ABBA886;?;AAA@@> RG:Z:HiMom.9
-HiMom:9:2:3:1123 516 * 0 0 * * 0 0 .CCTCTTCCACAACTTCCTTCTTCTCCTTT %.23)7475776876486:;67348867:8 RG:Z:HiMom.9
-HiMom:9:2:3:782 4 * 0 0 * * 0 0 AGCCATGGGCATATAGAATCACTGTAAACA B at BBBB>7;BCBCBB at BBB?BB>:=BAB at B RG:Z:HiMom.9
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/barcode.params b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/barcode.params
deleted file mode 100644
index cc307ed..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/barcode.params
+++ /dev/null
@@ -1,26 +0,0 @@
-BARCODE SAMPLE_ALIAS LIBRARY_NAME PI DS
-AACTTGAC SA_AACTTGAC LN_AACTTGAC 10001 DESC1
-AAGGATGT SA_AAGGATGT LN_AAGGATGT 10002 DESC2
-ACCAACTG SA_ACCAACTG LN_ACCAACTG 10003
-AGCAATTC SA_AGCAATTC LN_AGCAATTC 10004 DESC4
-AGTTGCTT SA_AGTTGCTT LN_AGTTGCTT 10005 DESC5
-ATTATGTT SA_ATTATGTT LN_ATTATGTT 10006 DESC6
-CACATCCT SA_CACATCCT LN_CACATCCT DESC7
-CAGGAGCC SA_CAGGAGCC LN_CAGGAGCC 10008 DESC8
-CATAGCGA SA_CATAGCGA LN_CATAGCGA 10009 DESC9
-CATGCTTA SA_CATGCTTA LN_CATGCTTA 10010 DESC10
-CCAGTTAG SA_CCAGTTAG LN_CCAGTTAG
-CCTACCAT SA_CCTACCAT LN_CCTACCAT 10012 DESC12
-CTACCAGG SA_CTACCAGG LN_CTACCAGG 10013 DESC13
-GCACACGA SA_GCACACGA LN_GCACACGA 10014 DESC14
-GCACATCT SA_GCACATCT LN_GCACATCT DESC15
-GGTCCAGA SA_GGTCCAGA LN_GGTCCAGA 10016 DESC16
-GTATAACA SA_GTATAACA LN_GTATAACA 10017 DESC17
-TACTTAGC SA_TACTTAGC LN_TACTTAGC 10018 DESC18
-TCGGAATG SA_TCGGAATG LN_TCGGAATG 10019 DESC19
-TCTGGCGA SA_TCTGGCGA LN_TCTGGCGA 10020 DESC20
-TGCTCGAC SA_TGCTCGAC LN_TGCTCGAC 10021 DESC21
-TGTCGGAT SA_TGTCGGAT LN_TGTCGGAT 10022 DESC22
-TTCGCTGA SA_TTCGCTGA LN_TTCGCTGA 10023 DESC23
-TTGAGCCT SA_TTGAGCCT LN_TTGAGCCT 10024 DESC24
-N SA_N LN_N 10025 DESC25
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/barcode_double.params b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/barcode_double.params
deleted file mode 100644
index 7d9f3d1..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/barcode_double.params
+++ /dev/null
@@ -1,26 +0,0 @@
-BARCODE_1 BARCODE_2 SAMPLE_ALIAS LIBRARY_NAME PI DS
-AACTTGAC TTGAGCCT SA_AACTTGACTTGAGCCT LN_AACTTGACTTGAGCCT 10001 DESC01
-AAGGATGT TTCGCTGA SA_AAGGATGTTTCGCTGA LN_AAGGATGTTTCGCTGA 10002 DESC02
-ACCAACTG TGTCGGAT SA_ACCAACTGTGTCGGAT LN_ACCAACTGTGTCGGAT 10003 DESC03
-AGCAATTC TGCTCGAC SA_AGCAATTCTGCTCGAC LN_AGCAATTCTGCTCGAC 10004 DESC04
-AGTTGCTT TCTGGCGA SA_AGTTGCTTTCTGGCGA LN_AGTTGCTTTCTGGCGA 10005 DESC05
-ATTATGTT TCGGAATG SA_ATTATGTTTCGGAATG LN_ATTATGTTTCGGAATG 10006 DESC06
-CACATCCT TACTTAGC SA_CACATCCTTACTTAGC LN_CACATCCTTACTTAGC 10007 DESC07
-CAGGAGCC GTATAACA SA_CAGGAGCCGTATAACA LN_CAGGAGCCGTATAACA 10008 DESC08
-CATAGCGA GGTCCAGA SA_CATAGCGAGGTCCAGA LN_CATAGCGAGGTCCAGA 10009 DESC09
-CATGCTTA GCACATCT SA_CATGCTTAGCACATCT LN_CATGCTTAGCACATCT 10010 DESC10
-CCAGTTAG GCACACGA SA_CCAGTTAGGCACACGA LN_CCAGTTAGGCACACGA 10011 DESC11
-CCTACCAT CTACCAGG SA_CCTACCATCTACCAGG LN_CCTACCATCTACCAGG 10012 DESC12
-CTACCAGG CCTACCAT SA_CTACCAGGCCTACCAT LN_CTACCAGGCCTACCAT 10013 DESC13
-GCACACGA CCAGTTAG SA_GCACACGACCAGTTAG LN_GCACACGACCAGTTAG 10014 DESC14
-GCACATCT CATGCTTA SA_GCACATCTCATGCTTA LN_GCACATCTCATGCTTA 10015 DESC15
-GGTCCAGA CATAGCGA SA_GGTCCAGACATAGCGA LN_GGTCCAGACATAGCGA 10016 DESC16
-GTATAACA CAGGAGCC SA_GTATAACACAGGAGCC LN_GTATAACACAGGAGCC 10017 DESC17
-TACTTAGC CACATCCT SA_TACTTAGCCACATCCT LN_TACTTAGCCACATCCT 10018 DESC18
-TCGGAATG ATTATGTT SA_TCGGAATGATTATGTT LN_TCGGAATGATTATGTT 10019 DESC19
-TCTGGCGA AGTTGCTT SA_TCTGGCGAAGTTGCTT LN_TCTGGCGAAGTTGCTT 10020 DESC20
-TGCTCGAC AGCAATTC SA_TGCTCGACAGCAATTC LN_TGCTCGACAGCAATTC 10021 DESC21
-TGTCGGAT ACCAACTG SA_TGTCGGATACCAACTG LN_TGTCGGATACCAACTG 10022 DESC22
-TTCGCTGA AAGGATGT SA_TTCGCTGAAAGGATGT LN_TTCGCTGAAAGGATGT 10023 DESC23
-TTGAGCCT AACTTGAC SA_TTGAGCCTAACTTGAC LN_TTGAGCCTAACTTGAC 10024 DESC24
-N N SA_N LN_N 10025 DESC25
\ No newline at end of file
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/barcode_single.params b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/barcode_single.params
deleted file mode 100644
index 95a8df4..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/barcode_single.params
+++ /dev/null
@@ -1,26 +0,0 @@
-BARCODE_1 SAMPLE_ALIAS LIBRARY_NAME
-AACTTGAC SA_AACTTGAC LN_AACTTGAC
-AAGGATGT SA_AAGGATGT LN_AAGGATGT
-ACCAACTG SA_ACCAACTG LN_ACCAACTG
-AGCAATTC SA_AGCAATTC LN_AGCAATTC
-AGTTGCTT SA_AGTTGCTT LN_AGTTGCTT
-ATTATGTT SA_ATTATGTT LN_ATTATGTT
-CACATCCT SA_CACATCCT LN_CACATCCT
-CAGGAGCC SA_CAGGAGCC LN_CAGGAGCC
-CATAGCGA SA_CATAGCGA LN_CATAGCGA
-CATGCTTA SA_CATGCTTA LN_CATGCTTA
-CCAGTTAG SA_CCAGTTAG LN_CCAGTTAG
-CCTACCAT SA_CCTACCAT LN_CCTACCAT
-CTACCAGG SA_CTACCAGG LN_CTACCAGG
-GCACACGA SA_GCACACGA LN_GCACACGA
-GCACATCT SA_GCACATCT LN_GCACATCT
-GGTCCAGA SA_GGTCCAGA LN_GGTCCAGA
-GTATAACA SA_GTATAACA LN_GTATAACA
-TACTTAGC SA_TACTTAGC LN_TACTTAGC
-TCGGAATG SA_TCGGAATG LN_TCGGAATG
-TCTGGCGA SA_TCTGGCGA LN_TCTGGCGA
-TGCTCGAC SA_TGCTCGAC LN_TGCTCGAC
-TGTCGGAT SA_TGTCGGAT LN_TGTCGGAT
-TTCGCTGA SA_TTCGCTGA LN_TTCGCTGA
-TTGAGCCT SA_TTGAGCCT LN_TTGAGCCT
-N SA_N LN_N
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/barcode_triple.params b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/barcode_triple.params
deleted file mode 100644
index 59d2c33..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/barcode_triple.params
+++ /dev/null
@@ -1,26 +0,0 @@
-BARCODE_1 BARCODE_2 BARCODE_3 SAMPLE_ALIAS LIBRARY_NAME
-AACTTGAC AACTTGAC AACTTGAC SA_AACTTGAC LN_AACTTGAC
-AAGGATGT AAGGATGT AAGGATGT SA_AAGGATGT LN_AAGGATGT
-ACCAACTG ACCAACTG ACCAACTG SA_ACCAACTG LN_ACCAACTG
-AGCAATTC AGCAATTC AGCAATTC SA_AGCAATTC LN_AGCAATTC
-AGTTGCTT AGTTGCTT AGTTGCTT SA_AGTTGCTT LN_AGTTGCTT
-ATTATGTT ATTATGTT ATTATGTT SA_ATTATGTT LN_ATTATGTT
-CACATCCT CACATCCT CACATCCT SA_CACATCCT LN_CACATCCT
-CAGGAGCC CAGGAGCC CAGGAGCC SA_CAGGAGCC LN_CAGGAGCC
-CATAGCGA CATAGCGA CATAGCGA SA_CATAGCGA LN_CATAGCGA
-CATGCTTA CATGCTTA CATGCTTA SA_CATGCTTA LN_CATGCTTA
-CCAGTTAG CCAGTTAG CCAGTTAG SA_CCAGTTAG LN_CCAGTTAG
-CCTACCAT CCTACCAT CCTACCAT SA_CCTACCAT LN_CCTACCAT
-CTACCAGG CTACCAGG CTACCAGG SA_CTACCAGG LN_CTACCAGG
-GCACACGA GCACACGA GCACACGA SA_GCACACGA LN_GCACACGA
-GCACATCT GCACATCT GCACATCT SA_GCACATCT LN_GCACATCT
-GGTCCAGA GGTCCAGA GGTCCAGA SA_GGTCCAGA LN_GGTCCAGA
-GTATAACA GTATAACA GTATAACA SA_GTATAACA LN_GTATAACA
-TACTTAGC TACTTAGC TACTTAGC SA_TACTTAGC LN_TACTTAGC
-TCGGAATG TCGGAATG TCGGAATG SA_TCGGAATG LN_TCGGAATG
-TCTGGCGA TCTGGCGA TCTGGCGA SA_TCTGGCGA LN_TCTGGCGA
-TGCTCGAC TGCTCGAC TGCTCGAC SA_TGCTCGAC LN_TGCTCGAC
-TGTCGGAT TGTCGGAT TGTCGGAT SA_TGTCGGAT LN_TGTCGGAT
-TTCGCTGA TTCGCTGA TTCGCTGA SA_TTCGCTGA LN_TTCGCTGA
-TTGAGCCT TTGAGCCT TTGAGCCT SA_TTGAGCCT LN_TTGAGCCT
-N N N SA_N LN_N
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/multiplexed_positive_rgtags.params b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/multiplexed_positive_rgtags.params
deleted file mode 100644
index b6f6816..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/multiplexed_positive_rgtags.params
+++ /dev/null
@@ -1,26 +0,0 @@
-BARCODE_1 SAMPLE_ALIAS LIBRARY_NAME PI DS
-AACTTGAC SA_AACTTGAC LN_AACTTGAC 10001 DESC1
-AAGGATGT SA_AAGGATGT LN_AAGGATGT 10002 DESC2
-ACCAACTG SA_ACCAACTG LN_ACCAACTG 10003
-AGCAATTC SA_AGCAATTC LN_AGCAATTC 10004 DESC4
-AGTTGCTT SA_AGTTGCTT LN_AGTTGCTT 10005 DESC5
-ATTATGTT SA_ATTATGTT LN_ATTATGTT 10006 DESC6
-CACATCCT SA_CACATCCT LN_CACATCCT DESC7
-CAGGAGCC SA_CAGGAGCC LN_CAGGAGCC 10008 DESC8
-CATAGCGA SA_CATAGCGA LN_CATAGCGA 10009 DESC9
-CATGCTTA SA_CATGCTTA LN_CATGCTTA 10010 DESC10
-CCAGTTAG SA_CCAGTTAG LN_CCAGTTAG
-CCTACCAT SA_CCTACCAT LN_CCTACCAT 10012 DESC12
-CTACCAGG SA_CTACCAGG LN_CTACCAGG 10013 DESC13
-GCACACGA SA_GCACACGA LN_GCACACGA 10014 DESC14
-GCACATCT SA_GCACATCT LN_GCACATCT DESC15
-GGTCCAGA SA_GGTCCAGA LN_GGTCCAGA 10016 DESC16
-GTATAACA SA_GTATAACA LN_GTATAACA 10017 DESC17
-TACTTAGC SA_TACTTAGC LN_TACTTAGC 10018 DESC18
-TCGGAATG SA_TCGGAATG LN_TCGGAATG 10019 DESC19
-TCTGGCGA SA_TCTGGCGA LN_TCTGGCGA 10020 DESC20
-TGCTCGAC SA_TGCTCGAC LN_TGCTCGAC 10021 DESC21
-TGTCGGAT SA_TGTCGGAT LN_TGTCGGAT 10022 DESC22
-TTCGCTGA SA_TTCGCTGA LN_TTCGCTGA 10023 DESC23
-TTGAGCCT SA_TTGAGCCT LN_TTGAGCCT 10024 DESC24
-N SA_N LN_N 10025 DESC25
\ No newline at end of file
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/negative_test.params b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/negative_test.params
deleted file mode 100644
index ae53386..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/negative_test.params
+++ /dev/null
@@ -1,25 +0,0 @@
-BARCODE_1 BARCODE_2 SAMPLE_ALIAS LIBRARY_NAME PI DS
-AACTTGAC TTGAGCCT SA_AACTTGACTTGAGCCT LN_AACTTGACTTGAGCCT 10001 DESC01
-AAGGATGT TTCGCTGA SA_AAGGATGTTTCGCTGA LN_AAGGATGTTTCGCTGA 10002 DESC02
-ACCAACTG TGTCGGAT SA_ACCAACTGTGTCGGAT LN_ACCAACTGTGTCGGAT 10003 DESC03
-AGCAATTC TGCTCGAC SA_AGCAATTCTGCTCGAC LN_AGCAATTCTGCTCGAC 10004 DESC04
-AGTTGCTT TCTGGCGA SA_AGTTGCTTTCTGGCGA LN_AGTTGCTTTCTGGCGA 10005 DESC05
-ATTATGTT TCGGAATG SA_ATTATGTTTCGGAATG LN_ATTATGTTTCGGAATG 10006 DESC06
-CACATCCT TACTTAGC SA_CACATCCTTACTTAGC LN_CACATCCTTACTTAGC 10007 DESC07
-CAGGAGCC GTATAACA SA_CAGGAGCCGTATAACA LN_CAGGAGCCGTATAACA 10008 DESC08
-CATAGCGA GGTCCAGA SA_CATAGCGAGGTCCAGA LN_CATAGCGAGGTCCAGA 10009 DESC09
-CATGCTTA GCACATCT SA_CATGCTTAGCACATCT LN_CATGCTTAGCACATCT 10010 DESC10
-CCAGTTAG GCACACGA SA_CCAGTTAGGCACACGA LN_CCAGTTAGGCACACGA 10011 DESC11
-CCTACCAT CTACCAGG SA_CCTACCATCTACCAGG LN_CCTACCATCTACCAGG 10012 DESC12
-CTACCAGG CCTACCAT SA_CTACCAGGCCTACCAT LN_CTACCAGGCCTACCAT 10013 DESC13
-GCACACGA CCAGTTAG SA_GCACACGACCAGTTAG LN_GCACACGACCAGTTAG 10014 DESC14
-GCACATCT CATGCTTA SA_GCACATCTCATGCTTA LN_GCACATCTCATGCTTA 10015 DESC15
-GGTCCAGA CATAGCGA SA_GGTCCAGACATAGCGA LN_GGTCCAGACATAGCGA 10016 DESC16
-GTATAACA CAGGAGCC SA_GTATAACACAGGAGCC LN_GTATAACACAGGAGCC 10017 DESC17
-TCGGAATG ATTATGTT SA_TCGGAATGATTATGTT LN_TCGGAATGATTATGTT 10019 DESC19
-TCTGGCGA AGTTGCTT SA_TCTGGCGAAGTTGCTT LN_TCTGGCGAAGTTGCTT 10020 DESC20
-TGCTCGAC AGCAATTC SA_TGCTCGACAGCAATTC LN_TGCTCGACAGCAATTC 10021 DESC21
-TGTCGGAT ACCAACTG SA_TGTCGGATACCAACTG LN_TGTCGGATACCAACTG 10022 DESC22
-TTCGCTGA AAGGATGT SA_TTCGCTGAAAGGATGT LN_TTCGCTGAAAGGATGT 10023 DESC23
-TTGAGCCT AACTTGAC SA_TTGAGCCTAACTTGAC LN_TTGAGCCTAACTTGAC 10024 DESC24
-N N SA_N LN_N 10025 DESC25
\ No newline at end of file
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/nonBarcoded.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/nonBarcoded.sam
deleted file mode 100644
index 22325ba..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/nonBarcoded.sam
+++ /dev/null
@@ -1,122 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.1 PL:illumina PU:HiMom.1 LB:Hello, World SM:HiDad CN:BI
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-HiMom:1:1:1793:1420 589 * 0 0 * * 0 0 G....................C.....................T.....................T.......... =%%%%%%%%%%%%%%%%%%%%=%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1420 653 * 0 0 * * 0 0 C...A................A.....................C.....................T.......... ?%%%*%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1441 589 * 0 0 * * 0 0 C....................C.....................G.....................G.......... (%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%+%%%%%%%%%%%%%%%%%%%%%5%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1441 653 * 0 0 * * 0 0 C...A................A.....................C.....................G.......... <%%%(%%%%%%%%%%%%%%%%'%%%%%%%%%%%%%%%%%%%%%:%%%%%%%%%%%%%%%%%%%%%&%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1483 589 * 0 0 * * 0 0 G....................G.....................A.....................A.......... :%%%%%%%%%%%%%%%%%%%%=%%%%%%%%%%%%%%%%%%%%%/%%%%%%%%%%%%%%%%%%%%%8%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1483 653 * 0 0 * * 0 0 G...A................A.....................T.....................C.......... <%%%%%%%%%%%%%%%%%%%%0%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%>%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1495 589 * 0 0 * * 0 0 G....................C.....................G.....................C.......... 7%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1495 653 * 0 0 * * 0 0 A...T................A.....................C.....................C.......... )%%%*%%%%%%%%%%%%%%%%(%%%%%%%%%%%%%%%%%%%%%:%%%%%%%%%%%%%%%%%%%%%4%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1527 589 * 0 0 * * 0 0 G....................G.....................G.....................T.......... .%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1527 653 * 0 0 * * 0 0 C...C................C.....................C.....................G.......... :%%%*%%%%%%%%%%%%%%%%7%%%%%%%%%%%%%%%%%%%%%5%%%%%%%%%%%%%%%%%%%%%*%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1545 589 * 0 0 * * 0 0 C....................A.....................A.....................C.......... )%%%%%%%%%%%%%%%%%%%%)%%%%%%%%%%%%%%%%%%%%%)%%%%%%%%%%%%%%%%%%%%%1%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1545 653 * 0 0 * * 0 0 C...T................G.....................T.....................G.......... 5%%%*%%%%%%%%%%%%%%%%2%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1583 589 * 0 0 * * 0 0 G....................G.....................G.....................A.......... :%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1583 653 * 0 0 * * 0 0 C...T................G.....................G.....................G.......... <%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%&%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1596 589 * 0 0 * * 0 0 G....................C.....................C.....................T.......... 5%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%5%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1596 653 * 0 0 * * 0 0 C...C................G.....................C.....................C.......... <%%%+%%%%%%%%%%%%%%%%5%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%+%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1602 589 * 0 0 * * 0 0 C....................G.....................G.....................A.......... <%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1602 653 * 0 0 * * 0 0 C...G................C.....................C.....................C.......... ;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%8%%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1658 589 * 0 0 * * 0 0 C....................C.....................T.....................A.......... (%%%%%%%%%%%%%%%%%%%%=%%%%%%%%%%%%%%%%%%%%%=%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1658 653 * 0 0 * * 0 0 T...C................C.....................C.....................C.......... :%%%+%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1681 589 * 0 0 * * 0 0 C....................T.....................A.....................A.......... ?%%%%%%%%%%%%%%%%%%%%)%%%%%%%%%%%%%%%%%%%%%&%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1681 653 * 0 0 * * 0 0 A...A................G.....................G.....................G.......... )%%%(%%%%%%%%%%%%%%%%7%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%%%%%%%%%%%%4%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1718 589 * 0 0 * * 0 0 G....................C.....................C.....................C.......... :%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%)%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1718 653 * 0 0 * * 0 0 A...A................A.....................A.....................G.......... (%%%%%%%%%%%%%%%%%%%%/%%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1745 589 * 0 0 * * 0 0 C....................C.....................C.....................A.......... 1%%%%%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%7%%%%%%%%%%%%%%%%%%%%%1%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1745 653 * 0 0 * * 0 0 A...T................T.....................C.....................A.......... (%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%%%%%%%%%%%%4%%%%%%%%%%%%%%%%%%%%%0%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1777 589 * 0 0 * * 0 0 G....................C.....................T.....................C.......... :%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%:%%%%%%%%%%%%%%%%%%%%%1%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1777 653 * 0 0 * * 0 0 A...A................C.....................C.....................C.......... )%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%(%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1813 589 * 0 0 * * 0 0 G....................C.....................A.....................C.......... 7%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%1%%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1813 653 * 0 0 * * 0 0 C...C................C.....................T.....................C.......... <%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%*%%%%%%%%%%%%%%%%%%%%%:%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1916 589 * 0 0 * * 0 0 G....................T.....................T.....................C.......... <%%%%%%%%%%%%%%%%%%%%6%%%%%%%%%%%%%%%%%%%%%=%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1916 653 * 0 0 * * 0 0 C...A................T.....................C.....................C.......... (%%%(%%%%%%%%%%%%%%%%0%%%%%%%%%%%%%%%%%%%%%5%%%%%%%%%%%%%%%%%%%%%4%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1959 589 * 0 0 * * 0 0 G....................C.....................T.....................C.......... <%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:1959 653 * 0 0 * * 0 0 A...C................C.....................A.....................C.......... 1%%%%%%%%%%%%%%%%%%%%'%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:602 589 * 0 0 * * 0 0 T....................A.....................A.....................A.......... <%%%%%%%%%%%%%%%%%%%%>%%%%%%%%%%%%%%%%%%%%%7%%%%%%%%%%%%%%%%%%%%%2%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:602 653 * 0 0 * * 0 0 C...A................T.....................T.....................G.......... ?%%%&%%%%%%%%%%%%%%%%;%%%%%%%%%%%%%%%%%%%%%:%%%%%%%%%%%%%%%%%%%%%6%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:808 589 * 0 0 * * 0 0 T....................C.....................C.....................T.......... :%%%%%%%%%%%%%%%%%%%%?%%%%%%%%%%%%%%%%%%%%%?%%%%%%%%%%%%%%%%%%%%%<%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:1:1793:808 653 * 0 0 * * 0 0 C...A................A.....................G.....................G.......... <%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%%%%%%%%%%%%%.%%%%%%%%%%%%%%%%%%%%%,%%%%%%%%%% RG:Z:HiMom.1
-HiMom:1:2:1793:1117 589 * 0 0 * * 0 0 G.GGG.......C.GGTCGTTAGCAAGTGATGGCTGTGTTCTGTATCTTTATTGTGGCGACACTTACATGACTGGA 3%;B7%%%%%%%=%9C*'5@?BCB><.9>?@BA)>>(B<3@)@4?B<8)5>67<6A5+5-0.(84-8637,7/7%) RG:Z:HiMom.1
-HiMom:1:2:1793:1117 653 * 0 0 * * 0 0 TTCTTCAGCTGTATTGAAGTATAATTTACAATACAGTACAATTCATATATTTTAATTGTATAATTTAATGACTTTG +4 at .:B=?<'<?@2+=38A4+;>.3:9A>(7??A09(0>((0=A::;,;+/(:+*769)..'09>.%+2-4>-'(7 RG:Z:HiMom.1
-HiMom:1:2:1793:1329 589 * 0 0 * * 0 0 C.TCT.......T.GATGCAGTAACTGGAAATATAGAAGATGCTGTGACTCCATTTGAATCTATAAAAAGCGTTGT 8%805%%%%%%%3%9?*7?(1(90'80;4(:??<<+9:5+/=A85,/=?3)=')6-+*,5=/902-2-0+5-%,-0 RG:Z:HiMom.1
-HiMom:1:2:1793:1329 653 * 0 0 * * 0 0 GAGCCCCGCGTCTGTCTCAGAGAACTTTTGCATTCTTCTTGTTCTCCAGGAGAAACGGCATCATCTTCCATGTCTT A@=*BC at -+:6B8'6 at BC@C>,;2)5BBBBB>;BCBBC at 6@@BAACCB>B;8)07*<@=':C><<9A@(68@=B59 RG:Z:HiMom.1
-HiMom:1:2:1793:1354 589 * 0 0 * * 0 0 T.GCT.......G.GGCGCCGCGAAGCGCACGGCGCCGACGCAGGGGGAAGGCGGGACATACACGACCCGCGAGCG 1%;A;%%%%%%%8%(5;@B7;(;*8;(8@;@<9/81((77*<(8 at -3<'(5=;(7((<')'<.0(/*(7/.2(9>1 RG:Z:HiMom.1
-HiMom:1:2:1793:1354 653 * 0 0 * * 0 0 CTGAACCTCAAGTCTCCACCAATCAGAATCTGGGGGAGGGCGCGCGTGCAGGGAGCCGCCTGCTCTCCACCTTCGC A24(06/+.2(21?49?:-+(5&8&5**4?1'13..0'.'%,,98&%(60&.++1(&+A,,0..8.18(.0&+,,/ RG:Z:HiMom.1
-HiMom:1:2:1793:1455 589 * 0 0 * * 0 0 C.TTC.......G.GACTGCAGTTGCTGTTGCCCATTAAGACCTTGAGAAAAGGCTTGCCTGCCCTTCGTCTGACT ?%8=?%%%%%%%:%9'=?@C*@2'=B<;/(;=%?,89'80(=B9=>7145.-(7B-)38/5)'=%5-=:/57)%6% RG:Z:HiMom.1
-HiMom:1:2:1793:1455 653 * 0 0 * * 0 0 GGAAACCAACCCCTCACATGGTAACCCGCTCCAACCCGCACGCCCTGTTCGGCCCCTGACCCGGCCCCCCGGCGCA >/,+'<:''',5'3(59'+.705,/8 at 94(,+'5@;'%7%%;3>86.*%04&'%17(&.5%%+%,>0624*%,*:% RG:Z:HiMom.1
-HiMom:1:2:1793:1478 589 * 0 0 * * 0 0 T.TTT.......C.AATTTTACCTCATAAAATTTTTTGAGGTTTGATGTATGTCTCTGTCTTATCAATAATGAGGC =%?C?%%%%%%%*%+, at CCB>BCBBA@=778BCBCBCB?BC?BCA4AC@;@C at CBCBBACA:)=B>';64=>6=AC RG:Z:HiMom.1
-HiMom:1:2:1793:1478 653 * 0 0 * * 0 0 CAGCCATTCAAATCCAGTATTTTTTAAGCCTCATTATTGATAAGACAGAGACATACATCACACCTCAACACCTTTT A:;C?'7<>(0*8B?*:4-4;A><8+-9BB>?/;;7:<702'+:(?/9(92<+12<,5;&'.>@<?*&%*&%3865 RG:Z:HiMom.1
-HiMom:1:2:1793:1793 589 * 0 0 * * 0 0 C.CCA.......C.GGGCCCTTTGTCTAAAGTCTGAATCAGCATTTGGATTTAGCCCTAATAGAGCCTGTTCATCC =%?%)%%%%%%%=%68>BBB9?>@:B:)2(7:A84'67>5;>/67889'385,9@?=-+(327+3@>8777</15@ RG:Z:HiMom.1
-HiMom:1:2:1793:1793 653 * 0 0 * * 0 0 GTTTATAACTTCTTCTGTGGGATCAGCGGGCACGCCTCTTCCCACCAGCACACTACACGTCTACCAGCGCGGATGG B?A>.90)(<@CB?C at B8BA>?=?*<&:@?=%;ABB:&85&=+>A=%7&+'. at 3&9&,=2&810626B7'<5%->: RG:Z:HiMom.1
-HiMom:1:2:1793:1812 589 * 0 0 * * 0 0 C.CTC.......C.GCATACTTAACAAGTCTGATCTTGCTTATAGAAATTGGATCTTACTACTTCATTCTCAGAAT (%?B>%%%%%%%?%>B7=- at BB;=@07B at CBB5?CBBBCB?+>:B944?BB at 1@CBB9/=7B at AB=@@BB@(>(8< RG:Z:HiMom.1
-HiMom:1:2:1793:1812 653 * 0 0 * * 0 0 TCCAGCATGAAGATAATGGCTAATACCAAAGCAGCCTTTTTGCTGTGGTAGGAAGATAATGGCTAATAAAAATGAG BCCCCB9A at ++@4?7+?CBCA@)=)''/2)8@)=?(;??AA=&=B at BB02<9.)3).%0-2<5&/+*1%(:'*,%9 RG:Z:HiMom.1
-HiMom:1:2:1793:1893 589 * 0 0 * * 0 0 G.TCC.......A.TCCCCGTGGATGAAAATGCTGTACATGTTCTTGTTGATAACAATGGGCAAGGTCTAGGACAG 0%;C<%%%%%%%)%9CC@(>?C at 1=A7(00=BCAB96A><A?@CAAB at AA5>7AB1'6>7>B9.9B7B5)7;5B<> RG:Z:HiMom.1
-HiMom:1:2:1793:1893 653 * 0 0 * * 0 0 GGGCAGGGGGCTTTTTCTCACTCTCTCTCATATCTTCTAGGGTAACTACATGAACACACGCTTCTCTCCCCTTCCG ABBB4=BBB:)=B<AAC?C>)?C at C?CBB3;)<C at BC9(>?A3 at -@=)@6@=4'?4(425C9=B<C at CB@(07((: RG:Z:HiMom.1
-HiMom:1:2:1793:1909 589 * 0 0 * * 0 0 G.CCT.......C.CTCACACCGCCCCCCTTCTCACCTGCCCTGCGTAACCTGTACTGACTGCCCACTCCTCACCC (%<@8%%%%%%%*%;(8@;*>7;*.(<B>5(.5@/*>93;(2@=-:'5>)0=+1;'5:';/(;1@*>,(;';((:) RG:Z:HiMom.1
-HiMom:1:2:1793:1909 653 * 0 0 * * 0 0 CTCACACCCACACCCCCCCCAATCCCACCCCCGGACACCACACCCCTCCAACTTCCCCCCCCGAGCGCAGCCGGGG B16+:&3:(%+'4+&6;/2(%,/29.'5,,--,('&.''%%,&.1+%*:%%1%%%%,((%'&(%(247-*%+11&% RG:Z:HiMom.1
-HiMom:1:2:1793:1931 589 * 0 0 * * 0 0 G.CTA.......T.CACTGTCGACACCGCACACGGGGCATACCCACATCAAAGCAGTCCCCCAAGTCCCTGCGCAG <%8.'%%%%%%%&%.(<B**(>3*775(*(;'.6''+;'&1(9.).*(7;5/'2(64A70>0.,23@)0%'5=<*' RG:Z:HiMom.1
-HiMom:1:2:1793:1931 653 * 0 0 * * 0 0 CTGAAGCGCCACCGCCGCGGCGTGGCGGGCCCCGCGCACCACCTCTTCCCGTCCTCTACCGGCCCTGGCCACGCCC 9+&'411'41,0'1/.%'%&9(0,%,'--%%-'%%.''.,((.+,(%-3+++,/(*+&'3,+*-%%**.&%,0'*( RG:Z:HiMom.1
-HiMom:1:2:1793:1969 589 * 0 0 * * 0 0 T.CGC.......A.CCCTGACTGGCAAGGCGGTGGCGGCTCCAGTGAAGGCTCCCCGTGTTCTTAAAGACTAGCGC 5%8((%%%%%%%1%;BBB>+)7BBB?-?10 at B7BBB9A@@A379'?*39BA4@>);'5:'BBAA;>2>A6+9+@*< RG:Z:HiMom.1
-HiMom:1:2:1793:1969 653 * 0 0 * * 0 0 GAGAACTCTCTGTGTAGTTGTGACTTCCATCCTTCCGCAACAGTAGTAAGGACCGCGACTTCTGACCACATTGACC :%===(,=B>=:-;7<B/?@8@=:8==>'.,=86 at B@A,,+07-(9'35>?58//?;-'+.8(50'619('''+/9 RG:Z:HiMom.1
-HiMom:1:2:1793:2004 589 * 0 0 * * 0 0 G.GTT.......C.TACTGGCATTTACTGTTTAACATCACACACCAAGCCAGGTTATTTCACACTCCTGCTACTGG 8%13<%%%%%%%:%?CCBBB?(>CCCCCBA@*9+ at +@C at +*1?;8 at +3*@*8C4 at 4>C>7 at 8115?),CC<7@?:A RG:Z:HiMom.1
-HiMom:1:2:1793:2004 653 * 0 0 * * 0 0 GAACTTGACTATCTCTTCTAATTTTATTGTTTATTTTGTGTTTACTGCCCAGCTACTTCCCACCTTCCACTTGCTT B?4 at C@<+>=57'3B>=)?4>BBA?+=@B@>7-;@@@A=B::7?4<>?*?<8B83A?=>(>;BB1A.%-@@:8 at 5= RG:Z:HiMom.1
-HiMom:1:2:1793:2031 589 * 0 0 * * 0 0 C.CCG.......G.GGTGCATGGGCTCCAACGTGGTGTCCTGTGGAGCTGTTGGGCCTGGGCAGGCGGCACAGATC :%'*:%%%%%%%:%:B;B@(<BBAB9BA3AAB9A@,B1(==A6 at A/??;=5=?A3%273<4A,;7;:=;+&&/,/3 RG:Z:HiMom.1
-HiMom:1:2:1793:2031 653 * 0 0 * * 0 0 TGCCAGTAGTTTTGGGTCAAGCCCTCACCTGATTCCACGCTTCATAGCTTCAGCCGTTCCCATCATACTACTAGCT BBBC=>==B=@@@@BB5@)-=CBA9'/B@=>16 at BB)(8'4=A54-=B:8@(;?(9'0?A7'1A.96>3/'4235- RG:Z:HiMom.1
-HiMom:1:2:1793:2038 589 * 0 0 * * 0 0 G.GCG.......G.CACCTTGGTACTGGGTGATGGGGAGGCACTGAATGGGCTTCAAGTCCTCAAACGCCTGATCT ?%:-;%%%%%%%.%=)@CCACB=8ABCB?7@&>B?AC=?CB9C4AAA>>6==>>;%5>3%:/:%,3.;@0,9*-1; RG:Z:HiMom.1
-HiMom:1:2:1793:2038 653 * 0 0 * * 0 0 CCTGTGTCTCAGTGAGCCTTCAGTGCAACATACGGGTAAGAGCAGCCTTCTCTTCACTGAGATGAGACCCCCCCAC B>626.288?89.5'5??60,477.3'%%)+112.21.&21330/75*)55(5+./,2*%-,/1)162/2'55662 RG:Z:HiMom.1
-HiMom:1:2:1793:310 589 * 0 0 * * 0 0 C.GGA.......T.GAACCTTTGGCAAGGCTGCTCTTACGAGTCCTCTCGCCCTGTTCCACCTATCCCCATAGCTA (%5;'%%%%%%%(%.*0 at 99@AB>CA5):=:A1;A<3':-''.'3';('5>BC at B=A(A<>511(6B?,''(<&-* RG:Z:HiMom.1
-HiMom:1:2:1793:310 653 * 0 0 * * 0 0 CGAAACTTGGGTCAGTAAACTGGTGAAGCTGACCTATTTGGCAAGCAGCATGATTCGGAAGCGCGGCAGGCAGAGT ?(5 at BB*>57 at 6B@*34)?=6B@()'18%'?=@A*:@?4 at +(4>A;8<'/@=366A@;/7@(-'()7(1(8(2''' RG:Z:HiMom.1
-HiMom:1:2:1793:404 589 * 0 0 * * 0 0 C.CCC.......T.CAATGCTATGCAGTATGTCTTCTTATCTCTGTCTTCAAGAGCATCCTCTGTCAGTCCTACAT :%)?0%%%%%%%9%*/0%,8.-->>>>9@?=975(=4/%0?74'/''39%-?8828,4412=0168;2+9A:74'5 RG:Z:HiMom.1
-HiMom:1:2:1793:404 653 * 0 0 * * 0 0 ACATGAATCCTCTCCCACAGGAATTATTCAGCTTACCGCGAGTACGCTTCCGTGTTGGAAAGATTCAACTCACCCC ;'7B62:2(=/8<>A at 9A=88>6<==:4?%5A8=;>@*73,.%6?<'%%5;+)%%-2'1)&%5(-937&0)%%0=B RG:Z:HiMom.1
-HiMom:1:2:1793:475 589 * 0 0 * * 0 0 C.GGG.......C.CCCCCCTAGGCAATATGCTACTGCATATATATTTGGTCTAGATATATAACAAGTTACTACTG ?%9?3%%%%%%%0%<<%5;(2*7<@?(1')6>7?,7=7@*)6)35'7:7)%%,'3(.(+2++482.:))-%0-''2 RG:Z:HiMom.1
-HiMom:1:2:1793:475 653 * 0 0 * * 0 0 AACTTTTTTACGCAATGTTAATATTCAACTCTTCCTTCCAATAGAAATTTTCTGCTGCTTTTCTTGCTCGTGCTAG BCB77433)@1)@*:>A9+>401>@?:*@6=(6C8*/2@<(2A8%)6?;97 at 9+9;<'3/4)-15:34+)'8'2-- RG:Z:HiMom.1
-HiMom:1:2:1793:666 589 * 0 0 * * 0 0 C.GAG.......T.GGGTAGGAAACACAGCCTTGCTCCACAGCGCACTGTCAGCAAGACGCTCCTTTCTTCGGAGA ?%9(9%%%%%%%%%7)9..<::>3>1;77<B05??)B>0=12(2A6=4:4956?/%5-%-;1;6542;/-&(26,( RG:Z:HiMom.1
-HiMom:1:2:1793:666 653 * 0 0 * * 0 0 ATTTTTGCTTTCCTTGGCCCCCACCAATTTATACATCTCCATTTTCCGACCTCTGGACTAACTGCTTGCTCAGCAC 6;BAC?AB@@>@8;@>@BBBBA:@B8=?;1>6 at AA<B4AB:94<;=,0'<@<A87)7B=73@;3)'/69(<,67'% RG:Z:HiMom.1
-HiMom:1:2:1793:829 589 * 0 0 * * 0 0 T.GGC.......C.TGGGCAAGCACCTGACCAGCAACAGCCCCCGCCTGGTGCAGCACTGCCTGTGGACCCTGCGC ;%;>*%%%%%%%<%:BAB at 0;BBBBBB@;@B at A@;*@*>BBBBBABBA?@3@@;<(5 at AAB@:>.=;,<BB;<BAB RG:Z:HiMom.1
-HiMom:1:2:1793:829 653 * 0 0 * * 0 0 TCGCTGTTGTTGCATGTCAGGTTGGAGAGTGTGCCCGTGGCCCCGGTGCGGCCGGTGGCCGCCCCCCCCCCCCGCC AB at BBA=AB?AA@)8@=@)>=>=A>3=0>4A3ABB at 6+<><(<'88*8%:8%:4%52(8%(55%4>2<7;*;2%7% RG:Z:HiMom.1
-HiMom:1:2:1794:490 589 * 0 0 * * 0 0 C.TCC.......T.TATTTACTATTTTCTGATTTTTAAAATGACAGTGGCAATTACCATTTATACTGTGTTATTTG ?%8C?%%%%%%%9%6(=?:(=@BAA@@B at A<<<<=@=;5?@9+?A@:?9 at 5&1=>A?+:6668=A9?7?9?=<9=6 RG:Z:HiMom.1
-HiMom:1:2:1794:490 653 * 0 0 * * 0 0 ATAAACTTGAAAATAATTTTCTATGATACAGCTTTCAGGTAGAAAAATGAATTTTCGTCGTGTTTAACAATGTTGT ABBCBCAAC@;5@@77BBB?CCBBB?@BCBBCAB@@3<A6>>)99?0<B at 6?>@@BB6A9>B5A<@6<%+>@<<:0 RG:Z:HiMom.1
-HiMom:1:3:1793:1031 589 * 0 0 * * 0 0 C.ACT.......G..GCATTGGAGAAGAACCAAGCTGGCTCTCTAAGGAAGTGCACACGAGTTGGAACACATATTC ?%<?(%%%%%%%:%%=B47?B=6?=2?/00 at 8), at BB=3,>).'50;:72))1)5=:)<19%)+(%5?:=;7.)1' RG:Z:HiMom.1
-HiMom:1:3:1793:1031 653 * 0 0 * * 0 0 CCCATACCAGCACAGAGCATACAGAAACACAGAAAAAATATTCCCAGTAAAACATGTGCAACTGTCCAGGCAGTCG +5AA at 92+>4AABBA6@;'(-;<=22)B8@@@7>A@<583498 at 62-45:-8>8;:0081*956-;7.)*%.4))0 RG:Z:HiMom.1
-HiMom:1:3:1793:1143 589 * 0 0 * * 0 0 T.GGG.......T.CATGGTGAGGAAGAGTCGGAAGCAGGCATGCGGCTGCAGGGAATGCAACTTCTTCTCCATCG :%(B3%%%%%%%:%=BCCC<CBBB<CCB3*@?BBBAA*=B at 9@?B?8<3;>3;A;+2:9<43:<;?9>A:8<+%<% RG:Z:HiMom.1
-HiMom:1:3:1793:1143 653 * 0 0 * * 0 0 CTGCAGAGCAGTTGTGGCACTGGGCTTTGGCCACTCAAACTCAGGCTGGTCCGGAACCTCCCCCACCCCGCCCCAC A==B59>>A at 8/7=,19:+:'344A..366?A9=4>168?1:113;42,%7:3-&177&59=;8&,=2%(8+7%%2 RG:Z:HiMom.1
-HiMom:1:3:1793:1282 589 * 0 0 * * 0 0 G.TAG.......C.GGACTCTGGCGTCACCTTTGGCGCTGAGCGCCCCAGGCCCGCCAGCCCGCCCGCCCACTGCC <%;(.%%%%%%%(%.6.(;B at 55+9>*8@(>*@;(.;@75'5';;@;;*4<5<2*@;/><@5>5(16;1;7)',.. RG:Z:HiMom.1
-HiMom:1:3:1793:1282 653 * 0 0 * * 0 0 AAGCACACCAAGCTTCCCGCAGCTGCGGCGCCCCCGCTCCAAGGCCAGCAGCTGCCCCCTCTGCCCCCACCCCCTC (*579.1(.//>B at -17+=../@9=*=(.(.;<.1'>;<:'''7=;'.':==:551938*7.7;:%7:'';@;609 RG:Z:HiMom.1
-HiMom:1:3:1793:1301 589 * 0 0 * * 0 0 G.AGG.......T.CAGGGTTGAGGTATTCTTAGGTTAGCCGAGCTCTTTCCTCCTTTCCCCCCCCCTCTCCCCCA ?%*:3%%%%%%%(%;*9)>3+-*-@=)3?CCBAA;)A8 at 2*25;A7,52=B;(=)47)=BC;+:C@)2 at 0=BA9(9 RG:Z:HiMom.1
-HiMom:1:3:1793:1301 653 * 0 0 * * 0 0 GCATTGCGTCCATCTCTTTACAGAAGAACTCAGCCCACACCCTAGAATGTACACCTTTGGAAAAAGGAGAAGTGCT =(6;9*AA;*BCBCCCABB at CB@)??@>@BBBCCCA6 at 8?CC>9@>=?@-2)9AB;6>>;5334=3=7+6-14?=- RG:Z:HiMom.1
-HiMom:1:3:1793:1311 589 * 0 0 * * 0 0 G.TAT.......T.TTCCTTCAGTCTGCACAAAGATTAAGGTAATTTACAGTCAATCTGTGAATGAATGTTGAGAC <%()<%%%%%%%7%<<BCBCCCABCCCC at CBB?BCCCCCBC>AACC?*@.BAB8*@CCCBC@:@?7?ABAA??B8B RG:Z:HiMom.1
-HiMom:1:3:1793:1311 653 * 0 0 * * 0 0 CAGCAAAAGTGCCGGCTAGTCCGGTTTGTTGAAAATACAGTAGAAAAGCTGATTCTGGTTATCTCTCTCAGGACAA B<ABBA4=A1?CCBB*B9?:>'>@)?A@<AA74;A@?B=>)'6'61<58(:/75A?7(0===@=@4*7%355/>40 RG:Z:HiMom.1
-HiMom:1:3:1793:1326 589 * 0 0 * * 0 0 G.CCA.......C.TCTTGGGCTCCACACCATTACCAGCATCAGAGGCAGGGGAACACAATCTGCTGCCTTATAAG ?%?@7%%%%%%%?%3C=+;.<@+@@8A?AC@@ABBB at BCB?+?;?-5- at BA92-7B<?-2/,*@A2?BB;A5?1'4 RG:Z:HiMom.1
-HiMom:1:3:1793:1326 653 * 0 0 * * 0 0 CAAGATCATACTAACACACTCCAGCCTGGGCAACAGAGTGGGACTCTGTATCCAAAAAAAATTCTCTACCAACTAC BABB==BA?@CB??BBCCCCBB- at AC0B<,CCCCA at 4<@A;;AC+CBCA,BCA1=A:=9<=A,C?+<?B?3<B,?C RG:Z:HiMom.1
-HiMom:1:3:1793:1389 589 * 0 0 * * 0 0 G.GGG.......G.CGCAGGTGGGGATGGGCACCCTCACAGCTTCCCTGGACCTTAGTTTTGTTGGGGTTCAGTCC :%<B;%%%%%%%7%;A at 1@>.>BB@:;ABAABBBBB<+<7?@8 at BBBBA72@>2<(>5+=7906A<;5*3<2 at -(4 RG:Z:HiMom.1
-HiMom:1:3:1793:1389 653 * 0 0 * * 0 0 ACCACAGGCACCACCAGCCACGGACCCACGCCTGCCACTCCCCACCCCCCCCCCCCCAGCCACGCCACCGTCCCAC 7@>*@0:3 at 2@@7BB=ABB3B=5%;B>(>0%:;<A=0@=8';&(:?A>2>7%<;%:A;3@>+.*%%.+<0/:)>-) RG:Z:HiMom.1
-HiMom:1:3:1793:1405 589 * 0 0 * * 0 0 G.TGG.......T.GCTGAGATGCTCTTTAACCAAAGGAGGAAAGAGAGGAGACCAAGGGCCAGCTGGTTGGTTGT 7%1C=%%%%%%%8%8CA=2@?ABB6BABBABBC;:>BB>B at 9(;A=@?B>3?)@A?=5(7?@1>B=A;(=@@,1=3 RG:Z:HiMom.1
-HiMom:1:3:1793:1405 653 * 0 0 * * 0 0 GCCTTGTTTGGCCCTGATCTCTGACTTCTAGAGCCCCAGCTGCTGGCGGCTGCTGGGATATCCTCCCCGCTCGGGT @BBBBBA@@9BBBBA11=BBBBBABBBBB9=9BBBBB9ABABB@*=B@@719.2=33%822@>'':A5%1+%77%( RG:Z:HiMom.1
-HiMom:1:3:1793:141 589 * 0 0 * * 0 0 T.CTC.......C.CTTAGCAGTGCGCCCCCCGAGCGCGGCACAGGGGCCAGGGAGACAGAGGACACCGGGATCTC ;%;9,%%%%%%%,%52(((3.8(+/*/B at 1<1((=.&4+9+/(::11+(&7600+.+A4'*%%%-%:/,%%,'9'B RG:Z:HiMom.1
-HiMom:1:3:1793:141 653 * 0 0 * * 0 0 CTCTCCCGCGCCTGCTACGGAGCCCGCTCGGGGGGGCCACGCCGCTCCCGAGGACGTAGCACCTCCTCCACTCACG 4:-*695*:&7(.333?9*'(@(6.((%%,;62+*..(./0(>3/&%14(,1((0-6&15%%.6>(&'%+20&+3( RG:Z:HiMom.1
-HiMom:1:3:1793:1507 589 * 0 0 * * 0 0 G.GTG.......T.GTTGCCAGCCTGCTGCCCGCCATCCTGGTCTTCATTCTCATCTTCATGGAGACACAGATCAC =%==8%%%%%%%?%5ABABBABCCBBCBBCCCBC at 09ACB==;CBB at 0;>ABBBACA>?'9A==>)@)?9;63?5@ RG:Z:HiMom.1
-HiMom:1:3:1793:1507 653 * 0 0 * * 0 0 CAGAGCGCGTTGGCGTGAGTGACAGAGCGGCCAGTGGCCGCCGCCCACCCGCCCACGCCCCCGAGGGCCCCCCTGC @11+1?4>44344=533,252.;11,->4.&7.**,-5++.,(.7*&,1*%%%.*(%...,*%*+,%%+1(&+%,. RG:Z:HiMom.1
-HiMom:1:3:1793:1557 589 * 0 0 * * 0 0 G.GGA.......C.TCGAGCCATTCCACTCCCGCCCGGGCACCAACAGCCAAACGCACGCTCATCAAAAAGGCCGA (%;*(%%%%%%%;%5>/(4?A;=6(><1*@1*-@@>/*0 at 9)9?>2.=8'<,8<,1((%:1<?+(.08'+55B?:% RG:Z:HiMom.1
-HiMom:1:3:1793:1557 653 * 0 0 * * 0 0 CGGCTTTTTTTTTATTGAGACCAGCTCCTGCCCTACCCCCGCGGCTGCGGAGCAAGGTCCCCTTCATGCGCCCCCC 5&0/(7*3>96=9)<*+%'+5,/%'&7%7+675%'%%+09*(*'2(5%%,&(.&,%%(,6%(&'7&+&,&-,+554 RG:Z:HiMom.1
-HiMom:1:3:1793:1570 589 * 0 0 * * 0 0 G.TCT.......T.TCTCCACTCTGCTGCCCTACCTCTCGGAGTCTTCTACCGCGTCTAACTAGTCATATTTACAA 6%3B6%%%%%%%,%'C@@BC>1?B at CC?C at CAB@B@?6&BACA4,?*<B@>1'13,<B;)@BB3'?%)+:A@;CB@ RG:Z:HiMom.1
-HiMom:1:3:1793:1570 653 * 0 0 * * 0 0 CAGACACCTTTCATATCTTTATGGCAACTTAATTTTTGGCCTTTTATCACTCTGTCATACCAGCATTCTGCCGTCA A@>;B at CB549'34=9B;?>/A@?8@@;=<(9/5++<74B;B<%..;C-(.8?@(>'9@>><6>(4;<%*.(.*=: RG:Z:HiMom.1
-HiMom:1:3:1793:1617 589 * 0 0 * * 0 0 C.GAA.......T.CGCCTTCTTCTTCAACTCGGAGCTGCTGAGCGCTGTGCGCTTCGCCCTGGGCAAGGGCCGCG :%75'%%%%%%%3%;;BA><A;=B;7 at 84>'9>:90<,7<,61132%*8//3471'349+6,36+:&+462+.&.% RG:Z:HiMom.1
-HiMom:1:3:1793:1617 653 * 0 0 * * 0 0 GTGGTCATAACTGTTTCTGGACCCATTTGAACTTCATCTGAATATAGAAATCTCAGCAGCGCCCGGACGGCTGCGG A<CBAB4>=, at BB@BAC at B=*A@*+>ABB94BB at B;>B?;>@@5A;B=046C@@(6A9;A2A<'90'(:-?%3:/: RG:Z:HiMom.1
-HiMom:1:3:1793:1709 589 * 0 0 * * 0 0 G.GGG.......T.CCATTGGTTTCTGAAAGTATTCACATCATTTGGGATACCAGATAGCTCAATACTCTCTGAGT 8%>B<%%%%%%%:%?B8BBBB?BBCAC?@6 at 1;AB@*@<>B9>?@@B?9<4BB8 at 82)<C at CA:?8B at C@C@?/=' RG:Z:HiMom.1
-HiMom:1:3:1793:1709 653 * 0 0 * * 0 0 AGCCACTGTCCCGTGTATAACTTGGCATTAGAGCACCAGGTCTGTTGGATGGTGGTGGCAGGCCCAATTAATTTTT ,?@)7 at B@6BCCC;C?@A;+ at A;BBB=;BA at 6@B6B@(>B8CAA6<B?69B?(B=-:@>-7 at 85:%.))3&73-%) RG:Z:HiMom.1
-HiMom:1:3:1793:1738 589 * 0 0 * * 0 0 G.GCC.......G.CTCTTGGGGAATATCTGAGGCTCTGTGGTCACCCACAGACCCGTTACTCCTTTAGGTGTCTG ?%:C?%%%%%%%8%=BCABBBBC?BBCBCBBBBBC at C?A1AB.?3?A2)@880@@)0%96?9 at B;><+=>5 at 0>=@ RG:Z:HiMom.1
-HiMom:1:3:1793:1738 653 * 0 0 * * 0 0 TCCCTGACTGGATACAGGCAGCTGACCCCTTCTCCCGACACCTCAAGGAGTAACTGGGCTGTTGGTGACCCCCGAC ABBBBA at BBBA<B7B at ABBAB;(:';BBA=A at 0@@*90@)@B<(>)>>(>(+;@9@:%;*<(54 at +.%3@(>5(%' RG:Z:HiMom.1
-HiMom:1:3:1793:1779 589 * 0 0 * * 0 0 G.GCA.......C.TGCGTATATTTACAGATATATATACAGAATTGTTTGCTCTGAGCCATTTATAAGCACTTACT =%5A0%%%%%%%?%)9*>'=@::>BBB:B@;7AAA at 7@=3/.*:?@8;,<*;B4=ABBC?).=4>(;BA=CA:-?; RG:Z:HiMom.1
-HiMom:1:3:1793:1779 653 * 0 0 * * 0 0 CACTGAAATGTTTAGGACCATATTATAAGTAAGTACTTATCAATGTACTTTAGGACCATATTATAAGTAAGTGCTT =:AB>(>64A=;27A@=B@)=64@@:5)@9<)=:BBB@:='?'9B*BC>)67B at AC@;=9>)0@*8?:40:<BC=< RG:Z:HiMom.1
-HiMom:1:3:1793:1793 589 * 0 0 * * 0 0 C.TCT.......A..ATGGGCTTTCTACAGCCTGCTTACCACTAACAGTAAGGAATCTTTCATAAACACACCTCAG :%1 at 6%%%%%%%&%%'-;:)62(9=)=>3)0A9>@501??:=5:583466.451,9 at 952<,94.2;88+2=8;3, RG:Z:HiMom.1
-HiMom:1:3:1793:1793 653 * 0 0 * * 0 0 GCTCAAATTTGTGCTACCAATGATATCGAGTTTATAGCAAATTTTCTACGGGAAGTCTATGCGGCAATTTTCTCAT BCA=8+3?C=A-8A@:ACB?,@;8;@+@*@;C3,8)8C?+9=;2*=+='2A?898*+0%())18)42:?A7B>?': RG:Z:HiMom.1
-HiMom:1:3:1793:1859 589 * 0 0 * * 0 0 G.GAG.......A.CCAAGCATCTATCCCAGTGTGGGGGCTGAGGCTGCGAGAGGAAAGCGGGGACGGAAGACGGG <%((;%%%%%%%<%(;=<B96<@B3?BBB=B11(A;BB/(0=-:?9)@-=,12<=2>>:@8@':%8<=.52(82(+ RG:Z:HiMom.1
-HiMom:1:3:1793:1859 653 * 0 0 * * 0 0 CGATTTTTAAGGACCCCGTGCCTCTGGGGGCCGATGAACTCCACGATGGGACGCACCTGGAGCTCTACCATCAATA BB55A9?@>.(7AAAB?3,A>A=A>A6@?>29(434(.'0B?2:?266<2/,91:B9.1)06451//&&78A10,2 RG:Z:HiMom.1
-HiMom:1:3:1793:1898 589 * 0 0 * * 0 0 G.ACA.......G.AATATGGGCTTATCCAACCCAACCAAGATGGAGAGTGAGGGGGTTGTCCCTGGGCCCAAGGC :%/=(%%%%%%%:%*/<1=5;BBBAAACCA8ABCAACB;)@?BBB+B6?4B:A7;??16@=BA?9509B?@-+844 RG:Z:HiMom.1
-HiMom:1:3:1793:1898 653 * 0 0 * * 0 0 CCGGCCAAGCAGGCATGTGTGAATGAACGTGGCCGCTGACTCAGAACAGAGGACATCCCAGGGCCGCAAGCGCGGA BB>ABB3=;>&5(1%2=4=552-',37A=,41>1(1',+.37'1,&9/331(/9/'6.+''0,(%,2&(.1,//.( RG:Z:HiMom.1
-HiMom:1:3:1793:456 589 * 0 0 * * 0 0 C.TAT.......C..CGGGTACCACAGTTGAGGACTGACATTCTGAACCCTGATGTTTCTAAAGAAACGACAGTAT ?%6 at 8%%%%%%%?%%?@?@6AAA??6<>>@6/7?A??6><<8=@252;>@84<9>58@?7.-6;78;<4'9-<:68 RG:Z:HiMom.1
-HiMom:1:3:1793:456 653 * 0 0 * * 0 0 TCCATCCACTTCCCTGAGCCTCAGAAAAGGGCAAGGCATGGCTCACATACTCTCAGCCACGGCCTGGCCTGCTGCC BBB<ABB at BBBBBB=@@ABB?B5 at 777=;;ABA9A;B?=><BB at 6@AA?B>B9>*>AA9A53?>(%89(.9>;<:( RG:Z:HiMom.1
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/nonMatchingBarcoded.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/nonMatchingBarcoded.sam
deleted file mode 100644
index 2c5c3eb..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/nonMatchingBarcoded.sam
+++ /dev/null
@@ -1,225 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7 LB:Hello, World SM:HiDad CN:BI
-HiMom:7:1:0:1038 516 * 0 0 * * 0 0 .....C..CA...C...C.CC...C..... ############################## RG:Z:HiMom.7
-HiMom:7:1:0:1093 516 * 0 0 * * 0 0 .....C..GT...A...G.AA...A..... ############################## RG:Z:HiMom.7
-HiMom:7:1:0:113 516 * 0 0 * * 0 0 ........G...........A......... ############################## RG:Z:HiMom.7
-HiMom:7:1:0:1193 516 * 0 0 * * 0 0 ........T....T...T..T...C..... ############################## RG:Z:HiMom.7
-HiMom:7:1:0:1291 516 * 0 0 * * 0 0 ........A........A..T......... ############################## RG:Z:HiMom.7
-HiMom:7:1:0:1307 516 * 0 0 * * 0 0 ........C....A...T..T...C..... ############################## RG:Z:HiMom.7
-HiMom:7:1:0:1434 516 * 0 0 * * 0 0 .............................. ############################## XN:i:1 RG:Z:HiMom.7
-HiMom:7:1:0:1475 516 * 0 0 * * 0 0 .....G..A....A...A..A...A..... ############################## RG:Z:HiMom.7
-HiMom:7:1:0:1690 516 * 0 0 * * 0 0 ........A........G..C...C..... ############################## RG:Z:HiMom.7
-HiMom:7:1:0:1703 516 * 0 0 * * 0 0 ........A...........A......... ############################## XN:i:1 RG:Z:HiMom.7
-HiMom:7:1:0:1940 516 * 0 0 * * 0 0 ........C........T..T......... ############################## RG:Z:HiMom.7
-HiMom:7:1:0:2001 516 * 0 0 * * 0 0 .....A..TG...G...A.GC...A..... ############################## RG:Z:HiMom.7
-HiMom:7:1:0:205 516 * 0 0 * * 0 0 ........A........A..T...A..... ############################## RG:Z:HiMom.7
-HiMom:7:1:0:275 516 * 0 0 * * 0 0 .....A..CA...T...G.CC...A..... ############################## RG:Z:HiMom.7
-HiMom:7:1:0:324 516 * 0 0 * * 0 0 ........T........T..A...A..... ############################## RG:Z:HiMom.7
-HiMom:7:1:0:37 516 * 0 0 * * 0 0 ........A........C..T...C..... ############################## RG:Z:HiMom.7
-HiMom:7:1:0:464 516 * 0 0 * * 0 0 .............................. ############################## XN:i:1 RG:Z:HiMom.7
-HiMom:7:1:0:586 516 * 0 0 * * 0 0 ........C........C..C...A..... ############################## RG:Z:HiMom.7
-HiMom:7:1:0:841 516 * 0 0 * * 0 0 ........C...........T......... ############################## RG:Z:HiMom.7
-HiMom:7:1:0:879 516 * 0 0 * * 0 0 ........T...........T......... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1013 516 * 0 0 * * 0 0 ..C..T.CAG...C...A.GT...G..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:111 516 * 0 0 * * 0 0 ..C..T.GCG...T...A.CT...T..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1153 516 * 0 0 * * 0 0 ..T..T.TGG...T...C.TC...T..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1184 516 * 0 0 * * 0 0 ..A..G.TCG...A...T.CA...T..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1241 516 * 0 0 * * 0 0 ..A..G.TGG...T...C.TG...A..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1243 516 * 0 0 * * 0 0 ..A..A.GGA...A...C.TA...T..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1247 516 * 0 0 * * 0 0 .CCAGC.TTT...T...T.CT...G..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1282 516 * 0 0 * * 0 0 ..A..A.GGG...T...G.AG...C..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:132 516 * 0 0 * * 0 0 ..A..G.GGG...G...G.GG...G..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1320 516 * 0 0 * * 0 0 ..A..T.AGT...G...G.TA...C..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1372 516 * 0 0 * * 0 0 .ACATTTTTTAG.T.A.TTGTT.AC.A... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1379 516 * 0 0 * * 0 0 .AATATAATT...T...TTAGA.TT..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1391 516 * 0 0 * * 0 0 ..G..T.TAA...A...T.AT...T..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:140 516 * 0 0 * * 0 0 ..A..T.TAA...G...C.TT...T..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1513 516 * 0 0 * * 0 0 .....A..TT...A...A.AA...C..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1521 516 * 0 0 * * 0 0 .AACAA.ATT...T...A.TA..TA..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:155 516 * 0 0 * * 0 0 ..G..C.AGT...C...A.TT...G..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1555 516 * 0 0 * * 0 0 ..T..G.AGA...A...C.TA...A..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:164 516 * 0 0 * * 0 0 ..A..A.TAA...T...T.AT...T..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1684 516 * 0 0 * * 0 0 ..G..A.GGT...G...T.TC...T..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1696 516 * 0 0 * * 0 0 ..A..G..GC...G...A.AC...T..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:170 516 * 0 0 * * 0 0 ..T..C.CAC...G...G.TC...G..... ############################## RG:Z:HiMom.7
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-HiMom:7:1:1:1733 516 * 0 0 * * 0 0 ..A..G.GTC...T...T.AG...A..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1770 516 * 0 0 * * 0 0 ..C..T.CTG...G...G.CA...A..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:18 516 * 0 0 * * 0 0 .ATCAG.CTG...A...T.GT..AA..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1815 516 * 0 0 * * 0 0 .ATGAAAATA...T...TAAAT.AT..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1836 516 * 0 0 * * 0 0 .....G..TA...G...T.CT...C..... ############################## RG:Z:HiMom.7
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-HiMom:7:1:1:1886 4 * 0 0 * * 0 0 .ACATATGCATACATATATAATAGATA... %.9:;<217;:999;<;;<<<;;####### RG:Z:HiMom.7
-HiMom:7:1:1:1906 516 * 0 0 * * 0 0 ..T..C.ATA...C...T.CT...G..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:1917 516 * 0 0 * * 0 0 .....T..GA...C...A.AA...A..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:195 516 * 0 0 * * 0 0 ..A..G.GTG...G...C.AT...A..... ############################## RG:Z:HiMom.7
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-HiMom:7:1:1:2 516 * 0 0 * * 0 0 ..A..G.GAA...C................ ############################## RG:Z:HiMom.7
-HiMom:7:1:1:2011 516 * 0 0 * * 0 0 .ACAGCTGGCA..T...AGAGC.AG.A... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:240 516 * 0 0 * * 0 0 ..G..A.GTA...T...T.CC...C..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:262 516 * 0 0 * * 0 0 ..C..G.CAT...A...C.TG...C..... ############################## RG:Z:HiMom.7
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-HiMom:7:1:1:299 516 * 0 0 * * 0 0 ..C..T.GCA...A...C.AA...T..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:30 516 * 0 0 * * 0 0 ..A..A.TTT...T...G.TC...T..... ############################## RG:Z:HiMom.7
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-HiMom:7:1:1:367 516 * 0 0 * * 0 0 ..A..T.AGC...G...A.GT...C..... ############################## RG:Z:HiMom.7
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-HiMom:7:1:1:508 516 * 0 0 * * 0 0 ..G..C.CAG...T...C.CT...C..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:517 516 * 0 0 * * 0 0 .TCATAAAACATCA.TATTGGAAAGGA... %.75:<999578################## RG:Z:HiMom.7
-HiMom:7:1:1:535 516 * 0 0 * * 0 0 .GCCCAAGTATTGA.TATGTGCTCTAA... %.599:7187:940%0::52599####### RG:Z:HiMom.7
-HiMom:7:1:1:55 516 * 0 0 * * 0 0 .TTTATGTCCTT.A.AACTTAG.AGTT... %/9<<83599#################### RG:Z:HiMom.7
-HiMom:7:1:1:554 516 * 0 0 * * 0 0 ..A..G.AGA...G...T.TC...A..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:567 516 * 0 0 * * 0 0 ..C..C.GTT...C...G.AC...C..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:59 516 * 0 0 * * 0 0 ..A..G.TGC...T...T.AC...A..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:613 516 * 0 0 * * 0 0 ..G..A.TAT...C...G.AT...A..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:622 516 * 0 0 * * 0 0 ..T..C.AGT...C...A.CT...T..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:627 516 * 0 0 * * 0 0 ..A..T.GAC...T...A.GC...C..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:684 516 * 0 0 * * 0 0 ..T..T.AGA...C...A.AG...A..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:72 516 * 0 0 * * 0 0 .ACACACATATCAC.CACATCATACAC... %..48696;5:6;.%)49;;;9######## RG:Z:HiMom.7
-HiMom:7:1:1:812 516 * 0 0 * * 0 0 ..A..C.AAG...T...A.TC...A..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:874 516 * 0 0 * * 0 0 ..A..A.GCC...G...T.TA...T..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:931 516 * 0 0 * * 0 0 ..T..G.GAT...G...C.TT...C..... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:965 516 * 0 0 * * 0 0 .ACTAATCTTCCGC.CATATCCCCAAA... ############################## RG:Z:HiMom.7
-HiMom:7:1:1:994 516 * 0 0 * * 0 0 ..A..T.GAT...T...G.TT...C..... ############################## RG:Z:HiMom.7
-HiMom:7:1:2:1158 4 * 0 0 * * 0 0 .GGGTCCTTCATAGTTTTTTTCTACTTTCC %0777646;099:::95;;;688::99### RG:Z:HiMom.7
-HiMom:7:1:2:1238 516 * 0 0 * * 0 0 .TCCTTATATTCAATTATTAATATTTTTAC ############################## RG:Z:HiMom.7
-HiMom:7:1:2:1275 4 * 0 0 * * 0 0 .AGTGAAATAAGCCAGACACAGAAAGACA. %/5204:99971773,44755-39717### RG:Z:HiMom.7
-HiMom:7:1:2:1301 516 * 0 0 * * 0 0 .AGTAGACTGCATTAATTAATTGGAAGAG. %0370)024263144:48;;########## RG:Z:HiMom.7
-HiMom:7:1:2:1453 4 * 0 0 * * 0 0 .ATATCTTATTTTCTTTTCTTTCAGGCTCT %.:7,,395255################## RG:Z:HiMom.7
-HiMom:7:1:2:150 516 * 0 0 * * 0 0 .AAGACTTGATTATATCCCTTGTATGA... ############################## RG:Z:HiMom.7
-HiMom:7:1:2:1592 4 * 0 0 * * 0 0 .GAAAACTGGCACAAGACAAGGATGCCCTC %,67786861,3466(8485868648583# RG:Z:HiMom.7
-HiMom:7:1:2:1706 4 * 0 0 * * 0 0 .GATATGTGGATACAGCTCACAAAGAG... %,99:6/566999/7############### RG:Z:HiMom.7
-HiMom:7:1:2:1722 516 * 0 0 * * 0 0 .AAAGAAAATTAAAGAAAAATATACACGT. ############################## RG:Z:HiMom.7
-HiMom:7:1:2:1727 516 * 0 0 * * 0 0 .TATTGAAGGACTTTTGTATCCTCCTTAT. ############################## RG:Z:HiMom.7
-HiMom:7:1:2:1753 516 * 0 0 * * 0 0 .GTTCACACAAGGATAATATTTTTGATTAT ############################## RG:Z:HiMom.7
-HiMom:7:1:2:1782 4 * 0 0 * * 0 0 .ACCAAGTGTTTGGAGTATGCTGCCTA... %0:::668885-5335/85########### RG:Z:HiMom.7
-HiMom:7:1:2:1827 4 * 0 0 * * 0 0 .AACCGAGGATGTACACTGTCCCTGTGAAA ############################## RG:Z:HiMom.7
-HiMom:7:1:2:1932 4 * 0 0 * * 0 0 .AGCGATCCTCCCGCCTCTGCCTCCCA... %,1545541455################## RG:Z:HiMom.7
-HiMom:7:1:2:1946 516 * 0 0 * * 0 0 .ATCTTCTGGAATTTCTAACAGCTTGGAA. %0515.,.35<997################ RG:Z:HiMom.7
-HiMom:7:1:2:209 516 * 0 0 * * 0 0 .GACTCAACTCCTGGGCTCCCTACGACCAT ############################## RG:Z:HiMom.7
-HiMom:7:1:2:246 516 * 0 0 * * 0 0 .GGAGGTTTCATTTAGCCGATATTGTG... ############################## RG:Z:HiMom.7
-HiMom:7:1:2:25 516 * 0 0 * * 0 0 .GCTTTGGCAAGACAAATCTCCCGTCTGG. ############################## RG:Z:HiMom.7
-HiMom:7:1:2:307 516 * 0 0 * * 0 0 .GGATGAACAGAAACTAAAATAACACA... ############################## RG:Z:HiMom.7
-HiMom:7:1:2:363 516 * 0 0 * * 0 0 .ATATTCTTTTTTTTTATTTATCAGAT... ############################## RG:Z:HiMom.7
-HiMom:7:1:2:449 516 * 0 0 * * 0 0 .ATTCTAATTCTAGGAAATTAACAATC... %.9315<936970%0############### RG:Z:HiMom.7
-HiMom:7:1:2:546 516 * 0 0 * * 0 0 .GGTTGTGTCTCTCTCAGCCTTTGGGATC. %,46888444685-35############## RG:Z:HiMom.7
-HiMom:7:1:2:605 4 * 0 0 * * 0 0 .GCATTGAGCAGACGTGGCATCCAGAT... %)085222/55453################ RG:Z:HiMom.7
-HiMom:7:1:2:69 516 * 0 0 * * 0 0 .TCAGTCTGCTGTTTTAAAAAAATACTGTG ############################## RG:Z:HiMom.7
-HiMom:7:1:2:747 516 * 0 0 * * 0 0 .AACAACAGCGGAAAATAATAAAAAAAAA. ############################## RG:Z:HiMom.7
-HiMom:7:1:2:786 4 * 0 0 * * 0 0 .TAAACAATAATCTGATGATTTATAATCC. %09<<<<;<;<8<9;<9<;<::<<::#### RG:Z:HiMom.7
-HiMom:7:1:2:858 4 * 0 0 * * 0 0 .AAACGTTGCTGATCTTCTGTTTTAAACTA %/;7-222265366-6977035:::;626; RG:Z:HiMom.7
-HiMom:7:1:2:943 4 * 0 0 * * 0 0 .AATACCAATAAACCTAGAATGTCTCATAC %08<9646<6378744774:1005799<4# RG:Z:HiMom.7
-HiMom:7:1:2:974 4 * 0 0 * * 0 0 .GATCAATGATCACATCTTTGGATATGTAT %/9979<99:999::9;;:7511<<<77<< RG:Z:HiMom.7
-HiMom:7:1:2:988 4 * 0 0 * * 0 0 .AAAGGAATGTTCAGCTCTGTGAGTTGAAC %/92/04:2-2785-3875/404362-162 RG:Z:HiMom.7
-HiMom:7:1:3:1233 516 * 0 0 * * 0 0 .AACCAATTTCTTTACATACCAAATACGCC ############################## RG:Z:HiMom.7
-HiMom:7:1:3:1294 516 * 0 0 * * 0 0 TGTAACTTTACTTTAGTTGCTTATTTGTAG BA############################ RG:Z:HiMom.7
-HiMom:7:1:3:405 516 * 0 0 * * 0 0 AAAAAACATAGAACGGGGTCAATATTTTAT (?A>8(7B?<(:')?@)8(:(*:<8:0>'> RG:Z:HiMom.7
-HiMom:7:1:3:579 516 * 0 0 * * 0 0 .GAAAAATGACCACACTTGCCTCCTGAGAA ############################## RG:Z:HiMom.7
-HiMom:7:1:3:673 516 * 0 0 * * 0 0 TCCTCAAAAACAAGATAAAACGGTTGAAAT >()>)''85BBC?################# RG:Z:HiMom.7
-HiMom:7:1:3:890 516 * 0 0 * * 0 0 TGCTTCTGTTTCCGTTAGCTAGATAAAGTT ############################## RG:Z:HiMom.7
-HiMom:7:1:3:905 516 * 0 0 * * 0 0 TGTTATGTTTAATTTTCTTTAGCACCCTTC >7>?A:-<BA at 0>@:@8=A;5%7;9?=:9@ RG:Z:HiMom.7
-HiMom:7:1:3:918 516 * 0 0 * * 0 0 TTTTCATTCCTAGTCATCCACCCCATCAGA 0()@A=:2>3:>(/((<22A>:0(20:@)@ RG:Z:HiMom.7
-HiMom:7:2:0:1073 516 * 0 0 * * 0 0 .....A.CAC...C...C.CA...C..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:1135 516 * 0 0 * * 0 0 .....G..GT...A...T.TA...G..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:1198 516 * 0 0 * * 0 0 .....T.CTA...T...C.CA...A..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:1278 516 * 0 0 * * 0 0 ........TA...T...C..A...G..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:135 516 * 0 0 * * 0 0 ........A...........G......... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:1547 516 * 0 0 * * 0 0 ........C...........G...A..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:1598 516 * 0 0 * * 0 0 ........AT...T...A..G...C..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:1620 516 * 0 0 * * 0 0 ........CA.......A..C...C..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:1668 516 * 0 0 * * 0 0 .....A.ATA...A...G.TG...T..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:186 516 * 0 0 * * 0 0 ........CC...A...T..T...T..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:205 516 * 0 0 * * 0 0 ........A........T..C...T..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:287 516 * 0 0 * * 0 0 ........CC...C...T..A...A..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:382 516 * 0 0 * * 0 0 ........CA...T...T..A...A..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:441 516 * 0 0 * * 0 0 ........TT...A...A..T...T..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:50 516 * 0 0 * * 0 0 ........T........T..G...G..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:501 516 * 0 0 * * 0 0 .....G..AG...A...C.CT...C..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:73 516 * 0 0 * * 0 0 .....A.CAT...G...A.AC...G..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:740 516 * 0 0 * * 0 0 ........TT...A...T..A...A..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:766 516 * 0 0 * * 0 0 ........TG...A...A..T...T..... ############################## RG:Z:HiMom.7
-HiMom:7:2:0:87 516 * 0 0 * * 0 0 ........G........A..T...T..... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1004 516 * 0 0 * * 0 0 .ATTTATCACTA.A.ATCCGCAAACCCTCC ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1034 516 * 0 0 * * 0 0 .ATCATTTTCAT.C.TTTCACTGATACATT %.737:887471%-%1:8555545;696:: RG:Z:HiMom.7
-HiMom:7:2:1:1159 516 * 0 0 * * 0 0 ..ACTT.TAG...G...AAAT..CC.A... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1168 516 * 0 0 * * 0 0 ..TCTA.CTT...T...ATTG..TT.T... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1180 516 * 0 0 * * 0 0 ..ATGG.CTT...C...AGAA..TC.A... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1214 516 * 0 0 * * 0 0 .AAAAAAAAAAA.A.TATAAGAAAGAATCA %035:######################### RG:Z:HiMom.7
-HiMom:7:2:1:1221 516 * 0 0 * * 0 0 .GGTCACACTCACATAGTGTTCAGAGCACT ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1306 516 * 0 0 * * 0 0 ..ACAT.AAA...T...AACA..GT.A... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1351 516 * 0 0 * * 0 0 .....C.ATA...T...A.AA...T..... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1424 516 * 0 0 * * 0 0 ..TCAT.TAG...C...ATGG..GT.C... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1452 516 * 0 0 * * 0 0 .GAAATTTGTAAAA.CACCTGCAGAATACT ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1515 516 * 0 0 * * 0 0 .ATTAAATAT.A.A..GTAATAATAATA.. %/9########################### RG:Z:HiMom.7
-HiMom:7:2:1:1521 516 * 0 0 * * 0 0 ..ACAC.AAA...G...ATCT..TT.C... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1536 516 * 0 0 * * 0 0 .AGCAAAGACTT.G.ACCAACCCAAATGTT ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1543 516 * 0 0 * * 0 0 ..TTGA.ATC...A...AATA..TA.C... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1617 516 * 0 0 * * 0 0 ..CCAT.ATC...G...CCAG..GT.T... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1627 516 * 0 0 * * 0 0 ..TGGT.AGA...C...AAAA..CA.T... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1646 516 * 0 0 * * 0 0 .TTAATTATA...A..TAAACATTCTAA.. ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1653 516 * 0 0 * * 0 0 ..AATT.AAA...T...ATCT..AG.A... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1682 516 * 0 0 * * 0 0 ..TCTT.TTT...G...AAAA..AA.T... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:170 4 * 0 0 * * 0 0 .AGAAGAAATGGGATCCTGCTGTGGCCAGT %/888865284168866767663(6874/5 RG:Z:HiMom.7
-HiMom:7:2:1:1731 516 * 0 0 * * 0 0 ..TATA.GAA...T...TGCT..AG.T... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1755 516 * 0 0 * * 0 0 ..GT.A.TCT...C...C.TG...G.A... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1812 516 * 0 0 * * 0 0 ..TTGC.CAC...C...CCAT..AA.G... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1853 516 * 0 0 * * 0 0 ..ATCT.TTC...A...AGTG..AT.C... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1919 516 * 0 0 * * 0 0 ..AATT.AAA...A...AGAA..AG.A... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1924 516 * 0 0 * * 0 0 .ATATTCTGAAG.A..CCAATGAACCAAA. %116<9579<7################### RG:Z:HiMom.7
-HiMom:7:2:1:1933 516 * 0 0 * * 0 0 .AGGGTACAT.T.C..AATGTGCGGGTT.. ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1938 4 * 0 0 * * 0 0 .AGTCCAGTGTCTCTGCTTCCGCAGGGACA %/818865/058858644866457646668 RG:Z:HiMom.7
-HiMom:7:2:1:1950 516 * 0 0 * * 0 0 ..TT.A.AAA...C...T.CA...T.C... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:1959 516 * 0 0 * * 0 0 .GACACATTCCTAC.ACAGAGAAAAATTTA %*77;;<;<<:<;,%.::;:6:9::<4488 RG:Z:HiMom.7
-HiMom:7:2:1:1987 516 * 0 0 * * 0 0 ..AT.G.ACA...C...T.GT...T..... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:2006 516 * 0 0 * * 0 0 ..GTAT.TGA...G...CCTT..AG.A... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:211 516 * 0 0 * * 0 0 ..CTGA.ACA...G...TGCA..AC.C... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:234 516 * 0 0 * * 0 0 .AAGCCTGTGGG.A..CCCAGTGGGAGCG. ############################## RG:Z:HiMom.7
-HiMom:7:2:1:242 516 * 0 0 * * 0 0 ..GCTC.AGC...A...ATAT..TT.G... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:262 516 * 0 0 * * 0 0 ..ATTG.AAT...C...TTCC..AT.T... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:298 516 * 0 0 * * 0 0 ..TCAA.TTG...T...CTGC..TT.T... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:312 516 * 0 0 * * 0 0 ..TTGC.AGA...A...AACT..TG.A... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:363 4 * 0 0 * * 0 0 .GAAAGGTTTTGCAGCATGTGCAAACTCAC %-5565678:8177656503512/377856 RG:Z:HiMom.7
-HiMom:7:2:1:37 516 * 0 0 * * 0 0 .TGTAAACGA...C..TTCCTGTTCAGC.. ############################## RG:Z:HiMom.7
-HiMom:7:2:1:370 516 * 0 0 * * 0 0 ..CTGG.AGC...T...CATA..AA.C... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:377 516 * 0 0 * * 0 0 ..AGAA.GTG...T...AAAT..AA.A... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:414 516 * 0 0 * * 0 0 ..TAGA.AGC...A...TCAG..AC.G... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:421 516 * 0 0 * * 0 0 ..GTTA.TTC...A...CGTG..AT.C... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:428 516 * 0 0 * * 0 0 .ATGTGAATA.T.A..TAGTTGGGATTCA. ############################## RG:Z:HiMom.7
-HiMom:7:2:1:44 516 * 0 0 * * 0 0 .ACTACCTCA.G.A..AAGCAGGTTCTAA. ############################## RG:Z:HiMom.7
-HiMom:7:2:1:466 516 * 0 0 * * 0 0 .ACACTCACA.C.A..TGTTTGGAATGA.. ############################## RG:Z:HiMom.7
-HiMom:7:2:1:555 516 * 0 0 * * 0 0 ..CAAT.TCT...G...TACA..CT.C... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:558 516 * 0 0 * * 0 0 .AAAATATCA.T.A..AATAAATAATCA.. ############################## RG:Z:HiMom.7
-HiMom:7:2:1:56 516 * 0 0 * * 0 0 ..GCCA.GGT...A...TCAC..GG.C... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:569 516 * 0 0 * * 0 0 ..AGGC.AGT...G...GTCC..GT.A... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:604 516 * 0 0 * * 0 0 .ATGATGAAACTCT.TCTCTACTAAAAATA ############################## RG:Z:HiMom.7
-HiMom:7:2:1:628 516 * 0 0 * * 0 0 .AGTATGCCC.C.C..ACCACTCCTATT.. ############################## RG:Z:HiMom.7
-HiMom:7:2:1:64 516 * 0 0 * * 0 0 .ATTAATCTT...T..GCACAATTCATT.. ############################## RG:Z:HiMom.7
-HiMom:7:2:1:684 516 * 0 0 * * 0 0 .AAAAATCAAATGA.CATAATTTTATAAAA ############################## RG:Z:HiMom.7
-HiMom:7:2:1:699 516 * 0 0 * * 0 0 ..AATT.TTG...T...ATTT..GA.T... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:714 516 * 0 0 * * 0 0 .ATTAACTTA.A.T..ACCACAACCTAA.. %.:########################### RG:Z:HiMom.7
-HiMom:7:2:1:722 516 * 0 0 * * 0 0 ..CCTC.CTG...C...CTGT..TG.C... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:749 516 * 0 0 * * 0 0 ..AGTG.TAC...T...CTTG..CT.T... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:760 516 * 0 0 * * 0 0 .GTCTGTTTTATGT.AAATATTTTGTTTAA ############################## RG:Z:HiMom.7
-HiMom:7:2:1:8 516 * 0 0 * * 0 0 ..TGCG.TGG...C...AGGC..TT.T... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:833 516 * 0 0 * * 0 0 ..GAGC.CCT...A...CTCC..GA.G... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:848 516 * 0 0 * * 0 0 ..TACT.AGT...G...TGTT..GC.T... ############################## RG:Z:HiMom.7
-HiMom:7:2:1:893 516 * 0 0 * * 0 0 .GAGACAGAGTCTC.CTCTGTTCCCTAGCC ############################## RG:Z:HiMom.7
-HiMom:7:2:1:998 516 * 0 0 * * 0 0 ..ATGT.TGC...A...TATA..GG.A... ############################## RG:Z:HiMom.7
-HiMom:7:2:2:0 516 * 0 0 * * 0 0 .ATTCCTT.A.................... ############################## RG:Z:HiMom.7
-HiMom:7:2:2:131 4 * 0 0 * * 0 0 .ATATATTGACAGCAGTCATGTTGTTGAAG %0<<<:<959874492:96999969:7784 RG:Z:HiMom.7
-HiMom:7:2:2:1636 516 * 0 0 * * 0 0 .GTGTAAAAGTAGGGAAATACTATAGCAAG ############################## RG:Z:HiMom.7
-HiMom:7:2:2:1974 516 * 0 0 * * 0 0 .ACGCCAATACAAAAATGTTGAAGCTAGCT ############################## RG:Z:HiMom.7
-HiMom:7:2:2:351 516 * 0 0 * * 0 0 .GGGGTTGAGGTGTAAATAGAACATTTGTA ############################## RG:Z:HiMom.7
-HiMom:7:2:2:646 516 * 0 0 * * 0 0 .GAATCTAAGAAGACACAAAACTAAGGAAA ############################## RG:Z:HiMom.7
-HiMom:7:2:2:828 516 * 0 0 * * 0 0 .TCAAGTCAATTTGGGACTTGAAACAGCTC ############################## RG:Z:HiMom.7
-HiMom:7:2:3:1529 516 * 0 0 * * 0 0 .TTATATGAATAGATAAATAAATAATCAAT ############################## RG:Z:HiMom.7
-HiMom:7:2:3:179 516 * 0 0 * * 0 0 CATTATTGTTAGACTGATTTTTTATAATCT B@)104..*0-A(@@(<A9A<(+9)-=6(B RG:Z:HiMom.7
-HiMom:7:2:3:198 516 * 0 0 * * 0 0 TGTCATTTTCTTTGCCTTAATTGTTCTTCT 5 at CBB7-*<=#################### RG:Z:HiMom.7
-HiMom:7:2:3:2030 516 * 0 0 * * 0 0 CGAGATAATTTTTTAAAAAAAGTCCAAAAA ((@;()@==*7<(5A@<C>########### RG:Z:HiMom.7
-HiMom:7:2:3:247 516 * 0 0 * * 0 0 TGTACATGACCAGGTAATTTGGTTATGTGA <@596353;)>@A7=:,A0'6>######## RG:Z:HiMom.7
-HiMom:7:2:3:4 516 * 0 0 * * 0 0 AGAGGCAATAAGTTTTAA............ A>BA at 9BAB3AA################## RG:Z:HiMom.7
-HiMom:7:2:3:862 516 * 0 0 * * 0 0 .CTTTAAGAAATCATTCATTCTGCAAACAC ############################## RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/singleBarcoded.sam b/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/singleBarcoded.sam
deleted file mode 100644
index 5fc99b8..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/singleBarcoded.sam
+++ /dev/null
@@ -1,8 +0,0 @@
- at HD VN:1.4 SO:queryname
- at RG ID:HiMom.7 PL:illumina PU:HiMom.7 LB:Hello, World SM:HiDad CN:BI
-HiMom:7:1:2:1995 4 * 0 0 * * 0 0 .ATTTCCTGAACACAGCACAGGGAAGAGGA %/78777738777:8877786776858225 RG:Z:HiMom.7
-HiMom:7:1:3:1358 516 * 0 0 * * 0 0 .TCCTTCCTCAAGGGGACCCCGCCTCCCCT ############################## RG:Z:HiMom.7
-HiMom:7:1:3:176 4 * 0 0 * * 0 0 ATATTTCATGAAAGACATAAATTTACAGTT BBBCCB at BBBABBBB?ABBBBBBBBABB at B RG:Z:HiMom.7
-HiMom:7:1:3:198 4 * 0 0 * * 0 0 TATAATTTAATGGTTTTTATATATTCAGAG BBC=BBCCA=@=8<BCBCBBABBCB=BB<9 RG:Z:HiMom.7
-HiMom:7:1:3:900 516 * 0 0 * * 0 0 TGAATCTTTGTTCAACACAGATTATTCCAG )>@+5*<B1':(5,23A>5)@:)(/>:=## RG:Z:HiMom.7
-HiMom:7:2:3:1970 4 * 0 0 * * 0 0 .TAATACTCTTTGAGAAAGGACTGAGGGAA %.:77558:68862.3;8455:0057535; RG:Z:HiMom.7
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_1_0001_qseq.txt
deleted file mode 100644
index 7190a89..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_1_0001_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 1 1 1793 1420 0 1 G....................C.....................T.....................T.......... \DDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1441 0 1 C....................C.....................G.....................G.......... GDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDJDDDDDDDDDDDDDDDDDDDDDTDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1483 0 1 G....................G.....................A.....................A.......... YDDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDDNDDDDDDDDDDDDDDDDDDDDDWDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1495 0 1 G....................C.....................G.....................C.......... VDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1527 0 1 G....................G.....................G.....................T.......... MDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1545 0 1 C....................A.....................A.....................C.......... HDDDDDDDDDDDDDDDDDDDDHDDDDDDDDDDDDDDDDDDDDDHDDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1583 0 1 G....................G.....................G.....................A.......... YDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1596 0 1 G....................C.....................C.....................T.......... TDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDTDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1658 0 1 C....................C.....................T.....................A.......... GDDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1718 0 1 G....................C.....................C.....................C.......... YDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDHDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1745 0 1 C....................C.....................C.....................A.......... PDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDVDDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1777 0 1 G....................C.....................T.....................C.......... YDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDYDDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1813 0 1 G....................C.....................A.....................C.......... VDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1916 0 1 G....................T.....................T.....................C.......... [DDDDDDDDDDDDDDDDDDDDUDDDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1959 0 1 G....................C.....................T.....................C.......... [DDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 808 0 1 T....................C.....................C.....................T.......... YDDDDDDDDDDDDDDDDDDDD^DDDDDDDDDDDDDDDDDDDDD^DDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 1 1 1793 602 0 1 T....................A.....................A.....................A.......... [DDDDDDDDDDDDDDDDDDDD]DDDDDDDDDDDDDDDDDDDDDVDDDDDDDDDDDDDDDDDDDDDQDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1602 0 1 C....................G.....................G.....................A.......... [DDDDDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1681 0 1 C....................T.....................A.....................A.......... ^DDDDDDDDDDDDDDDDDDDDHDDDDDDDDDDDDDDDDDDDDDEDDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1011 0 1 A....................C.....................G.....................G.......... GDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDD 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_1_0002_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_1_0002_qseq.txt
deleted file mode 100644
index 808165a..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_1_0002_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 1 2 1793 1893 0 1 G.TCC.......A.TCCCCGTGGATGAAAATGCTGTACATGTTCTTGTTGATAACAATGGGCAAGGTCTAGGACAG ODZb[DDDDDDDHDXbb_G]^b_P\`VGOO\ab`aXU`][`^_b``a_``T]V`aPFU]V]aXMXaVaTHVZTa[] 0
-SL-XBA 1 1 2 1793 1909 0 1 G.CCT.......C.CTCACACCGCCCCCCTTCTCACCTGCCCTGCGTAACCTGTACTGACTGCCCACTCCTCACCC GD[_WDDDDDDDIDZGW_ZI]VZIMG[a]TGMT_NI]XRZGQ_\LYFT]HO\JPZFTYFZNGZP_I]KGZFZGGYH 0
-SL-XBA 1 1 2 1793 1931 0 1 G.CTA.......T.CACTGTCGACACCGCACACGGGGCATACCCACATCAAAGCAGTCCCCCAAGTCCCTGCGCAG [DWMFDDDDDDDEDMG[aIIG]RIVVTGIGZFMUFFJZFEPGXMHMIGVZTNFQGUS`VO]OMKQR_HODFT\[IF 0
-SL-XBA 1 1 2 1793 2004 0 1 G.GTT.......C.TACTGGCATTTACTGTTTAACATCACACACCAAGCCAGGTTATTTCACACTCCTGCTACTGG WDPR[DDDDDDDYD^bbaaa^G]bbbbba`_IXJ_J_b_JIP^ZW_JRI_IWbS_S]b]V_WPPT^HKbb[V_^Y` 0
-SL-XBA 1 1 2 1793 2038 0 1 G.GCG.......G.CACCTTGGTACTGGGTGATGGGGAGGCACTGAATGGGCTTCAAGTCCTCAAACGCCTGATCT ^DYLZDDDDDDDMD\H_bb`ba\W`aba^V_E]a^`b\^baXbS```]]U\\]]ZDT]RDYNYDKRMZ_OKXILPZ 0
-SL-XBA 1 1 2 1793 829 0 1 T.GGC.......C.TGGGCAAGCACCTGACCAGCAACAGCCCCCGCCTGGTGCAGCACTGCCTGTGGACCCTGCGC ZDZ]IDDDDDDD[DYa`a_OZaaaaaa_Z_a_`_ZI_I]aaaaa`aa`^_R__Z[GT_``a_Y]M\ZK[aaZ[a`a 0
-SL-XBA 1 1 2 1793 1117 0 1 G.GGG.......C.GGTCGTTAGCAAGTGATGGCTGTGTTCTGTATCTTTATTGTGGCGACACTTACATGACTGGA RDZaVDDDDDDD\DXbIFT_^aba][MX]^_a`H]]Ga[R_H_S^a[WHT]UV[U`TJTLOMGWSLWURVKVNVDH 0
-SL-XBA 1 1 2 1793 1478 0 1 T.TTT.......C.AATTTTACCTCATAAAATTTTTTGAGGTTTGATGTATGTCTCTGTCTTATCAATAATGAGGC \D^b^DDDDDDDIDJK_bba]abaa`_\VVWabababa^ab^ab`S`b_Z_b_babaa`b`YH\a]FZUS\]U\`b 0
-SL-XBA 1 1 2 1793 1354 0 1 T.GCT.......G.GGCGCCGCGAAGCGCACGGCGCCGACGCAGGGGGAAGGCGGGACATACACGACCCGCGAGCG PDZ`ZDDDDDDDWDGTZ_aVZGZIWZGW_Z_[XNWPGGVVI[GW_LR[FGT\ZGVGG[FHF[MOGNIGVNMQGX]P 0
-SL-XBA 1 1 2 1793 666 0 1 C.GAG.......T.GGGTAGGAAACACAGCCTTGCTCCACAGCGCACTGTCAGCAAGACGCTCCTTTCTTCGGAGA ^DXGXDDDDDDDDDVHXMM[YY]R]PZVV[aOT^^Ha]O\PQGQ`U\SYSXTU^NDTLDLZPZUTSQZNLEGQUKG 0
-SL-XBA 1 1 2 1793 2031 0 1 C.CCG.......G.GGTGCATGGGCTCCAACGTGGTGTCCTGTGGAGCTGTTGGGCCTGGGCAGGCGGCACAGATC YDFIYDDDDDDDYDYaZa_G[aa`aXa`R``aX`_KaPG\\`U_`N^^Z\T\^`RDQVR[S`KZVZY\ZJEENKNR 0
-SL-XBA 1 1 2 1793 1812 0 1 C.CTC.......C.GCATACTTAACAAGTCTGATCTTGCTTATAGAAATTGGATCTTACTACTTCATTCTCAGAAT GD^a]DDDDDDD^D]aV\L_aaZ\_OVa_baaT^baaaba^J]YaXSS^aa_P_baaXN\Va_`a\__aa_G]GW[ 0
-SL-XBA 1 1 2 1793 475 0 1 C.GGG.......C.CCCCCCTAGGCAATATGCTACTGCATATATATTTGGTCTAGATATATAACAAGTTACTACTG ^DX^RDDDDDDDOD[[DTZGQIV[_^GPFHU]V^KV\V_IHUHRTFVYVHDDKFRGMGJQJJSWQMYHHLDOLFFQ 0
-SL-XBA 1 1 2 1793 1329 0 1 C.TCT.......T.GATGCAGTAACTGGAAATATAGAAGATGCTGTGACTCCATTTGAATCTATAAAAAGCGTTGT WDWOTDDDDDDDRDX^IV^GPGXOFWOZSGY^^[[JXYTJN\`WTKN\^RH\FHULJIKT\NXOQLQLOJTLDKLO 0
-SL-XBA 1 1 2 1793 404 0 1 C.CCC.......T.CAATGCTATGCAGTATGTCTTCTTATCTCTGTCTTCAAGAGCATCCTCTGTCAGTCCTACAT YDH^ODDDDDDDXDINODKWMLL]]]]X_^\XVTG\SNDO^VSFNFFRXDL^WWQWKSSPQ\OPUWZQJX`YVSFT 0
-SL-XBA 1 1 2 1793 1455 0 1 C.TTC.......G.GACTGCAGTTGCTGTTGCCCATTAAGACCTTGAGAAAAGGCTTGCCTGCCCTTCGTCTGACT ^DW\^DDDDDDDYDXF\^_bI_QF\a[ZNGZ\D^KWXFWOG\aX\]VPSTMLGVaLHRWNTHF\DTL\YNTVHDUD 0
-SL-XBA 1 1 2 1793 1793 0 1 C.CCA.......C.GGGCCCTTTGTCTAAAGTCTGAATCAGCATTTGGATTTAGCCCTAATAGAGCCTGTTCATCC \D^DHDDDDDDD\DUW]aaaX^]_YaYHQGVY`WSFUV]TZ]NUVWWXFRWTKX_^\LJGRQVJR_]WVVV[NPT_ 0
-SL-XBA 1 1 2 1793 310 0 1 C.GGA.......T.GAACCTTTGGCAAGGCTGCTCTTACGAGTCCTCTCGCCCTGTTCCACCTATCCCCATAGCTA GDTZFDDDDDDDGDMIO_XX_`a]b`THY\Y`PZ`[RFYLFFMFRFZGFT]ab_a\`G`[]TPPGUa^KFFG[ELI 0
-SL-XBA 1 1 2 1793 1969 0 1 T.CGC.......A.CCCTGACTGGCAAGGCGGTGGCGGCTCCAGTGAAGGCTCCCCGTGTTCTTAAAGACTAGCGC TDWGGDDDDDDDPDZaaa]JHVaaa^L^PO_aVaaaX`__`RVXF^IRXa`S_]HZFTYFaa``Z]Q]`UJXJ_I[ 0
-SL-XBA 1 1 2 1794 490 0 1 C.TCC.......T.TATTTACTATTTTCTGATTTTTAAAATGACAGTGGCAATTACCATTTATACTGTGTTATTTG ^DWb^DDDDDDDXDUG\^YG\_a``__a_`[[[[\_\ZT^_XJ^`_Y^X_TEP\]`^JYUUUW\`X^V^X^\[X\U 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_1_0003_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_1_0003_qseq.txt
deleted file mode 100644
index da8dbcd..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_1_0003_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 1 3 1793 1282 0 1 G.TAG.......C.GGACTCTGGCGTCACCTTTGGCGCTGAGCGCCCCAGGCCCGCCAGCCCGCCCGCCCACTGCC [DZGMDDDDDDDGDMUMGZa_TTJX]IW_G]I_ZGMZ_VTFTFZZ_ZZIS[T[QI_ZN][_T]TGPUZPZVHFKMM 0
-SL-XBA 1 1 3 1793 1301 0 1 G.AGG.......T.CAGGGTTGAGGTATTCTTAGGTTAGCCGAGCTCTTTCCTCCTTTCCCCCCCCCTCTCCCCCA ^DIYRDDDDDDDGDZIXH]RJLIL_\HR^bba``ZH`W_QIQTZ`VKTQ\aZG\HSVH\abZJYb_HQ_O\a`XGX 0
-SL-XBA 1 1 3 1793 1311 0 1 G.TAT.......T.TTCCTTCAGTCTGCACAAAGATTAAGGTAATTTACAGTCAATCTGTGAATGAATGTTGAGAC [DGH[DDDDDDDVD[[ababbb`abbbb_baa^abbbbbab]``bb^I_Ma`aWI_bbbab_Y_^V^`a``^^aWa 0
-SL-XBA 1 1 3 1793 1326 0 1 G.CCA.......C.TCTTGGGCTCCACACCATTACCAGCATCAGAGGCAGGGGAACACAATCTGCTGCCTTATAAG ^D^_VDDDDDDD^DRb\JZM[_J__W`^`b__`aaa_aba^J^Z^LTL_a`XQLVa[^LQNKI_`Q^aaZ`T^PFS 0
-SL-XBA 1 1 3 1793 1389 0 1 G.GGG.......G.CGCAGGTGGGGATGGGCACCCTCACAGCTTCCCTGGACCTTAGTTTTGTTGGGGTTCAGTCC YD[aZDDDDDDDVDZ`_P_]M]aa_YZ`a``aaaaa[J[V^_W_aaaa`VQ_]Q[G]TJ\VXOU`[ZTIR[Q_LGS 0
-SL-XBA 1 1 3 1793 1405 0 1 G.TGG.......T.GCTGAGATGCTCTTTAACCAAAGGAGGAAAGAGAGGAGACCAAGGGCCAGCTGGTTGGTTGT VDPb\DDDDDDDWDWb`\Q_^`aaUa`aa`aabZY]aa]a_XGZ`\_^a]R^H_`^\TGV^_P]a\`ZG\__KP\R 0
-SL-XBA 1 1 3 1793 1507 0 1 G.GTG.......T.GTTGCCAGCCTGCTGCCCGCCATCCTGGTCTTCATTCTCATCTTCATGGAGACACAGATCAC \D\\WDDDDDDD^DT`a`aa`abbaabaabbbab_OX`ba\\Zbaa_OZ]`aaa`b`]^FX`\\]H_H^XZUR^T_ 0
-SL-XBA 1 1 3 1793 1557 0 1 G.GGA.......C.TCGAGCCATTCCACTCCCGCCCGGGCACCAACAGCCAAACGCACGCTCATCAAAAAGGCCGA GDZIGDDDDDDDZDT]NGS^`Z\UG][PI_PIL__]NIO_XHX^]QM\WF[KW[KPGGDYP[^JGMOWFJTTa^YD 0
-SL-XBA 1 1 3 1793 1570 0 1 G.TCT.......T.TCTCCACTCTGCTGCCCTACCTCTCGGAGTCTTCTACCGCGTCTAACTAGTCATATTTACAA UDRaUDDDDDDDKDFb__ab]P^a_bb^b_b`a_a_^UEa`b`SK^I[a_]PFPRK[aZH_aaRF^DHJY`_Zba_ 0
-SL-XBA 1 1 3 1793 1709 0 1 G.GGG.......T.CCATTGGTTTCTGAAAGTATTCACATCATTTGGGATACCAGATAGCTCAATACTCTCTGAGT WD]a[DDDDDDDYD^aWaaaa^aab`b^_U_PZ`a_I_[]aX]^__a^X[SaaW_WQH[b_b`Y^Wa_b_b_^N\F 0
-SL-XBA 1 1 3 1793 1738 0 1 G.GCC.......G.CTCTTGGGGAATATCTGAGGCTCTGTGGTCACCCACAGACCCGTTACTCCTTTAGGTGTCTG ^DYb^DDDDDDDWD\ab`aaaab^aababaaaaab_b^`P`aM^R^`QH_WWO__HODXU^X_aZ][J\]T_O]\_ 0
-SL-XBA 1 1 3 1793 1779 0 1 G.GCA.......C.TGCGTATATTTACAGATATATATACAGAATTGTTTGCTCTGAGCCATTTATAAGCACTTACT \DT`ODDDDDDD^DHXI]F\_YY]aaaYa_ZV```_V_\RNMIY^_WZK[IZaS\`aab^HM\S]GZa`\b`YL^Z 0
-SL-XBA 1 1 3 1793 1859 0 1 G.GAG.......A.CCAAGCATCTATCCCAGTGTGGGGGCTGAGGCTGCGAGAGGAAAGCGGGGACGGAAGACGGG [DGGZDDDDDDD[DGZ\[aXU[_aR^aaa\aPPG`ZaaNGO\LY^XH_L\KPQ[\Q]]Y_W_FYDW[\MTQGWQGJ 0
-SL-XBA 1 1 3 1793 1898 0 1 G.ACA.......G.AATATGGGCTTATCCAACCCAACCAAGATGGAGAGTGAGGGGGTTGTCCCTGGGCCCAAGGC YDN\GDDDDDDDYDIN[P\TZaaa```bb`W`ab``baZH_^aaaJaU^SaY`VZ^^PU_\a`^XTOXa^_LJWSS 0
-SL-XBA 1 1 3 1793 1143 0 1 T.GGG.......T.CATGGTGAGGAAGAGTCGGAAGCAGGCATGCGGCTGCAGGGAATGCAACTTCTTCTCCATCG YDGaRDDDDDDDYD\abbb[baaa[bbaRI_^aaa``I\a_X_^a^W[RZ]RZ`ZJQYX[SRY[Z^X]`YW[JD[D 0
-SL-XBA 1 1 3 1793 141 0 1 T.CTC.......C.CTTAGCAGTGCGCCCCCCGAGCGCGGCACAGGGGCCAGGGAGACAGAGGACACCGGGATCTC ZDZXKDDDDDDDKDTQGGGRMWGJNINa_P[PGG\MESJXJNGYYPPJGEVUOOJMJ`SFIDDDLDYNKDDKFXFa 0
-SL-XBA 1 1 3 1793 1617 0 1 C.GAA.......T.CGCCTTCTTCTTCAACTCGGAGCTGCTGAGCGCTGTGCGCTTCGCCCTGGGCAAGGGCCGCG YDVTFDDDDDDDRDZZa`][`Z\aZV_WS]FX]YXO[KV[KUPPRQDIWNNRSVPFRSXJUKRUJYEJSUQJMEMD 0
-SL-XBA 1 1 3 1793 1031 0 1 C.ACT.......G..GCATTGGAGAAGAACCAAGCTGGCTCTCTAAGGAAGTGCACACGAGTTGGAACACATATTC ^D[^GDDDDDDDYDD\aSV^a\U^\Q^NOO_WHK_aa\RK]HMFTOZYVQHHPHT\YH[PXDHJGDT^Y\ZVMHPF 0
-SL-XBA 1 1 3 1793 1793 0 1 C.TCT.......A..ATGGGCTTTCTACAGCCTGCTTACCACTAACAGTAAGGAATCTTTCATAAACACACCTCAG YDP_UDDDDDDDEDDFLZYHUQGX\H\]RHO`X]_TOP^^Y\TYTWRSUUMSTPKX_XTQ[KXSMQZWWJQ\WZRK 0
-SL-XBA 1 1 3 1793 456 0 1 C.TAT.......C..CGGGTACCACAGTTGAGGACTGACATTCTGAACCCTGATGTTTCTAAAGAAACGACAGTAT ^DU_WDDDDDDD^DD^_^_U```^^U[]]_UNV^`^^U][[W\_QTQZ]_WS[X]TW_^VMLUZVWZ[SFXL[YUW 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_2_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_2_0001_qseq.txt
deleted file mode 100644
index b9be13b..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_2_0001_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 1 1 1793 1420 0 2 C...A................A.....................C.....................T.......... ^DDDIDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1441 0 2 C...A................A.....................C.....................G.......... [DDDGDDDDDDDDDDDDDDDDFDDDDDDDDDDDDDDDDDDDDDYDDDDDDDDDDDDDDDDDDDDDEDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1483 0 2 G...A................A.....................T.....................C.......... [DDDDDDDDDDDDDDDDDDDDODDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDD]DDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1495 0 2 A...T................A.....................C.....................C.......... HDDDIDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDDYDDDDDDDDDDDDDDDDDDDDDSDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1527 0 2 C...C................C.....................C.....................G.......... YDDDIDDDDDDDDDDDDDDDDVDDDDDDDDDDDDDDDDDDDDDTDDDDDDDDDDDDDDDDDDDDDIDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1545 0 2 C...T................G.....................T.....................G.......... TDDDIDDDDDDDDDDDDDDDDQDDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1583 0 2 C...T................G.....................G.....................G.......... [DDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDEDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1596 0 2 C...C................G.....................C.....................C.......... [DDDJDDDDDDDDDDDDDDDDTDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDJDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1658 0 2 T...C................C.....................C.....................C.......... YDDDJDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1718 0 2 A...A................A.....................A.....................G.......... GDDDDDDDDDDDDDDDDDDDDNDDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1745 0 2 A...T................T.....................C.....................A.......... GDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDDSDDDDDDDDDDDDDDDDDDDDDODDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1777 0 2 A...A................C.....................C.....................C.......... HDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1813 0 2 C...C................C.....................T.....................C.......... [DDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDIDDDDDDDDDDDDDDDDDDDDDYDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1916 0 2 C...A................T.....................C.....................C.......... GDDDGDDDDDDDDDDDDDDDDODDDDDDDDDDDDDDDDDDDDDTDDDDDDDDDDDDDDDDDDDDDSDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1959 0 2 A...C................C.....................A.....................C.......... PDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 1 1 1793 808 0 2 C...A................A.....................G.....................G.......... [DDDDDDDDDDDDDDDDDDDDMDDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 602 0 2 C...A................T.....................T.....................G.......... ^DDDEDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDYDDDDDDDDDDDDDDDDDDDDDUDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1602 0 2 C...G................C.....................C.....................C.......... ZDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDWDDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1681 0 2 A...A................G.....................G.....................G.......... HDDDGDDDDDDDDDDDDDDDDVDDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDDDDDDDDDDDDDSDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1011 0 2 A...T................T.....................C.....................C.......... RDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDD^DDDDDDDDDDDDDDDDDDDDDIDDDDDDDDDD 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_2_0002_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_2_0002_qseq.txt
deleted file mode 100644
index abe44d5..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_2_0002_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 1 2 1793 1893 0 2 GGGCAGGGGGCTTTTTCTCACTCTCTCTCATATCTTCTAGGGTAACTACATGAACACACGCTTCTCTCCCCTTCCG `aaaS\aaaYH\a[``b^b]H^b_b^baaRZH[b_abXG]^`R_L_\H_U_\SF^SGSQTbX\a[b_ba_GOVGGY 0
-SL-XBA 1 1 2 1793 1909 0 2 CTCACACCCACACCCCCCCCAATCCCACCCCCGGACACCACACCCCTCCAACTTCCCCCCCCGAGCGCAGCCGGGG aPUJYERYGDJFSJEUZNQGDKNQXMFTKKLLKGFEMFFDDKEMPJDIYDDPDDDDKGGDFEGDGQSVLIDJPPED 0
-SL-XBA 1 1 2 1793 1931 0 2 CTGAAGCGCCACCGCCGCGGCGTGGCGGGCCCCGCGCACCACCTCTTCCCGTCCTCTACCGGCCCTGGCCACGCCC XJEFSPPFSPKOFPNMDFDEXGOKDKFLLDDLFDDMFFMKGGMJKGDLRJJJKNGIJEFRKJILDDIIMEDKOFIG 0
-SL-XBA 1 1 2 1793 2004 0 2 GAACTTGACTATCTCTTCTAATTTTATTGTTTATTTTGTGTTTACTGCCCAGCTACTTCCCACCTTCCACTTGCTT a^S_b_[J]\TVFRa]\H^S]aa`^J\_a_]VLZ___`\aYYV^S[]^I^[WaWR`^\]G]ZaaP`MDL__YW_T\ 0
-SL-XBA 1 1 2 1793 2038 0 2 CCTGTGTCTCAGTGAGCCTTCAGTGCAACATACGGGTAAGAGCAGCCTTCTCTTCACTGAGATGAGACCCCCCCAC a]UQUMQWW^WXMTFT^^UOKSVVMRFDDHJPPQMQPMEQPRRONVTIHTTGTJMNKQIDLKNPHPUQNQFTTUUQ 0
-SL-XBA 1 1 2 1793 829 0 2 TCGCTGTTGTTGCATGTCAGGTTGGAGAGTGTGCCCGTGGCCCCGGTGCGGCCGGTGGCCGCCCCCCCCCCCCGCC `a_aa`\`a^``_HW_\_H]\]\`]R\O]S`R`aa_UJ[][G[FWWIWDYWDYSDTQGWDGTTDS]Q[VZIZQDVD 0
-SL-XBA 1 1 2 1793 1117 0 2 TTCTTCAGCTGTATTGAAGTATAATTTACAATACAGTACAATTCATATATTTTAATTGTATAATTTAATGACTTTG JS_MYa\^[F[^_QJ\RW`SJZ]MRYX`]GV^^`OXGO]GGO\`YYZKZJNGYJIVUXHMMFOX]MDJQLS]LFGV 0
-SL-XBA 1 1 2 1793 1478 0 2 CAGCCATTCAAATCCAGTATTTTTTAAGCCTCATTATTGATAAGACAGAGACATACATCACACCTCAACACCTTTT `YZb^FV[]GOIWa^IYSLSZ`][WJLXaa]^NZZVY[VOQFJYG^NXGXQ[JPQ[KTZEFM]_[^IEDIEDRWUT 0
-SL-XBA 1 1 2 1793 1354 0 2 CTGAACCTCAAGTCTCCACCAATCAGAATCTGGGGGAGGGCGCGCGTGCAGGGAGCCGCCTGCTCTCCACCTTCGC `QSGOUNJMQGQP^SX^YLJGTEWETIIS^PFPRMMOFMFDKKXWEDGUOEMJJPGEJ`KKOMMWMPWGMOEJKKN 0
-SL-XBA 1 1 2 1793 666 0 2 ATTTTTGCTTTCCTTGGCCCCCACCAATTTATACATCTCCATTTTCCGACCTCTGGACTAACTGCTTGCTCAGCAC UZa`b^`a__]_WZ_]_aaaa`Y_aW\^ZP]U_``[aS`aYXS[Z\KOF[_[`WVHVa\VR_ZRHFNUXG[KUVFD 0
-SL-XBA 1 1 2 1793 2031 0 2 TGCCAGTAGTTTTGGGTCAAGCCCTCACCTGATTCCACGCTTCATAGCTTCAGCCGTTCCCATCATACTACTAGCT aaab\]\\a\____aaT_HL\ba`XFNa_\]PU_aaHGWFS\`TSL\aYW_GZ^GXFO^`VFP`MXU]RNFSQRTL 0
-SL-XBA 1 1 2 1793 1812 0 2 TCCAGCATGAAGATAATGGCTAATACCAAAGCAGCCTTTTTGCTGTGGTAGGAAGATAATGGCTAATAAAAATGAG abbbbaX`_JJ_S^VJ^bab`_H\HFFNQHW_H\^GZ^^``\E\a_aaOQ[XMHRHMDOLQ[TENJIPDGYFIKDX 0
-SL-XBA 1 1 2 1793 475 0 2 AACTTTTTTACGCAATGTTAATATTCAACTCTTCCTTCCAATAGAAATTTTCTGCTGCTTTTCTTGCTCGTGCTAG abaVVSRRH_PH_IY]`XJ]SOP]_^YI_U\GUbWINQ_[GQ`WDHU^ZXV_XJXZ[FRNSHLPTYRSJHFWFQLL 0
-SL-XBA 1 1 2 1793 1329 0 2 GAGCCCCGCGTCTGTCTCAGAGAACTTTTGCATTCTTCTTGTTCTCCAGGAGAAACGGCATCATCTTCCATGTCTT `_\Iab_LJYUaWFU_ab_b]KZQHTaaaaa]Zabaab_U__a``bba]aZWHOVI[_\FYb][[X`_GUW_\aTX 0
-SL-XBA 1 1 2 1793 404 0 2 ACATGAATCCTCTCCCACAGGAATTATTCAGCTTACCGCGAGTACGCTTCCGTGTTGGAAAGATTCAACTCACCCC ZFVaUQYQG\NW[]`_X`\WW]U[\\YS^DT`W\Z]_IVRKMDU^[FDDTZJHDDLQFPHEDTGLXRVEOHDDO\a 0
-SL-XBA 1 1 2 1793 1455 0 2 GGAAACCAACCCCTCACATGGTAACCCGCTCCAACCCGCACGCCCTGTTCGGCCCCTGACCCGGCCCCCCGGCGCA ]NKJF[YFFFKTFRGTXFJMVOTKNW_XSGKJFT_ZFDVDDZR]WUMIDOSEFDPVGEMTDDJDK]OUQSIDKIYD 0
-SL-XBA 1 1 2 1793 1793 0 2 GTTTATAACTTCTTCTGTGGGATCAGCGGGCACGCCTCTTCCCACCAGCACACTACACGTCTACCAGCGCGGATGG a^`]MXOHG[_ba^b_aWa`]^\^I[EY_^\DZ`aaYEWTE\J]`\DVEJFM_REXEK\QEWPOUQUaVF[TDL]Y 0
-SL-XBA 1 1 2 1793 310 0 2 CGAAACTTGGGTCAGTAAACTGGTGAAGCTGACCTATTTGGCAAGCAGCATGATTCGGAAGCGCGGCAGGCAGAGT ^GT_aaI]TV_Ua_IRSH^\Ua_GHFPWDF^\_`IY_^S_JGS]`ZW[FN_\RUU`_ZNV_GLFGHVGPGWGQFFF 0
-SL-XBA 1 1 2 1793 1969 0 2 GAGAACTCTCTGTGTAGTTGTGACTTCCATCCTTCCGCAACAGTAGTAAGGACCGCGACTTCTGACCACATTGACC YD\\\GK\a]\YLZV[aN^_W_\YW\\]FMK\WU_a_`KKJOVLGXFRT]^TWNN^ZLFJMWGTOFUPXGFFFJNX 0
-SL-XBA 1 1 2 1794 490 0 2 ATAAACTTGAAAATAATTTTCTATGATACAGCTTTCAGGTAGAAAAATGAATTTTCGTCGTGTTTAACAATGTTGT `aabab``b_ZT__VVaaa^bbaaa^_abaab`a__R[`U]]HXX^O[a_U^]__aaU`X]aT`[_U[DJ]_[[YO 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_2_0003_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_2_0003_qseq.txt
deleted file mode 100644
index 20c4acb..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_1_2_0003_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 1 3 1793 1282 0 2 AAGCACACCAAGCTTCCCGCAGCTGCGGCGCCCCCGCTCCAAGGCCAGCAGCTGCCCCCTCTGCCCCCACCCCCTC GITVXMPGMNN]a_LPVJ\MMN_X\I\GMGMZ[MPF]Z[YFFFV\ZFMFY\\YTTPXRWIVMVZYDVYFFZ_ZUOX 0
-SL-XBA 1 1 3 1793 1301 0 2 GCATTGCGTCCATCTCTTTACAGAAGAACTCAGCCCACACCCTAGAATGTACACCTTTGGAAAAAGGAGAAGTGCT \GUZXI``ZIababbb`aa_ba_H^^_]_aaabbb`U_W^bb]X_]\^_LQHX`aZU]]ZTRRS\R\VJULPS^\L 0
-SL-XBA 1 1 3 1793 1311 0 2 CAGCAAAAGTGCCGGCTAGTCCGGTTTGTTGAAAATACAGTAGAAAAGCTGATTCTGGTTATCTCTCTCAGGACAA a[`aa`S\`P^bbaaIaX^Y]F]_H^`_[``VSZ`_^a\]HFUFUP[TWGYNVT`^VGO\\\_\_SIVDRTTN]SO 0
-SL-XBA 1 1 3 1793 1326 0 2 CAAGATCATACTAACACACTCCAGCCTGGGCAACAGAGTGGGACTCTGTATCCAAAAAAAATTCTCTACCAACTAC a`aa\\a`^_ba^^aabbbbaaL_`bOa[Kbbbb`_S[_`ZZ`bJbab`Kab`P\`Y\X[\`Kb^J[^a^R[aK^b 0
-SL-XBA 1 1 3 1793 1389 0 2 ACCACAGGCACCACCAGCCACGGACCCACGCCTGCCACTCCCCACCCCCCCCCCCCCAGCCACGCCACCGTCCCAC V_]I_OYR_Q__Vaa\`aaRa\TDZa]G]ODYZ[`\O_\WFZEGY^`]Q]VD[ZDY`ZR_]JMIDDMJ[ONYH]LH 0
-SL-XBA 1 1 3 1793 1405 0 2 GCCTTGTTTGGCCCTGATCTCTGACTTCTAGAGCCCCAGCTGCTGGCGGCTGCTGGGATATCCTCCCCGCTCGGGT _aaaaa`__Xaaaa`PP\aaaaa`aaaaaX\XaaaaaX`a`aa_I\a__VPXMQ\RRDWQQ_]FFY`TDPJDVVDG 0
-SL-XBA 1 1 3 1793 1507 0 2 CAGAGCGCGTTGGCGTGAGTGACAGAGCGGCCAGTGGCCGCCGCCCACCCGCCCACGCCCCCGAGGGCCCCCCTGC _PPJP^S]SSRSS\TRRKQTQMZPPKL]SMEVMIIKLTJJMKGMVIEKPIDDDMIGDMMMKIDIJKDDJPGEJDKM 0
-SL-XBA 1 1 3 1793 1557 0 2 CGGCTTTTTTTTTATTGAGACCAGCTCCTGCCCTACCCCCGCGGCTGCGGAGCAAGGTCCCCTTCATGCGCCCCCC TEONGVIR]XU\XH[IJDFJTKNDFEVDVJUVTDFDDJOXIGIFQGTDDKEGMEKDDGKUDGEFVEJEKELKJTTS 0
-SL-XBA 1 1 3 1793 1570 0 2 CAGACACCTTTCATATCTTTATGGCAACTTAATTTTTGGCCTTTTATCACTCTGTCATACCAGCATTCTGCCGTCA `_]Za_baTSXFRS\XaZ^]N`_^W__Z\[GXNTJJ[VSaZa[DMMZbLGMW^_G]FX_]][U]GSZ[DIMGMI\Y 0
-SL-XBA 1 1 3 1793 1709 0 2 AGCCACTGTCCCGTGTATAACTTGGCATTAGAGCACCAGGTCTGTTGGATGGTGGTGGCAGGCCCAATTAATTTTT K^_HV_a_UabbbZb^_`ZJ_`Zaaa\Za`_U_aUa_G]aWb``U[a^UXa^Ga\LY_]LV_WTYDMHHREVRLDH 0
-SL-XBA 1 1 3 1793 1738 0 2 TCCCTGACTGGATACAGGCAGCTGACCCCTTCTCCCGACACCTCAAGGAGTAACTGGGCTGTTGGTGACCCCCGAC `aaaa`_aaa`[aVa_`aa`aZGYFZaa`\`_O__IXO_H_a[G]H]]G]GJZ_X_YDZI[GTS_JMDR_G]TGDF 0
-SL-XBA 1 1 3 1793 1779 0 2 CACTGAAATGTTTAGGACCATATTATAAGTAAGTACTTATCAATGTACTTTAGGACCATATTATAAGTAAGTGCTT \Y`a]G]US`\ZQV`_\a_H\US__YTH_X[H\Yaaa_Y\F^FXaIab]HUVa_`b_Z\X]HO_IW^YSOY[ab\[ 0
-SL-XBA 1 1 3 1793 1859 0 2 CGATTTTTAAGGACCCCGTGCCTCTGGGGGCCGATGAACTCCACGATGGGACGCACCTGGAGCTCTACCATCAATA aaTT`X^_]MGV```a^RK`]`\`]`U_^]QXGSRSGMFOa^QY^QUU[QNKXPYaXMPHOUSTPNNEEVW`POKQ 0
-SL-XBA 1 1 3 1793 1898 0 2 CCGGCCAAGCAGGCATGTGTGAATGAACGTGGCCGCTGACTCAGAACAGAGGACATCCCAGGGCCGCAAGCGCGGA aa]`aaR\Z]ETGPDQ\S\TTQLFKRV`\KSP]PGPFKJMRVFPKEXNRRPGNXNFUMJFFOKGDKQEGMPKNNMG 0
-SL-XBA 1 1 3 1793 1143 0 2 CTGCAGAGCAGTTGTGGCACTGGGCTTTGGCCACTCAAACTCAGGCTGGTCCGGAACCTCCCCCACCCCGCCCCAC `\\aTX]]`_WNV\KPXYJYFRSS`MMRUU^`X\S]PUW^PYPPRZSQKDVYRLEPVVETX\ZWEK\QDGWJVDDQ 0
-SL-XBA 1 1 3 1793 141 0 2 CTCTCCCGCGCCTGCTACGGAGCCCGCTCGGGGGGGCCACGCCGCTCCCGAGGACGTAGCACCTCCTCCACTCACG SYLIUXTIYEVGMRRR^XIFG_GUMGGDDKZUQJIMMGMNOG]RNEDPSGKPGGOLUEPTDDMU]GEFDJQOEJRG 0
-SL-XBA 1 1 3 1793 1617 0 2 GTGGTCATAACTGTTTCTGGACCCATTTGAACTTCATCTGAATATAGAAATCTCAGCAGCGCCCGGACGGCTGCGG `[ba`aS]\K_aa_a`b_a\I`_IJ]`aaXSaa_aZ]a^Z]__T`Za\OSUb__GU`XZ`Q`[FXOFGYL^DRYNY 0
-SL-XBA 1 1 3 1793 1031 0 2 CCCATACCAGCACAGAGCATACAGAAACACAGAAAAAATATTCCCAGTAAAACATGTGCAACTGTCCAGGCAGTCG JT``_XQJ]S``aa`U_ZFGLZ[\QQHaW___V]`_[TWRSXW_UQLSTYLW]WZYOOWPIXTULZVMHIDMSHHO 0
-SL-XBA 1 1 3 1793 1793 0 2 GCTCAAATTTGTGCTACCAATGATATCGAGTTTATAGCAAATTTTCTACGGGAAGTCTATGCGGCAATTTTCTCAT ab`\WJR^b\`LW`_Y`ba^K_ZWZ_J_I_ZbRKWHWb^JX\ZQI\J\FQ`^WXWIJODGHHPWHSQY^`Va]^FY 0
-SL-XBA 1 1 3 1793 456 0 2 TCCATCCACTTCCCTGAGCCTCAGAAAAGGGCAAGGCATGGCTCACATACTCTCAGCCACGGCCTGGCCTGCTGCC aaa[`aa_aaaaaa\__`aa^aT_VVV\ZZ`a`X`Za^\][aa_U_``^a]aX]I]``X`TR^]GDWXGMX]Z[YG 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_2_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_2_1_0001_qseq.txt
deleted file mode 100644
index 2e7626a..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_2_1_0001_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBB 2 2 1 0 357 0 1 GACTTTGGGAAGGGTCATTACTGCCCTTGTAGAAAGAACACCTCATGTTCCTTATCGAGAGCGGCCGCTGCTGATC W[`bbbb_baS\`_\bbabbaWR`bba``ab_bbbbbabbbaabb^^^\aa_ab`a_`[`VaST[^SWTXWNYEHM 1
-SL-XBB 2 2 1 0 300 0 1 CGGGTTGGGGCTCTGGAAGCGGATGTGTACGGGTGGAGTGTTAGTTACATTCTGGCCCGAGTGACTTTTGGTATCA [GI\LTNG[_KOIOWGGYOKOH^HYGTNRGU[HRGTPG[YHNGF[RV[PFNJFFFDKQMFKFQQMVLDMDDDGDDK 0
-SL-XBB 2 2 1 0 872 0 1 TTTTAAATTGAGACGCATGAAGGCTAAGCGGCCGCGGAAAGACACAGGGAGGTTTACTTATTTTATTAATCAGACT abbbb`aab`\W`aaaba^Z_WX]Z`_]a`[`^_[^`R[YXZZ]]^XXYXXWMXUTTZXSV\^[TTWUSQLMKHMD 1
-SL-XBB 2 2 1 0 458 0 1 CGCGTTGCGGCCGCTGAATCCAAATCCAATAGACTCACTTTTTATTTTTATTTTTAAAATTAAAGGTTGATCTCTC ZS`b^ab[Z^__L\a[`[``a^aZX_O\\TZJ]UXaZF[``_YP^a`[\Z]`a``NV[X_aYYSPRLXFOQX_UDI 1
-SL-XBB 2 2 1 0 1934 0 1 CGTCAGCGGGCGGAAGCGGGAGGGCGAACTGGAAAGCATGAACGGAGTGGCGGACTTACTGAGATAAGTGAGAGAG IIIIX_XHZG[IWG[`_R]GZ`JRJV^Z[GMP_TNN_[_HTX\QPFZ\PTGG]RUMGSRVFFGTZGPIDSTTFSKD 0
-SL-XBB 2 2 1 0 1688 0 1 AGAAGGAGGACGACCTCGAAGCCATGAACGCAGAGGAGGACTCACTGAGGAACGGGGGAGAGGAGGAGTACGAAGC I]_`_]TV[``]ZZa``b]TG_aaaa```XXZXG]aaaa^^a[^]`[Wa_^`[[[___XaTaXK]RRXFKPSUPNI 0
-SL-XBB 2 2 1 0 1366 0 1 AGTCATCTTCTTCTTTTTGGGGCCGCGTCTCTTGGGCTTTTGATCGTCATCCTCCTCTTCCTCTTCTTCCTCCTCT \bbbababbbbbbbbbb``abYb`ba\aa___aSWa`bbba\^b``^abba^_aba_abbabaa`]\^SWK_`RMD 1
-SL-XBB 2 2 1 0 287 0 1 AGGAGATTTATTACCTATTTAAAAAATGCATTTGTAATTGTAAAATGAAAAATCACTTGCAAACAGTCTGCGCGTC Z[a`aa^^`b`_aab_bbbabbbb_aaaabbbbbaab^ab^bbbbbbbaabbbbbaa^aa`aa_a^NSRSYSaYH^ 1
-SL-XBB 2 2 1 0 538 0 1 AATTGGGCAAGAAAATAAAGTCGTTGTGGGCGGCTGGGGAACCTGGCGTCAGTCCCCCGTGGCTGTTCGCCGGCAC TGZ]Z]XGI]\\aX^a`_a`]V]_a[[^^`PVZ^a_`_Z^```X\X_`ZYVUVVZa\XUQRTU]VIGMKJJDPKDI 0
-SL-XBB 2 2 1 0 1484 0 1 CAAAACAACTCAGTTTGTTCCAAAACAATGTGAGTTCCCAGATTTAGCCTTGTCTTAATATATTGACCTTAGTTCC a``aUI]^_Q_aaaabV\b`[`abb_Saa`ab]babb_Y`_aa]aa`^aabbXWa\`aaabaaa\ZYJQ\VY^SNJ 0
-SL-XBB 2 2 1 0 650 0 1 CATGCAACATCTCCACAGCCAGCCTCCTGATCCACTGACCCAGGGACCCCTAAAGCTGGAGGCCCCAGACTCTCTC a__a```a`aaaaa__aaaa``a`^`a`_```^^]\\^_VW]VXV\S\\\TXXTJMPUQQQSSRQRMJMPFRKDGD 1
-SL-XBB 2 2 1 0 932 0 1 TGAGGAGAAACATTCTTTTTGTAGGGGGTGCTAACTATGGCCTATGCAAAATTCTGAATTTTACCACCGTCTAAGC \GH]PSQ[I_\YHaabaaaWGZSSU`]NOXLMGS]aYFPRFV[\[FTP_Y^[NMZXNPLYYQNXSPSOKOMLTQNY 0
-SL-XBB 2 2 1 0 431 0 1 CCGATGAAAGCAACAAGGTAGGGTTAACTCATCTATGAATAAGCCTGACATGTGAGGAATCACAAGCAAATTGCAC ^NQLW\H\GLFFFZ\Q_\JGVY\Q_aK`^a_aa`XT]DF[[\QDIVZNTTZ]VXOYNSZXSPDLPFGPHNUMOJGS 0
-SL-XBB 2 2 1 0 978 0 1 AACCGGTGCATTATGCGGACCGGGAGGGCTTTCGAAACACCTGGGTGGTGCTGAACCCGGGAGTGGCGTCTCCCTC GGGI]_THV_GIW_]QTIGZZTGWZTOZ\`_NGGGGHZTZGGGMZ[HZRXU_IOKO_GQR\OVOYDLDPGTGJVFE 0
-SL-XBB 2 2 1 0 122 0 1 GCCCGCGCGTCCCTTGCCGCCGTGGGCAGGGACGGGGGGGAGGCAAGACCCCACCGATGCTCGTCATACGACCAGG L`aa\\J\\^X[_I]X_TI]TGFMZVIH`VIHXEG_aZTRXLH_PUFFFMMWNFPFFH^QNLPEUKKDGINKKVKF 0
-SL-XBB 2 2 1 0 1549 0 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA _Z_]JRR]ZVR[^^`X^aX^\\XPVGTPKTU]\TU\Y[S`\^V]NUFKMJJMUYQDQHFPKEMKMOKGIIFOJMOJ 1
-SL-XBB 2 2 1 0 1783 0 1 CACACCTCTCTCGTTTTGGGGCAAAACGGCTCAGCCATTGGAATATGGCACACTCGTCTGGCACAAGAAGGACATC a`_[W__\W[T_ZPZ_H_W_V`bJ`ba_aa[a_YROOW[]YGUI_T]RKGG^O]WGZSK[_ZGZZKNXRPRVZGUW 1
-SL-XBB 2 2 1 0 254 0 1 CCGCAAACAGCATACTTTGGTACTCTTGAAGTTTCAGGGCATACTTGTAATCTGCAACCACTGGATCTGTTCTTGT a`[_`Zaa]J_R_a\abbaaXbbaaa\VW_aQaT[Z[_GTa^_P^]aY^ababa``\aMaa]`[^XWWSOOX]MDD 1
-SL-XBB 2 2 1 0 1660 0 1 AACACTCATGGACATTATTCCTAATAATGGTTCTTATGGCAAAGTGAAAAAATAATCATCCAAGTACCTGTATCGC R^aa__bb```baaabbbb_bbaaabba`a^a^abb`^ababaaV`^`bbba^aba`aabaabb_`][V^V`aFF\ 1
-SL-XBB 2 2 1 0 1250 0 1 CACACACACACACACACACACACCACCTTTTGGCTTATCTGCACGCGGCCGCGTGCCCTACCCTACCCCATGGGAT a_aa^\Ra\`aaXa_aa_aaaaaaa[^X^``V[`_`a^aaO``^_SJUELTVMKVTPFOKJJMNKTRRJEEPFKTR 1
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_1_0001_qseq.txt
deleted file mode 100644
index 43797d0..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_1_0001_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 4 1 1793 1420 0 1 G....................C.....................T.....................T.......... \DDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1441 0 1 C....................C.....................G.....................G.......... GDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDJDDDDDDDDDDDDDDDDDDDDDTDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1483 0 1 G....................G.....................A.....................A.......... YDDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDDNDDDDDDDDDDDDDDDDDDDDDWDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1495 0 1 G....................C.....................G.....................C.......... VDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1527 0 1 G....................G.....................G.....................T.......... MDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1545 0 1 C....................A.....................A.....................C.......... HDDDDDDDDDDDDDDDDDDDDHDDDDDDDDDDDDDDDDDDDDDHDDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1583 0 1 G....................G.....................G.....................A.......... YDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1596 0 1 G....................C.....................C.....................T.......... TDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDTDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1658 0 1 C....................C.....................T.....................A.......... GDDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1718 0 1 G....................C.....................C.....................C.......... YDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDHDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1745 0 1 C....................C.....................C.....................A.......... PDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDVDDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1777 0 1 G....................C.....................T.....................C.......... YDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDYDDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1813 0 1 G....................C.....................A.....................C.......... VDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1916 0 1 G....................T.....................T.....................C.......... [DDDDDDDDDDDDDDDDDDDDUDDDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1959 0 1 G....................C.....................T.....................C.......... [DDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 808 0 1 T....................C.....................C.....................T.......... YDDDDDDDDDDDDDDDDDDDD^DDDDDDDDDDDDDDDDDDDDD^DDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 4 1 1793 602 0 1 T....................A.....................A.....................A.......... [DDDDDDDDDDDDDDDDDDDD]DDDDDDDDDDDDDDDDDDDDDVDDDDDDDDDDDDDDDDDDDDDQDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1602 0 1 C....................G.....................G.....................A.......... [DDDDDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1681 0 1 C....................T.....................A.....................A.......... ^DDDDDDDDDDDDDDDDDDDDHDDDDDDDDDDDDDDDDDDDDDEDDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1011 0 1 A....................C.....................G.....................G.......... GDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDD 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_1_0002_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_1_0002_qseq.txt
deleted file mode 100644
index 99de789..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_1_0002_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 4 2 1793 1893 0 1 G.TCC.......A.TCCCCGTGGATGAAAATGCTGTACATGTTCTTGTTGATAACAATGGGCAAGGTCTAGGACAG ODZb[DDDDDDDHDXbb_G]^b_P\`VGOO\ab`aXU`][`^_b``a_``T]V`aPFU]V]aXMXaVaTHVZTa[] 0
-SL-XBA 1 4 2 1793 1909 0 1 G.CCT.......C.CTCACACCGCCCCCCTTCTCACCTGCCCTGCGTAACCTGTACTGACTGCCCACTCCTCACCC GD[_WDDDDDDDIDZGW_ZI]VZIMG[a]TGMT_NI]XRZGQ_\LYFT]HO\JPZFTYFZNGZP_I]KGZFZGGYH 0
-SL-XBA 1 4 2 1793 1931 0 1 G.CTA.......T.CACTGTCGACACCGCACACGGGGCATACCCACATCAAAGCAGTCCCCCAAGTCCCTGCGCAG [DWMFDDDDDDDEDMG[aIIG]RIVVTGIGZFMUFFJZFEPGXMHMIGVZTNFQGUS`VO]OMKQR_HODFT\[IF 0
-SL-XBA 1 4 2 1793 2004 0 1 G.GTT.......C.TACTGGCATTTACTGTTTAACATCACACACCAAGCCAGGTTATTTCACACTCCTGCTACTGG WDPR[DDDDDDDYD^bbaaa^G]bbbbba`_IXJ_J_b_JIP^ZW_JRI_IWbS_S]b]V_WPPT^HKbb[V_^Y` 0
-SL-XBA 1 4 2 1793 2038 0 1 G.GCG.......G.CACCTTGGTACTGGGTGATGGGGAGGCACTGAATGGGCTTCAAGTCCTCAAACGCCTGATCT ^DYLZDDDDDDDMD\H_bb`ba\W`aba^V_E]a^`b\^baXbS```]]U\\]]ZDT]RDYNYDKRMZ_OKXILPZ 0
-SL-XBA 1 4 2 1793 829 0 1 T.GGC.......C.TGGGCAAGCACCTGACCAGCAACAGCCCCCGCCTGGTGCAGCACTGCCTGTGGACCCTGCGC ZDZ]IDDDDDDD[DYa`a_OZaaaaaa_Z_a_`_ZI_I]aaaaa`aa`^_R__Z[GT_``a_Y]M\ZK[aaZ[a`a 0
-SL-XBA 1 4 2 1793 1117 0 1 G.GGG.......C.GGTCGTTAGCAAGTGATGGCTGTGTTCTGTATCTTTATTGTGGCGACACTTACATGACTGGA RDZaVDDDDDDD\DXbIFT_^aba][MX]^_a`H]]Ga[R_H_S^a[WHT]UV[U`TJTLOMGWSLWURVKVNVDH 0
-SL-XBA 1 4 2 1793 1478 0 1 T.TTT.......C.AATTTTACCTCATAAAATTTTTTGAGGTTTGATGTATGTCTCTGTCTTATCAATAATGAGGC \D^b^DDDDDDDIDJK_bba]abaa`_\VVWabababa^ab^ab`S`b_Z_b_babaa`b`YH\a]FZUS\]U\`b 0
-SL-XBA 1 4 2 1793 1354 0 1 T.GCT.......G.GGCGCCGCGAAGCGCACGGCGCCGACGCAGGGGGAAGGCGGGACATACACGACCCGCGAGCG PDZ`ZDDDDDDDWDGTZ_aVZGZIWZGW_Z_[XNWPGGVVI[GW_LR[FGT\ZGVGG[FHF[MOGNIGVNMQGX]P 0
-SL-XBA 1 4 2 1793 666 0 1 C.GAG.......T.GGGTAGGAAACACAGCCTTGCTCCACAGCGCACTGTCAGCAAGACGCTCCTTTCTTCGGAGA ^DXGXDDDDDDDDDVHXMM[YY]R]PZVV[aOT^^Ha]O\PQGQ`U\SYSXTU^NDTLDLZPZUTSQZNLEGQUKG 0
-SL-XBA 1 4 2 1793 2031 0 1 C.CCG.......G.GGTGCATGGGCTCCAACGTGGTGTCCTGTGGAGCTGTTGGGCCTGGGCAGGCGGCACAGATC YDFIYDDDDDDDYDYaZa_G[aa`aXa`R``aX`_KaPG\\`U_`N^^Z\T\^`RDQVR[S`KZVZY\ZJEENKNR 0
-SL-XBA 1 4 2 1793 1812 0 1 C.CTC.......C.GCATACTTAACAAGTCTGATCTTGCTTATAGAAATTGGATCTTACTACTTCATTCTCAGAAT GD^a]DDDDDDD^D]aV\L_aaZ\_OVa_baaT^baaaba^J]YaXSS^aa_P_baaXN\Va_`a\__aa_G]GW[ 0
-SL-XBA 1 4 2 1793 475 0 1 C.GGG.......C.CCCCCCTAGGCAATATGCTACTGCATATATATTTGGTCTAGATATATAACAAGTTACTACTG ^DX^RDDDDDDDOD[[DTZGQIV[_^GPFHU]V^KV\V_IHUHRTFVYVHDDKFRGMGJQJJSWQMYHHLDOLFFQ 0
-SL-XBA 1 4 2 1793 1329 0 1 C.TCT.......T.GATGCAGTAACTGGAAATATAGAAGATGCTGTGACTCCATTTGAATCTATAAAAAGCGTTGT WDWOTDDDDDDDRDX^IV^GPGXOFWOZSGY^^[[JXYTJN\`WTKN\^RH\FHULJIKT\NXOQLQLOJTLDKLO 0
-SL-XBA 1 4 2 1793 404 0 1 C.CCC.......T.CAATGCTATGCAGTATGTCTTCTTATCTCTGTCTTCAAGAGCATCCTCTGTCAGTCCTACAT YDH^ODDDDDDDXDINODKWMLL]]]]X_^\XVTG\SNDO^VSFNFFRXDL^WWQWKSSPQ\OPUWZQJX`YVSFT 0
-SL-XBA 1 4 2 1793 1455 0 1 C.TTC.......G.GACTGCAGTTGCTGTTGCCCATTAAGACCTTGAGAAAAGGCTTGCCTGCCCTTCGTCTGACT ^DW\^DDDDDDDYDXF\^_bI_QF\a[ZNGZ\D^KWXFWOG\aX\]VPSTMLGVaLHRWNTHF\DTL\YNTVHDUD 0
-SL-XBA 1 4 2 1793 1793 0 1 C.CCA.......C.GGGCCCTTTGTCTAAAGTCTGAATCAGCATTTGGATTTAGCCCTAATAGAGCCTGTTCATCC \D^DHDDDDDDD\DUW]aaaX^]_YaYHQGVY`WSFUV]TZ]NUVWWXFRWTKX_^\LJGRQVJR_]WVVV[NPT_ 0
-SL-XBA 1 4 2 1793 310 0 1 C.GGA.......T.GAACCTTTGGCAAGGCTGCTCTTACGAGTCCTCTCGCCCTGTTCCACCTATCCCCATAGCTA GDTZFDDDDDDDGDMIO_XX_`a]b`THY\Y`PZ`[RFYLFFMFRFZGFT]ab_a\`G`[]TPPGUa^KFFG[ELI 0
-SL-XBA 1 4 2 1793 1969 0 1 T.CGC.......A.CCCTGACTGGCAAGGCGGTGGCGGCTCCAGTGAAGGCTCCCCGTGTTCTTAAAGACTAGCGC TDWGGDDDDDDDPDZaaa]JHVaaa^L^PO_aVaaaX`__`RVXF^IRXa`S_]HZFTYFaa``Z]Q]`UJXJ_I[ 0
-SL-XBA 1 4 2 1794 490 0 1 C.TCC.......T.TATTTACTATTTTCTGATTTTTAAAATGACAGTGGCAATTACCATTTATACTGTGTTATTTG ^DWb^DDDDDDDXDUG\^YG\_a``__a_`[[[[\_\ZT^_XJ^`_Y^X_TEP\]`^JYUUUW\`X^V^X^\[X\U 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_1_0003_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_1_0003_qseq.txt
deleted file mode 100644
index 20446c9..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_1_0003_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 4 3 1793 1282 0 1 G.TAG.......C.GGACTCTGGCGTCACCTTTGGCGCTGAGCGCCCCAGGCCCGCCAGCCCGCCCGCCCACTGCC [DZGMDDDDDDDGDMUMGZa_TTJX]IW_G]I_ZGMZ_VTFTFZZ_ZZIS[T[QI_ZN][_T]TGPUZPZVHFKMM 0
-SL-XBA 1 4 3 1793 1301 0 1 G.AGG.......T.CAGGGTTGAGGTATTCTTAGGTTAGCCGAGCTCTTTCCTCCTTTCCCCCCCCCTCTCCCCCA ^DIYRDDDDDDDGDZIXH]RJLIL_\HR^bba``ZH`W_QIQTZ`VKTQ\aZG\HSVH\abZJYb_HQ_O\a`XGX 0
-SL-XBA 1 4 3 1793 1311 0 1 G.TAT.......T.TTCCTTCAGTCTGCACAAAGATTAAGGTAATTTACAGTCAATCTGTGAATGAATGTTGAGAC [DGH[DDDDDDDVD[[ababbb`abbbb_baa^abbbbbab]``bb^I_Ma`aWI_bbbab_Y_^V^`a``^^aWa 0
-SL-XBA 1 4 3 1793 1326 0 1 G.CCA.......C.TCTTGGGCTCCACACCATTACCAGCATCAGAGGCAGGGGAACACAATCTGCTGCCTTATAAG ^D^_VDDDDDDD^DRb\JZM[_J__W`^`b__`aaa_aba^J^Z^LTL_a`XQLVa[^LQNKI_`Q^aaZ`T^PFS 0
-SL-XBA 1 4 3 1793 1389 0 1 G.GGG.......G.CGCAGGTGGGGATGGGCACCCTCACAGCTTCCCTGGACCTTAGTTTTGTTGGGGTTCAGTCC YD[aZDDDDDDDVDZ`_P_]M]aa_YZ`a``aaaaa[J[V^_W_aaaa`VQ_]Q[G]TJ\VXOU`[ZTIR[Q_LGS 0
-SL-XBA 1 4 3 1793 1405 0 1 G.TGG.......T.GCTGAGATGCTCTTTAACCAAAGGAGGAAAGAGAGGAGACCAAGGGCCAGCTGGTTGGTTGT VDPb\DDDDDDDWDWb`\Q_^`aaUa`aa`aabZY]aa]a_XGZ`\_^a]R^H_`^\TGV^_P]a\`ZG\__KP\R 0
-SL-XBA 1 4 3 1793 1507 0 1 G.GTG.......T.GTTGCCAGCCTGCTGCCCGCCATCCTGGTCTTCATTCTCATCTTCATGGAGACACAGATCAC \D\\WDDDDDDD^DT`a`aa`abbaabaabbbab_OX`ba\\Zbaa_OZ]`aaa`b`]^FX`\\]H_H^XZUR^T_ 0
-SL-XBA 1 4 3 1793 1557 0 1 G.GGA.......C.TCGAGCCATTCCACTCCCGCCCGGGCACCAACAGCCAAACGCACGCTCATCAAAAAGGCCGA GDZIGDDDDDDDZDT]NGS^`Z\UG][PI_PIL__]NIO_XHX^]QM\WF[KW[KPGGDYP[^JGMOWFJTTa^YD 0
-SL-XBA 1 4 3 1793 1570 0 1 G.TCT.......T.TCTCCACTCTGCTGCCCTACCTCTCGGAGTCTTCTACCGCGTCTAACTAGTCATATTTACAA UDRaUDDDDDDDKDFb__ab]P^a_bb^b_b`a_a_^UEa`b`SK^I[a_]PFPRK[aZH_aaRF^DHJY`_Zba_ 0
-SL-XBA 1 4 3 1793 1709 0 1 G.GGG.......T.CCATTGGTTTCTGAAAGTATTCACATCATTTGGGATACCAGATAGCTCAATACTCTCTGAGT WD]a[DDDDDDDYD^aWaaaa^aab`b^_U_PZ`a_I_[]aX]^__a^X[SaaW_WQH[b_b`Y^Wa_b_b_^N\F 0
-SL-XBA 1 4 3 1793 1738 0 1 G.GCC.......G.CTCTTGGGGAATATCTGAGGCTCTGTGGTCACCCACAGACCCGTTACTCCTTTAGGTGTCTG ^DYb^DDDDDDDWD\ab`aaaab^aababaaaaab_b^`P`aM^R^`QH_WWO__HODXU^X_aZ][J\]T_O]\_ 0
-SL-XBA 1 4 3 1793 1779 0 1 G.GCA.......C.TGCGTATATTTACAGATATATATACAGAATTGTTTGCTCTGAGCCATTTATAAGCACTTACT \DT`ODDDDDDD^DHXI]F\_YY]aaaYa_ZV```_V_\RNMIY^_WZK[IZaS\`aab^HM\S]GZa`\b`YL^Z 0
-SL-XBA 1 4 3 1793 1859 0 1 G.GAG.......A.CCAAGCATCTATCCCAGTGTGGGGGCTGAGGCTGCGAGAGGAAAGCGGGGACGGAAGACGGG [DGGZDDDDDDD[DGZ\[aXU[_aR^aaa\aPPG`ZaaNGO\LY^XH_L\KPQ[\Q]]Y_W_FYDW[\MTQGWQGJ 0
-SL-XBA 1 4 3 1793 1898 0 1 G.ACA.......G.AATATGGGCTTATCCAACCCAACCAAGATGGAGAGTGAGGGGGTTGTCCCTGGGCCCAAGGC YDN\GDDDDDDDYDIN[P\TZaaa```bb`W`ab``baZH_^aaaJaU^SaY`VZ^^PU_\a`^XTOXa^_LJWSS 0
-SL-XBA 1 4 3 1793 1143 0 1 T.GGG.......T.CATGGTGAGGAAGAGTCGGAAGCAGGCATGCGGCTGCAGGGAATGCAACTTCTTCTCCATCG YDGaRDDDDDDDYD\abbb[baaa[bbaRI_^aaa``I\a_X_^a^W[RZ]RZ`ZJQYX[SRY[Z^X]`YW[JD[D 0
-SL-XBA 1 4 3 1793 141 0 1 T.CTC.......C.CTTAGCAGTGCGCCCCCCGAGCGCGGCACAGGGGCCAGGGAGACAGAGGACACCGGGATCTC ZDZXKDDDDDDDKDTQGGGRMWGJNINa_P[PGG\MESJXJNGYYPPJGEVUOOJMJ`SFIDDDLDYNKDDKFXFa 0
-SL-XBA 1 4 3 1793 1617 0 1 C.GAA.......T.CGCCTTCTTCTTCAACTCGGAGCTGCTGAGCGCTGTGCGCTTCGCCCTGGGCAAGGGCCGCG YDVTFDDDDDDDRDZZa`][`Z\aZV_WS]FX]YXO[KV[KUPPRQDIWNNRSVPFRSXJUKRUJYEJSUQJMEMD 0
-SL-XBA 1 4 3 1793 1031 0 1 C.ACT.......G..GCATTGGAGAAGAACCAAGCTGGCTCTCTAAGGAAGTGCACACGAGTTGGAACACATATTC ^D[^GDDDDDDDYDD\aSV^a\U^\Q^NOO_WHK_aa\RK]HMFTOZYVQHHPHT\YH[PXDHJGDT^Y\ZVMHPF 0
-SL-XBA 1 4 3 1793 1793 0 1 C.TCT.......A..ATGGGCTTTCTACAGCCTGCTTACCACTAACAGTAAGGAATCTTTCATAAACACACCTCAG YDP_UDDDDDDDEDDFLZYHUQGX\H\]RHO`X]_TOP^^Y\TYTWRSUUMSTPKX_XTQ[KXSMQZWWJQ\WZRK 0
-SL-XBA 1 4 3 1793 456 0 1 C.TAT.......C..CGGGTACCACAGTTGAGGACTGACATTCTGAACCCTGATGTTTCTAAAGAAACGACAGTAT ^DU_WDDDDDDD^DD^_^_U```^^U[]]_UNV^`^^U][[W\_QTQZ]_WS[X]TW_^VMLUZVWZ[SFXL[YUW 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_2_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_2_0001_qseq.txt
deleted file mode 100644
index 9d11334..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_2_0001_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 4 1 1793 1420 0 2 C...A................A.....................C.....................T.......... ^DDDIDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1441 0 2 C...A................A.....................C.....................G.......... [DDDGDDDDDDDDDDDDDDDDFDDDDDDDDDDDDDDDDDDDDDYDDDDDDDDDDDDDDDDDDDDDEDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1483 0 2 G...A................A.....................T.....................C.......... [DDDDDDDDDDDDDDDDDDDDODDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDD]DDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1495 0 2 A...T................A.....................C.....................C.......... HDDDIDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDDYDDDDDDDDDDDDDDDDDDDDDSDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1527 0 2 C...C................C.....................C.....................G.......... YDDDIDDDDDDDDDDDDDDDDVDDDDDDDDDDDDDDDDDDDDDTDDDDDDDDDDDDDDDDDDDDDIDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1545 0 2 C...T................G.....................T.....................G.......... TDDDIDDDDDDDDDDDDDDDDQDDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1583 0 2 C...T................G.....................G.....................G.......... [DDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDEDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1596 0 2 C...C................G.....................C.....................C.......... [DDDJDDDDDDDDDDDDDDDDTDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDJDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1658 0 2 T...C................C.....................C.....................C.......... YDDDJDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1718 0 2 A...A................A.....................A.....................G.......... GDDDDDDDDDDDDDDDDDDDDNDDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1745 0 2 A...T................T.....................C.....................A.......... GDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDDSDDDDDDDDDDDDDDDDDDDDDODDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1777 0 2 A...A................C.....................C.....................C.......... HDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1813 0 2 C...C................C.....................T.....................C.......... [DDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDIDDDDDDDDDDDDDDDDDDDDDYDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1916 0 2 C...A................T.....................C.....................C.......... GDDDGDDDDDDDDDDDDDDDDODDDDDDDDDDDDDDDDDDDDDTDDDDDDDDDDDDDDDDDDDDDSDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1959 0 2 A...C................C.....................A.....................C.......... PDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 4 1 1793 808 0 2 C...A................A.....................G.....................G.......... [DDDDDDDDDDDDDDDDDDDDMDDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 602 0 2 C...A................T.....................T.....................G.......... ^DDDEDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDYDDDDDDDDDDDDDDDDDDDDDUDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1602 0 2 C...G................C.....................C.....................C.......... ZDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDWDDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1681 0 2 A...A................G.....................G.....................G.......... HDDDGDDDDDDDDDDDDDDDDVDDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDDDDDDDDDDDDDSDDDDDDDDDD 0
-SL-XBA 1 4 1 1793 1011 0 2 A...T................T.....................C.....................C.......... RDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDD^DDDDDDDDDDDDDDDDDDDDDIDDDDDDDDDD 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_2_0002_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_2_0002_qseq.txt
deleted file mode 100644
index bfdaecf..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_2_0002_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 4 2 1793 1893 0 2 GGGCAGGGGGCTTTTTCTCACTCTCTCTCATATCTTCTAGGGTAACTACATGAACACACGCTTCTCTCCCCTTCCG `aaaS\aaaYH\a[``b^b]H^b_b^baaRZH[b_abXG]^`R_L_\H_U_\SF^SGSQTbX\a[b_ba_GOVGGY 0
-SL-XBA 1 4 2 1793 1909 0 2 CTCACACCCACACCCCCCCCAATCCCACCCCCGGACACCACACCCCTCCAACTTCCCCCCCCGAGCGCAGCCGGGG aPUJYERYGDJFSJEUZNQGDKNQXMFTKKLLKGFEMFFDDKEMPJDIYDDPDDDDKGGDFEGDGQSVLIDJPPED 0
-SL-XBA 1 4 2 1793 1931 0 2 CTGAAGCGCCACCGCCGCGGCGTGGCGGGCCCCGCGCACCACCTCTTCCCGTCCTCTACCGGCCCTGGCCACGCCC XJEFSPPFSPKOFPNMDFDEXGOKDKFLLDDLFDDMFFMKGGMJKGDLRJJJKNGIJEFRKJILDDIIMEDKOFIG 0
-SL-XBA 1 4 2 1793 2004 0 2 GAACTTGACTATCTCTTCTAATTTTATTGTTTATTTTGTGTTTACTGCCCAGCTACTTCCCACCTTCCACTTGCTT a^S_b_[J]\TVFRa]\H^S]aa`^J\_a_]VLZ___`\aYYV^S[]^I^[WaWR`^\]G]ZaaP`MDL__YW_T\ 0
-SL-XBA 1 4 2 1793 2038 0 2 CCTGTGTCTCAGTGAGCCTTCAGTGCAACATACGGGTAAGAGCAGCCTTCTCTTCACTGAGATGAGACCCCCCCAC a]UQUMQWW^WXMTFT^^UOKSVVMRFDDHJPPQMQPMEQPRRONVTIHTTGTJMNKQIDLKNPHPUQNQFTTUUQ 0
-SL-XBA 1 4 2 1793 829 0 2 TCGCTGTTGTTGCATGTCAGGTTGGAGAGTGTGCCCGTGGCCCCGGTGCGGCCGGTGGCCGCCCCCCCCCCCCGCC `a_aa`\`a^``_HW_\_H]\]\`]R\O]S`R`aa_UJ[][G[FWWIWDYWDYSDTQGWDGTTDS]Q[VZIZQDVD 0
-SL-XBA 1 4 2 1793 1117 0 2 TTCTTCAGCTGTATTGAAGTATAATTTACAATACAGTACAATTCATATATTTTAATTGTATAATTTAATGACTTTG JS_MYa\^[F[^_QJ\RW`SJZ]MRYX`]GV^^`OXGO]GGO\`YYZKZJNGYJIVUXHMMFOX]MDJQLS]LFGV 0
-SL-XBA 1 4 2 1793 1478 0 2 CAGCCATTCAAATCCAGTATTTTTTAAGCCTCATTATTGATAAGACAGAGACATACATCACACCTCAACACCTTTT `YZb^FV[]GOIWa^IYSLSZ`][WJLXaa]^NZZVY[VOQFJYG^NXGXQ[JPQ[KTZEFM]_[^IEDIEDRWUT 0
-SL-XBA 1 4 2 1793 1354 0 2 CTGAACCTCAAGTCTCCACCAATCAGAATCTGGGGGAGGGCGCGCGTGCAGGGAGCCGCCTGCTCTCCACCTTCGC `QSGOUNJMQGQP^SX^YLJGTEWETIIS^PFPRMMOFMFDKKXWEDGUOEMJJPGEJ`KKOMMWMPWGMOEJKKN 0
-SL-XBA 1 4 2 1793 666 0 2 ATTTTTGCTTTCCTTGGCCCCCACCAATTTATACATCTCCATTTTCCGACCTCTGGACTAACTGCTTGCTCAGCAC UZa`b^`a__]_WZ_]_aaaa`Y_aW\^ZP]U_``[aS`aYXS[Z\KOF[_[`WVHVa\VR_ZRHFNUXG[KUVFD 0
-SL-XBA 1 4 2 1793 2031 0 2 TGCCAGTAGTTTTGGGTCAAGCCCTCACCTGATTCCACGCTTCATAGCTTCAGCCGTTCCCATCATACTACTAGCT aaab\]\\a\____aaT_HL\ba`XFNa_\]PU_aaHGWFS\`TSL\aYW_GZ^GXFO^`VFP`MXU]RNFSQRTL 0
-SL-XBA 1 4 2 1793 1812 0 2 TCCAGCATGAAGATAATGGCTAATACCAAAGCAGCCTTTTTGCTGTGGTAGGAAGATAATGGCTAATAAAAATGAG abbbbaX`_JJ_S^VJ^bab`_H\HFFNQHW_H\^GZ^^``\E\a_aaOQ[XMHRHMDOLQ[TENJIPDGYFIKDX 0
-SL-XBA 1 4 2 1793 475 0 2 AACTTTTTTACGCAATGTTAATATTCAACTCTTCCTTCCAATAGAAATTTTCTGCTGCTTTTCTTGCTCGTGCTAG abaVVSRRH_PH_IY]`XJ]SOP]_^YI_U\GUbWINQ_[GQ`WDHU^ZXV_XJXZ[FRNSHLPTYRSJHFWFQLL 0
-SL-XBA 1 4 2 1793 1329 0 2 GAGCCCCGCGTCTGTCTCAGAGAACTTTTGCATTCTTCTTGTTCTCCAGGAGAAACGGCATCATCTTCCATGTCTT `_\Iab_LJYUaWFU_ab_b]KZQHTaaaaa]Zabaab_U__a``bba]aZWHOVI[_\FYb][[X`_GUW_\aTX 0
-SL-XBA 1 4 2 1793 404 0 2 ACATGAATCCTCTCCCACAGGAATTATTCAGCTTACCGCGAGTACGCTTCCGTGTTGGAAAGATTCAACTCACCCC ZFVaUQYQG\NW[]`_X`\WW]U[\\YS^DT`W\Z]_IVRKMDU^[FDDTZJHDDLQFPHEDTGLXRVEOHDDO\a 0
-SL-XBA 1 4 2 1793 1455 0 2 GGAAACCAACCCCTCACATGGTAACCCGCTCCAACCCGCACGCCCTGTTCGGCCCCTGACCCGGCCCCCCGGCGCA ]NKJF[YFFFKTFRGTXFJMVOTKNW_XSGKJFT_ZFDVDDZR]WUMIDOSEFDPVGEMTDDJDK]OUQSIDKIYD 0
-SL-XBA 1 4 2 1793 1793 0 2 GTTTATAACTTCTTCTGTGGGATCAGCGGGCACGCCTCTTCCCACCAGCACACTACACGTCTACCAGCGCGGATGG a^`]MXOHG[_ba^b_aWa`]^\^I[EY_^\DZ`aaYEWTE\J]`\DVEJFM_REXEK\QEWPOUQUaVF[TDL]Y 0
-SL-XBA 1 4 2 1793 310 0 2 CGAAACTTGGGTCAGTAAACTGGTGAAGCTGACCTATTTGGCAAGCAGCATGATTCGGAAGCGCGGCAGGCAGAGT ^GT_aaI]TV_Ua_IRSH^\Ua_GHFPWDF^\_`IY_^S_JGS]`ZW[FN_\RUU`_ZNV_GLFGHVGPGWGQFFF 0
-SL-XBA 1 4 2 1793 1969 0 2 GAGAACTCTCTGTGTAGTTGTGACTTCCATCCTTCCGCAACAGTAGTAAGGACCGCGACTTCTGACCACATTGACC YD\\\GK\a]\YLZV[aN^_W_\YW\\]FMK\WU_a_`KKJOVLGXFRT]^TWNN^ZLFJMWGTOFUPXGFFFJNX 0
-SL-XBA 1 4 2 1794 490 0 2 ATAAACTTGAAAATAATTTTCTATGATACAGCTTTCAGGTAGAAAAATGAATTTTCGTCGTGTTTAACAATGTTGT `aabab``b_ZT__VVaaa^bbaaa^_abaab`a__R[`U]]HXX^O[a_U^]__aaU`X]aT`[_U[DJ]_[[YO 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_2_0003_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_2_0003_qseq.txt
deleted file mode 100644
index 6c90804..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_4_2_0003_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 4 3 1793 1282 0 2 AAGCACACCAAGCTTCCCGCAGCTGCGGCGCCCCCGCTCCAAGGCCAGCAGCTGCCCCCTCTGCCCCCACCCCCTC GITVXMPGMNN]a_LPVJ\MMN_X\I\GMGMZ[MPF]Z[YFFFV\ZFMFY\\YTTPXRWIVMVZYDVYFFZ_ZUOX 0
-SL-XBA 1 4 3 1793 1301 0 2 GCATTGCGTCCATCTCTTTACAGAAGAACTCAGCCCACACCCTAGAATGTACACCTTTGGAAAAAGGAGAAGTGCT \GUZXI``ZIababbb`aa_ba_H^^_]_aaabbb`U_W^bb]X_]\^_LQHX`aZU]]ZTRRS\R\VJULPS^\L 0
-SL-XBA 1 4 3 1793 1311 0 2 CAGCAAAAGTGCCGGCTAGTCCGGTTTGTTGAAAATACAGTAGAAAAGCTGATTCTGGTTATCTCTCTCAGGACAA a[`aa`S\`P^bbaaIaX^Y]F]_H^`_[``VSZ`_^a\]HFUFUP[TWGYNVT`^VGO\\\_\_SIVDRTTN]SO 0
-SL-XBA 1 4 3 1793 1326 0 2 CAAGATCATACTAACACACTCCAGCCTGGGCAACAGAGTGGGACTCTGTATCCAAAAAAAATTCTCTACCAACTAC a`aa\\a`^_ba^^aabbbbaaL_`bOa[Kbbbb`_S[_`ZZ`bJbab`Kab`P\`Y\X[\`Kb^J[^a^R[aK^b 0
-SL-XBA 1 4 3 1793 1389 0 2 ACCACAGGCACCACCAGCCACGGACCCACGCCTGCCACTCCCCACCCCCCCCCCCCCAGCCACGCCACCGTCCCAC V_]I_OYR_Q__Vaa\`aaRa\TDZa]G]ODYZ[`\O_\WFZEGY^`]Q]VD[ZDY`ZR_]JMIDDMJ[ONYH]LH 0
-SL-XBA 1 4 3 1793 1405 0 2 GCCTTGTTTGGCCCTGATCTCTGACTTCTAGAGCCCCAGCTGCTGGCGGCTGCTGGGATATCCTCCCCGCTCGGGT _aaaaa`__Xaaaa`PP\aaaaa`aaaaaX\XaaaaaX`a`aa_I\a__VPXMQ\RRDWQQ_]FFY`TDPJDVVDG 0
-SL-XBA 1 4 3 1793 1507 0 2 CAGAGCGCGTTGGCGTGAGTGACAGAGCGGCCAGTGGCCGCCGCCCACCCGCCCACGCCCCCGAGGGCCCCCCTGC _PPJP^S]SSRSS\TRRKQTQMZPPKL]SMEVMIIKLTJJMKGMVIEKPIDDDMIGDMMMKIDIJKDDJPGEJDKM 0
-SL-XBA 1 4 3 1793 1557 0 2 CGGCTTTTTTTTTATTGAGACCAGCTCCTGCCCTACCCCCGCGGCTGCGGAGCAAGGTCCCCTTCATGCGCCCCCC TEONGVIR]XU\XH[IJDFJTKNDFEVDVJUVTDFDDJOXIGIFQGTDDKEGMEKDDGKUDGEFVEJEKELKJTTS 0
-SL-XBA 1 4 3 1793 1570 0 2 CAGACACCTTTCATATCTTTATGGCAACTTAATTTTTGGCCTTTTATCACTCTGTCATACCAGCATTCTGCCGTCA `_]Za_baTSXFRS\XaZ^]N`_^W__Z\[GXNTJJ[VSaZa[DMMZbLGMW^_G]FX_]][U]GSZ[DIMGMI\Y 0
-SL-XBA 1 4 3 1793 1709 0 2 AGCCACTGTCCCGTGTATAACTTGGCATTAGAGCACCAGGTCTGTTGGATGGTGGTGGCAGGCCCAATTAATTTTT K^_HV_a_UabbbZb^_`ZJ_`Zaaa\Za`_U_aUa_G]aWb``U[a^UXa^Ga\LY_]LV_WTYDMHHREVRLDH 0
-SL-XBA 1 4 3 1793 1738 0 2 TCCCTGACTGGATACAGGCAGCTGACCCCTTCTCCCGACACCTCAAGGAGTAACTGGGCTGTTGGTGACCCCCGAC `aaaa`_aaa`[aVa_`aa`aZGYFZaa`\`_O__IXO_H_a[G]H]]G]GJZ_X_YDZI[GTS_JMDR_G]TGDF 0
-SL-XBA 1 4 3 1793 1779 0 2 CACTGAAATGTTTAGGACCATATTATAAGTAAGTACTTATCAATGTACTTTAGGACCATATTATAAGTAAGTGCTT \Y`a]G]US`\ZQV`_\a_H\US__YTH_X[H\Yaaa_Y\F^FXaIab]HUVa_`b_Z\X]HO_IW^YSOY[ab\[ 0
-SL-XBA 1 4 3 1793 1859 0 2 CGATTTTTAAGGACCCCGTGCCTCTGGGGGCCGATGAACTCCACGATGGGACGCACCTGGAGCTCTACCATCAATA aaTT`X^_]MGV```a^RK`]`\`]`U_^]QXGSRSGMFOa^QY^QUU[QNKXPYaXMPHOUSTPNNEEVW`POKQ 0
-SL-XBA 1 4 3 1793 1898 0 2 CCGGCCAAGCAGGCATGTGTGAATGAACGTGGCCGCTGACTCAGAACAGAGGACATCCCAGGGCCGCAAGCGCGGA aa]`aaR\Z]ETGPDQ\S\TTQLFKRV`\KSP]PGPFKJMRVFPKEXNRRPGNXNFUMJFFOKGDKQEGMPKNNMG 0
-SL-XBA 1 4 3 1793 1143 0 2 CTGCAGAGCAGTTGTGGCACTGGGCTTTGGCCACTCAAACTCAGGCTGGTCCGGAACCTCCCCCACCCCGCCCCAC `\\aTX]]`_WNV\KPXYJYFRSS`MMRUU^`X\S]PUW^PYPPRZSQKDVYRLEPVVETX\ZWEK\QDGWJVDDQ 0
-SL-XBA 1 4 3 1793 141 0 2 CTCTCCCGCGCCTGCTACGGAGCCCGCTCGGGGGGGCCACGCCGCTCCCGAGGACGTAGCACCTCCTCCACTCACG SYLIUXTIYEVGMRRR^XIFG_GUMGGDDKZUQJIMMGMNOG]RNEDPSGKPGGOLUEPTDDMU]GEFDJQOEJRG 0
-SL-XBA 1 4 3 1793 1617 0 2 GTGGTCATAACTGTTTCTGGACCCATTTGAACTTCATCTGAATATAGAAATCTCAGCAGCGCCCGGACGGCTGCGG `[ba`aS]\K_aa_a`b_a\I`_IJ]`aaXSaa_aZ]a^Z]__T`Za\OSUb__GU`XZ`Q`[FXOFGYL^DRYNY 0
-SL-XBA 1 4 3 1793 1031 0 2 CCCATACCAGCACAGAGCATACAGAAACACAGAAAAAATATTCCCAGTAAAACATGTGCAACTGTCCAGGCAGTCG JT``_XQJ]S``aa`U_ZFGLZ[\QQHaW___V]`_[TWRSXW_UQLSTYLW]WZYOOWPIXTULZVMHIDMSHHO 0
-SL-XBA 1 4 3 1793 1793 0 2 GCTCAAATTTGTGCTACCAATGATATCGAGTTTATAGCAAATTTTCTACGGGAAGTCTATGCGGCAATTTTCTCAT ab`\WJR^b\`LW`_Y`ba^K_ZWZ_J_I_ZbRKWHWb^JX\ZQI\J\FQ`^WXWIJODGHHPWHSQY^`Va]^FY 0
-SL-XBA 1 4 3 1793 456 0 2 TCCATCCACTTCCCTGAGCCTCAGAAAAGGGCAAGGCATGGCTCACATACTCTCAGCCACGGCCTGGCCTGCTGCC aaa[`aa_aaaaaa\__`aa^aT_VVV\ZZ`a`X`Za^\][aa_U_``^a]aX]I]``X`TR^]GDWXGMX]Z[YG 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_5_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_5_1_0001_qseq.txt
deleted file mode 100644
index 7350cae..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_5_1_0001_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBB 2 5 1 0 357 0 1 GACTTTGGGAAGGGTCATTACTGCCCTTGTAGAAAGAACACCTCATGTTCCTTATCGAGAGCGGCCGCTGCTGATC W[`bbbb_baS\`_\bbabbaWR`bba``ab_bbbbbabbbaabb^^^\aa_ab`a_`[`VaST[^SWTXWNYEHM 1
-SL-XBB 2 5 1 0 300 0 1 CGGGTTGGGGCTCTGGAAGCGGATGTGTACGGGTGGAGTGTTAGTTACATTCTGGCCCGAGTGACTTTTGGTATCA [GI\LTNG[_KOIOWGGYOKOH^HYGTNRGU[HRGTPG[YHNGF[RV[PFNJFFFDKQMFKFQQMVLDMDDDGDDK 0
-SL-XBB 2 5 1 0 872 0 1 TTTTAAATTGAGACGCATGAAGGCTAAGCGGCCGCGGAAAGACACAGGGAGGTTTACTTATTTTATTAATCAGACT abbbb`aab`\W`aaaba^Z_WX]Z`_]a`[`^_[^`R[YXZZ]]^XXYXXWMXUTTZXSV\^[TTWUSQLMKHMD 1
-SL-XBB 2 5 1 0 458 0 1 CGCGTTGCGGCCGCTGAATCCAAATCCAATAGACTCACTTTTTATTTTTATTTTTAAAATTAAAGGTTGATCTCTC ZS`b^ab[Z^__L\a[`[``a^aZX_O\\TZJ]UXaZF[``_YP^a`[\Z]`a``NV[X_aYYSPRLXFOQX_UDI 1
-SL-XBB 2 5 1 0 1934 0 1 CGTCAGCGGGCGGAAGCGGGAGGGCGAACTGGAAAGCATGAACGGAGTGGCGGACTTACTGAGATAAGTGAGAGAG IIIIX_XHZG[IWG[`_R]GZ`JRJV^Z[GMP_TNN_[_HTX\QPFZ\PTGG]RUMGSRVFFGTZGPIDSTTFSKD 0
-SL-XBB 2 5 1 0 1688 0 1 AGAAGGAGGACGACCTCGAAGCCATGAACGCAGAGGAGGACTCACTGAGGAACGGGGGAGAGGAGGAGTACGAAGC I]_`_]TV[``]ZZa``b]TG_aaaa```XXZXG]aaaa^^a[^]`[Wa_^`[[[___XaTaXK]RRXFKPSUPNI 0
-SL-XBB 2 5 1 0 1366 0 1 AGTCATCTTCTTCTTTTTGGGGCCGCGTCTCTTGGGCTTTTGATCGTCATCCTCCTCTTCCTCTTCTTCCTCCTCT \bbbababbbbbbbbbb``abYb`ba\aa___aSWa`bbba\^b``^abba^_aba_abbabaa`]\^SWK_`RMD 1
-SL-XBB 2 5 1 0 287 0 1 AGGAGATTTATTACCTATTTAAAAAATGCATTTGTAATTGTAAAATGAAAAATCACTTGCAAACAGTCTGCGCGTC Z[a`aa^^`b`_aab_bbbabbbb_aaaabbbbbaab^ab^bbbbbbbaabbbbbaa^aa`aa_a^NSRSYSaYH^ 1
-SL-XBB 2 5 1 0 538 0 1 AATTGGGCAAGAAAATAAAGTCGTTGTGGGCGGCTGGGGAACCTGGCGTCAGTCCCCCGTGGCTGTTCGCCGGCAC TGZ]Z]XGI]\\aX^a`_a`]V]_a[[^^`PVZ^a_`_Z^```X\X_`ZYVUVVZa\XUQRTU]VIGMKJJDPKDI 0
-SL-XBB 2 5 1 0 1484 0 1 CAAAACAACTCAGTTTGTTCCAAAACAATGTGAGTTCCCAGATTTAGCCTTGTCTTAATATATTGACCTTAGTTCC a``aUI]^_Q_aaaabV\b`[`abb_Saa`ab]babb_Y`_aa]aa`^aabbXWa\`aaabaaa\ZYJQ\VY^SNJ 0
-SL-XBB 2 5 1 0 650 0 1 CATGCAACATCTCCACAGCCAGCCTCCTGATCCACTGACCCAGGGACCCCTAAAGCTGGAGGCCCCAGACTCTCTC a__a```a`aaaaa__aaaa``a`^`a`_```^^]\\^_VW]VXV\S\\\TXXTJMPUQQQSSRQRMJMPFRKDGD 1
-SL-XBB 2 5 1 0 932 0 1 TGAGGAGAAACATTCTTTTTGTAGGGGGTGCTAACTATGGCCTATGCAAAATTCTGAATTTTACCACCGTCTAAGC \GH]PSQ[I_\YHaabaaaWGZSSU`]NOXLMGS]aYFPRFV[\[FTP_Y^[NMZXNPLYYQNXSPSOKOMLTQNY 0
-SL-XBB 2 5 1 0 431 0 1 CCGATGAAAGCAACAAGGTAGGGTTAACTCATCTATGAATAAGCCTGACATGTGAGGAATCACAAGCAAATTGCAC ^NQLW\H\GLFFFZ\Q_\JGVY\Q_aK`^a_aa`XT]DF[[\QDIVZNTTZ]VXOYNSZXSPDLPFGPHNUMOJGS 0
-SL-XBB 2 5 1 0 978 0 1 AACCGGTGCATTATGCGGACCGGGAGGGCTTTCGAAACACCTGGGTGGTGCTGAACCCGGGAGTGGCGTCTCCCTC GGGI]_THV_GIW_]QTIGZZTGWZTOZ\`_NGGGGHZTZGGGMZ[HZRXU_IOKO_GQR\OVOYDLDPGTGJVFE 0
-SL-XBB 2 5 1 0 122 0 1 GCCCGCGCGTCCCTTGCCGCCGTGGGCAGGGACGGGGGGGAGGCAAGACCCCACCGATGCTCGTCATACGACCAGG L`aa\\J\\^X[_I]X_TI]TGFMZVIH`VIHXEG_aZTRXLH_PUFFFMMWNFPFFH^QNLPEUKKDGINKKVKF 0
-SL-XBB 2 5 1 0 1549 0 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA _Z_]JRR]ZVR[^^`X^aX^\\XPVGTPKTU]\TU\Y[S`\^V]NUFKMJJMUYQDQHFPKEMKMOKGIIFOJMOJ 1
-SL-XBB 2 5 1 0 1783 0 1 CACACCTCTCTCGTTTTGGGGCAAAACGGCTCAGCCATTGGAATATGGCACACTCGTCTGGCACAAGAAGGACATC a`_[W__\W[T_ZPZ_H_W_V`bJ`ba_aa[a_YROOW[]YGUI_T]RKGG^O]WGZSK[_ZGZZKNXRPRVZGUW 1
-SL-XBB 2 5 1 0 254 0 1 CCGCAAACAGCATACTTTGGTACTCTTGAAGTTTCAGGGCATACTTGTAATCTGCAACCACTGGATCTGTTCTTGT a`[_`Zaa]J_R_a\abbaaXbbaaa\VW_aQaT[Z[_GTa^_P^]aY^ababa``\aMaa]`[^XWWSOOX]MDD 1
-SL-XBB 2 5 1 0 1660 0 1 AACACTCATGGACATTATTCCTAATAATGGTTCTTATGGCAAAGTGAAAAAATAATCATCCAAGTACCTGTATCGC R^aa__bb```baaabbbb_bbaaabba`a^a^abb`^ababaaV`^`bbba^aba`aabaabb_`][V^V`aFF\ 1
-SL-XBB 2 5 1 0 1250 0 1 CACACACACACACACACACACACCACCTTTTGGCTTATCTGCACGCGGCCGCGTGCCCTACCCTACCCCATGGGAT a_aa^\Ra\`aaXa_aa_aaaaaaa[^X^``V[`_`a^aaO``^_SJUELTVMKVTPFOKJJMNKTRRJEEPFKTR 1
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_6_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_6_1_0001_qseq.txt
deleted file mode 100644
index e8b1743..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_6_1_0001_qseq.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-SL-XAT 843091117 6 1 4 1969 0 1 TAGAGATGGC.CT.........T......C........G...TCCAGACCGCCCATTCTCTGCCTGCC ^`^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAT 843091117 6 1 4 1934 0 1 AAACAAGAGC.TG.........A......T........T...CAAAAAAGCGGAGGGAGAGGCCAGGC ab`aaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAT 843091117 6 1 4 1152 0 1 AGCCTCTGGA.TT........GG......C........C...CACCATGGGAGAGACGTTCCTATTTT VM_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAT 843091117 6 1 4 1201 0 1 CCCAATCCTT.TA........CG......T........A...TTAGAAGCCTTCTTTTTTTTTTTTTT IH]MBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAT 843091117 6 1 4 1248 0 1 TAAACAGATG.TT........CA......T........A...CCAATCCCTAATCTCCAGTAATCCGG ^bb`_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAT 843091117 6 1 4 893 0 1 GATGTGTATA.AC........GT......A........C...CCCGTGTGCATACACGTGTGCATACA _N`__BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAT 843091117 6 1 4 1912 0 1 ACCTTACCCC.AA........TC......A........G...CAACTCAGCCTTCACTGCATTAAGGC aabbBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAT 843091117 6 1 4 1236 0 1 GCTTACCCCA.TG........TC......G........G...ATTCGTGGCCTTTGGCACGCACCCAG X_aa^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAT 843091117 6 1 4 473 0 1 ATTTTATGTG.GG........AA......T........T...ACCCAGCGAAACCAACAGGTTGGATA J]BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAT 843091117 6 1 4 151 0 1 CAACTCTTGT.GT........GT......A........G...AATATATTCTGAAACTCAGCAATGTT aaabaaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_6_2_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_6_2_0001_qseq.txt
deleted file mode 100644
index f750408..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_6_2_0001_qseq.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-SL-XAT 843091117 6 1 4 1969 0 2 CCACCCAC _ZFZ^]BB 0
-SL-XAT 843091117 6 1 4 1934 0 2 AGTTGCTT a^_`\b__ 0
-SL-XAT 843091117 6 1 4 1152 0 2 GCACCCGA S_V_P]_B 0
-SL-XAT 843091117 6 1 4 1201 0 2 TACTAAGC QK`BBBBB 0
-SL-XAT 843091117 6 1 4 1248 0 2 GCACCCGA T_X_J_BB 0
-SL-XAT 843091117 6 1 4 893 0 2 CACCTCCT aXaLK_`B 0
-SL-XAT 843091117 6 1 4 1912 0 2 GCACCCGA ZZP_O_XW 0
-SL-XAT 843091117 6 1 4 1236 0 2 CCCTTCAC GI]I]JZ_ 0
-SL-XAT 843091117 6 1 4 473 0 2 CCAGTTAG aZDVUZZB 0
-SL-XAT 843091117 6 1 4 151 0 2 TCGGAATG abY`bb_^ 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_6_3_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_6_3_0001_qseq.txt
deleted file mode 100644
index c542df0..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_6_3_0001_qseq.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-SL-XAT 843091117 6 1 4 1969 0 3 CCTCTAATCCCAGCACTATCCGAGACCAAATCAGGCAAATCACTTGAAGTCAGGAGTTCGAGACCAGC ]]VISQK_M\`MHX\ZFMaPWHXYUa]ZHJGaULGPXTRS\W[`ZH_GMUa_[]M]PTUZX]VaZaU\ 0
-SL-XAT 843091117 6 1 4 1934 0 3 GATTTCACCATGTTGGCCAGGCTGGTCTCAAACTCCTAGCCTCAAGTGATCCGCTCACCTCGGCCTCC ]bbabbbbbbbbbaS`baaTR\babUbZ]JVbbbb]abaabbbb[b]J^bab`baab__bbb`bbbba 0
-SL-XAT 843091117 6 1 4 1152 0 3 CGGTGCTTTTCCTTCATGGCCAACAATCAGAACTTCTCTCCCATGTTGCACAGCAAGGGTGCCACGCC TTbJ^^TaRGZb_`b]`U`b[T`abZMI]Z`ZTIQQ]ZDZ`VQXQTY^bZS_TYX_babZ^GVIS[ab 0
-SL-XAT 843091117 6 1 4 1201 0 3 AGTCCCACCTACTTGGGAGGCTGAGGCCGGAAACTCACTTGAACCGGGGAGGTGGAGGTTGACCGGAG _[Sa_ZJZ_TJ_I\``SPSKa[[XSSYGZJDDXO[\\QZRH]BBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAT 843091117 6 1 4 1248 0 3 AATATTCTTTTAAGGTCTCTGGTTTTCCTAGGCAGAGGACCCTGCGGCCTTCCGCAGTGTTTGTGTCC IUQ[WP_aaa]Wbb[ab`bUZ_abbIbbb[b[_\_abbaabaaabQ_abUN_bbb`b`b^`_LMYU`b 0
-SL-XAT 843091117 6 1 4 893 0 3 TATACCCGTGTATGCACATATATGTAGATGTGTCCACACGTGTATGCCCACGTGTATGCACACGTGTA `aa``I_]]ZWMaab`ba^K``baaMWK_]__UUa`baba_aTbUba`bVabR`SbK`a]`_bV[\Za 0
-SL-XAT 843091117 6 1 4 1912 0 3 ACCCACCTGTTTAACAAAGCACATCTTGCACTCCCCTTAATCCATTTAACCCTGCGTTGACACAGCAC VGVUGLaMWaaU^H_HXSN_YbaU[HNDWH_\H_ba`R`bbbb_\a\SK\bab]M\U]^Naaa[abba 0
-SL-XAT 843091117 6 1 4 1236 0 3 AGCAACGGAATTCACATTGTCTTCTCTTCCATCTTTTAGAAAAGCTCCAGAGGAGAACAAGAAAATCG [`a_JQH_LGF^]T_SZaa[bVa\_aa[\KV`_F`aa]N\`_XTa^b\_NSa[aI_UYWYabXSaH`B 0
-SL-XAT 843091117 6 1 4 473 0 3 CTGAATTAGAATATTGGGTTTGCTACTTGTTTGCTGGGTGACTTTAGGCAAGTTGCTTAACCTTGCTG ``U_HFV^``Z`b`W`YYZ_\Y_^aa_JbQaYT_]_T[GbbbVWNaXP`aaaS^RJ[]b_\MMU\]Z_ 0
-SL-XAT 843091117 6 1 4 151 0 3 TAACTTTCAGAGGCCCTTCAGGAGGCCCTGGCCTGTCAAGTACCTTTACAGTGATGGGTATAGACTTT abbbabba_bbabb_]S]ab_ab__^abSORYX^RF[aa`_a_[XVa`[WUN`a^__a\ZL\BBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_0001_barcode.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_0001_barcode.txt
deleted file mode 100644
index e5ada71..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_0001_barcode.txt
+++ /dev/null
@@ -1,200 +0,0 @@
-........ N
-........ N
-........ N
-........ N
-........ N
-........ N
-.....G.. N
-.....C.. N
-.....C.. N
-.....A.. N
-.....G.. N
-.....GT. N
-.....CG. N
-.....TA. N
-.....GT. N
-.....CC. N
-.....AT. N
-.....GA. N
-.....TG. N
-.....GT. N
-.....CC. N
-.....GT. N
-.....CT. N
-.....AC. N
-.....CT. N
-.....GA. N
-........ N
-.....CA. N
-.....TG. N
-.....AC. N
-.....GA. N
-.....AC. N
-.....CG. N
-.....TG. N
-.....CA. N
-.....CA. N
-.....TT. N
-.....AC. N
-.....GT. N
-.....CG. N
-.....GA. N
-.....CA. N
-.....CG. N
-.....CG. N
-.....AG. N
-.....GA. N
-.....TA. N
-.....TG. N
-.....GA. N
-.....CT. N
-.....TA. N
-.....CC. N
-.....AG. N
-.....AG. N
-.....GA. N
-.....GA. N
-.....GT. N
-.....CA. N
-.....CG. N
-.....GA. N
-.....CT. N
-.....AG. N
-.....CT. N
-.....CC. N
-.....CG. N
-.....AG. N
-.....CG. N
-.....GA. N
-.....TC. N
-.....CG. N
-.....CC. N
-.....AC. N
-.....CG. N
-.....CC. N
-.....CGA N
-...T.GAC N
-...C.GAT N
-...G.TAG N
-...G.TTA N
-...G.TTA N
-...C.AGA N
-...T.TAA N
-...C.CGA N
-...T.GAC N
-...G.GCC N
-...C.AGA N
-...C.GAT N
-...T.CTT N
-...T.GAC N
-...G.TGT N
-...T.AGC N
-...A.TTC N
-...T.GAC N
-...A.CCT N
-...A.GTT N
-...T.CTT N
-...T.GAC N
-...A.CTG N
-...GATGT N
-...CCAGG N
-...GATGA N
-...TCGAC N
-...TAACA N
-...GAGCC N
-..ACCAGG N
-..TATGTT N
-..ACATCT N
-..CATTTC N
-..TGGCGA N
-..ACCAGG N
-..GGAGCC N
-..CTTAGC N
-..TGCTTA N
-..CTAAGC N
-..CAACTG N
-.TCGCTGA Y TTCGCTGA
-.AGGATGT Y AAGGATGT
-CAGGAGCC Y CAGGAGCC
-AGCAATTC Y AGCAATTC
-CATAGCGA Y CATAGCGA
-AAGGATGT Y AAGGATGT
-CATAGCGA Y CATAGCGA
-TGCTCGAC Y TGCTCGAC
-TACTTAGC Y TACTTAGC
-TTCGCTGA Y TTCGCTGA
-TACTTAGC Y TACTTAGC
-CAGGAGCC Y CAGGAGCC
-CACATCCT Y CACATCCT
-AGCAATTC Y AGCAATTC
-TGTCGGAT Y TGTCGGAT
-AACTTGAC Y AACTTGAC
-CAGGAGCC Y CAGGAGCC
-CATAGCGA Y CATAGCGA
-CTACCAGG Y CTACCAGG
-CAGGAGCC Y CAGGAGCC
-GTATAACT Y GTATAACA
-GTATAAGA Y GTATAACA
-CCTACCAT Y CCTACCAT
-GTATAACA Y GTATAACA
-ACCAACTG Y ACCAACTG
-TCTGGCGA Y TCTGGCGA
-AGTTGCTT Y AGTTGCTT
-GCACATCT Y GCACATCT
-CACATCCT Y CACATCCT
-AAGGATGT Y AAGGATGT
-CATAGCGA Y CATAGCGA
-GCACACGA Y GCACACGA
-ATTATGTT Y ATTATGTT
-AATCATGT N
-AAGGATGT Y AAGGATGT
-AGTTGCTT Y AGTTGCTT
-GCACACGA Y GCACACGA
-TTGAGCCT Y TTGAGCCT
-CCAACAGG N
-TGCTCGAC Y TGCTCGAC
-CTACAAGG Y CTACCAGG
-AACTTGAC Y AACTTGAC
-TACTTAGC Y TACTTAGC
-CCAGTTAG Y CCAGTTAG
-TCTGGCGA Y TCTGGCGA
-AAGGATGT Y AAGGATGT
-GTATAACA Y GTATAACA
-TGCTCGAC Y TGCTCGAC
-CTACCAGG Y CTACCAGG
-CAGGAGCC Y CAGGAGCC
-AACTTGAC Y AACTTGAC
-CACATCCT Y CACATCCT
-ACTACCTT N
-AACTTGAC Y AACTTGAC
-AACTTGAC Y AACTTGAC
-AACTTGAC Y AACTTGAC
-GTCACCAT N
-ACACAAGA N
-GCACACGA Y GCACACGA
-ACCAACTG Y ACCAACTG
-TCACAATG N
-ATTATGTT Y ATTATGTT
-AGATGCTT Y AGTTGCTT
-GATCCAGA Y GGTCCAGA
-GTATAACA Y GTATAACA
-GCACACGA Y GCACACGA
-CTCCCAGG Y CTACCAGG
-AAGGATGT Y AAGGATGT
-CCAGTTAG Y CCAGTTAG
-GTATAACA Y GTATAACA
-GGTCCAGA Y GGTCCAGA
-ACATCCTA N
-CATGCTTA Y CATGCTTA
-CCAGTTAG Y CCAGTTAG
-TCGGAATG Y TCGGAATG
-ACCAACTG Y ACCAACTG
-CATAGCGA Y CATAGCGA
-GTATAACA Y GTATAACA
-TGCCCAAA N
-GGTCCAGA Y GGTCCAGA
-TCGGAATG Y TCGGAATG
-AACTTGAC Y AACTTGAC
-CTACCAGG Y CTACCAGG
-TTCGCTGA Y TTCGCTGA
-TCGGAATG Y TCGGAATG
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_0002_barcode.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_0002_barcode.txt
deleted file mode 100644
index 9848a58..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_0002_barcode.txt
+++ /dev/null
@@ -1,200 +0,0 @@
-.....CG. N
-.....CA. N
-.....CG. N
-.....AG. N
-.....GA. N
-.....TG. N
-.....TA. N
-.....CC. N
-.....GA. N
-.....AG. N
-.....CC. N
-.....AG. N
-.....TA. N
-.....GG. N
-.....TA. N
-.....AG. N
-.....CG. N
-.....CT. N
-.....CC. N
-.....CA. N
-.....TT. N
-.....TA. N
-.....CA. N
-.....GT. N
-...A.... N
-...T.AGC N
-...G.TGT N
-...C.CGC N
-...C.AGG N
-...G.TAG N
-...A.GTT N
-...A.CAT N
-...C.TCT N
-...G.TTA N
-...A.CCT N
-...C.GAT N
-...A.CTG N
-...C.CGA N
-...C.AGG N
-...T.GAC N
-...A.CCT N
-...A.CGA N
-...A.GTT N
-...T.GAC N
-...G.TAG N
-...T.AGC N
-...A.CTG N
-...C.TCT N
-...C.AGG N
-...A.TTC N
-...C.AGG N
-...A.CTG N
-...G.TGT N
-...G.GCC N
-...T.AGC N
-...C.TAT N
-...C.CGA N
-...A.CTG N
-...G.GCC N
-...A.GTT N
-...T.GAC N
-...G.CGA N
-...G.ATG N
-...T.ACA N
-...A.CGA N
-...AGCGA N
-...TTAGC N
-...TAACA N
-...AGCGA N
-...ATGTT N
-...AACTG N
-...GCTTA N
-...GCCGA N
-...CATGA N
-...AGCCT N
-..ACATCT N
-..AAACGA N
-..CAATTC N
-..CAACTG N
-..ACAACA N
-..AGATCC N
-..TGCTTA N
-..CTCGAC N
-..GGATGT N
-..TATGTT N
-..GAGCCT N
-C.TAGCGA Y CATAGCGA
-ATCAACCC N
-TATATCGA N
-TCGGAATG Y TCGGAATG
-TACTTAGC Y TACTTAGC
-TGATAGAA N
-TTGAGCCT Y TTGAGCCT
-CCAGTTAG Y CCAGTTAG
-........ N
-GTATAACA Y GTATAACA
-AAGGATGT Y AAGGATGT
-TACTTAGC Y TACTTAGC
-AGCAATTC Y AGCAATTC
-TGCTCGAC Y TGCTCGAC
-CCAGTTAG Y CCAGTTAG
-ACCAACTG Y ACCAACTG
-TTCGCTGA Y TTCGCTGA
-CACAATCC N
-ACCAACTG Y ACCAACTG
-GGTCCAGA Y GGTCCAGA
-TTCGCTGA Y TTCGCTGA
-TTGAGCCT Y TTGAGCCT
-CAGGAACC Y CAGGAGCC
-CCAATTAG Y CCAGTTAG
-AAGGATGT Y AAGGATGT
-GCACATCT Y GCACATCT
-CATGCTTA Y CATGCTTA
-AAGGATGT Y AAGGATGT
-CACATCCT Y CACATCCT
-ACCAACTG Y ACCAACTG
-CATAGCGA Y CATAGCGA
-AGCAATCT N
-CACATCCT Y CACATCCT
-CAGGAGCC Y CAGGAGCC
-AACTTGAC Y AACTTGAC
-GCACACGA Y GCACACGA
-ATCAATTA N
-GTATAACA Y GTATAACA
-ACCAACTG Y ACCAACTG
-AAGGATGT Y AAGGATGT
-CCAGTTAG Y CCAGTTAG
-GGTCCAGA Y GGTCCAGA
-AAGGATGT Y AAGGATGT
-GCACACGA Y GCACACGA
-ACCAACTG Y ACCAACTG
-TCTGGCGA Y TCTGGCGA
-AGCAATTC Y AGCAATTC
-TAACAAGA N
-ATTATGTT Y ATTATGTT
-GCACACGA Y GCACACGA
-GCACATCT Y GCACATCT
-TTGAGCCT Y TTGAGCCT
-AACTTGAC Y AACTTGAC
-GCACACGA Y GCACACGA
-CCAGTTAG Y CCAGTTAG
-TAGAACCT N
-CCAGTTAG Y CCAGTTAG
-GTATAACA Y GTATAACA
-GGTCCAGA Y GGTCCAGA
-CATGCTTA Y CATGCTTA
-AACTTGAC Y AACTTGAC
-TACTTAGC Y TACTTAGC
-CATAGCGA Y CATAGCGA
-GCACACGA Y GCACACGA
-CTACCAGG Y CTACCAGG
-TCTGGCGA Y TCTGGCGA
-AACTTGAC Y AACTTGAC
-TGCTCGAC Y TGCTCGAC
-AACTTGAC Y AACTTGAC
-AGCAATTC Y AGCAATTC
-CAGGAGCG Y CAGGAGCC
-TGTCGGAT Y TGTCGGAT
-CAAATCCT Y CACATCCT
-CATGCTTA Y CATGCTTA
-CCAGTTAG Y CCAGTTAG
-CCTACCAT Y CCTACCAT
-CATAGCGA Y CATAGCGA
-CAGGATCT N
-AAGGATGT Y AAGGATGT
-CACATCCT Y CACATCCT
-TTGAGCCT Y TTGAGCCT
-AGCAATTC Y AGCAATTC
-AGTTGCTT Y AGTTGCTT
-TTGAGCCT Y TTGAGCCT
-ACCAACTG Y ACCAACTG
-AACTTGAC Y AACTTGAC
-TACTTAGC Y TACTTAGC
-AGTTGCTT Y AGTTGCTT
-GGTCCAGA Y GGTCCAGA
-TGTCGGAT Y TGTCGGAT
-TCTCGCGA Y TCTGGCGA
-AGCAATTC Y AGCAATTC
-CATAGCGA Y CATAGCGA
-CACATCCT Y CACATCCT
-CATAGCGA Y CATAGCGA
-TGTCGGAT Y TGTCGGAT
-CACATCCT Y CACATCCT
-GTTTATTA N
-CAGGAGCC Y CAGGAGCC
-CATAGCGA Y CATAGCGA
-TCGGAATG Y TCGGAATG
-AGTTGCTT Y AGTTGCTT
-TCGGAATG Y TCGGAATG
-CATGCTTA Y CATGCTTA
-AGTTGCTT Y AGTTGCTT
-AGCAATTC Y AGCAATTC
-........ N
-TCGGAATG Y TCGGAATG
-TACTTAGC Y TACTTAGC
-CCAGTTAG Y CCAGTTAG
-AAGGATGT Y AAGGATGT
-AGTTGCTT Y AGTTGCTT
-GATCAAGA N
-CGGTAGCT N
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_1_0001_qseq.txt
deleted file mode 100644
index fa3b9ff..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_1_0001_qseq.txt
+++ /dev/null
@@ -1,200 +0,0 @@
-SL-XAQ 505091110 7 1 0 1434 0 1 .............................. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 464 0 1 .............................. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 113 0 1 ........G...........A......... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1703 0 1 ........A...........A......... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 879 0 1 ........T...........T......... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 841 0 1 ........C...........T......... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1291 0 1 ........A........A..T......... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1940 0 1 ........C........T..T......... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 586 0 1 ........C........C..C...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1690 0 1 ........A........G..C...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 37 0 1 ........A........C..T...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 324 0 1 ........T........T..A...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 205 0 1 ........A........A..T...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1307 0 1 ........C....A...T..T...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1193 0 1 ........T....T...T..T...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1475 0 1 .....G..A....A...A..A...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 275 0 1 .....A..CA...T...G.CC...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 2001 0 1 .....A..TG...G...A.GC...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1093 0 1 .....C..GT...A...G.AA...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1038 0 1 .....C..CA...C...C.CC...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 173 0 1 .....A..AT...T...C.TT...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1836 0 1 .....G..TA...G...T.CT...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1513 0 1 .....A..TT...A...A.AA...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1917 0 1 .....T..GA...C...A.AA...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1696 0 1 ..A..G..GC...G...A.AC...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 812 0 1 ..A..C.AAG...T...A.TC...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 2 0 1 ..A..G.GAA...C................ BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1555 0 1 ..T..G.AGA...A...C.TA...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1243 0 1 ..A..A.GGA...A...C.TA...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 30 0 1 ..A..A.TTT...T...G.TC...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 41 0 1 ..A..C.AAA...G...T.CA...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 59 0 1 ..A..G.TGC...T...T.AC...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 111 0 1 ..C..T.GCG...T...A.CT...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 132 0 1 ..A..G.GGG...G...G.GG...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 140 0 1 ..A..T.TAA...G...C.TT...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 155 0 1 ..G..C.AGT...C...A.TT...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 164 0 1 ..A..A.TAA...T...T.AT...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 170 0 1 ..T..C.CAC...G...G.TC...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 184 0 1 ..C..T.TAA...A...T.AT...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 195 0 1 ..A..G.GTG...G...C.AT...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 240 0 1 ..G..A.GTA...T...T.CC...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 262 0 1 ..C..G.CAT...A...C.TG...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 299 0 1 ..C..T.GCA...A...C.AA...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 353 0 1 ..A..T.TAG...A...T.AT...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 367 0 1 ..A..T.AGC...G...A.GT...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 416 0 1 ..A..C.AAT...G...G.AC...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 483 0 1 ..G..G.GGG...G...G.TT...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 486 0 1 ..A..A.TTT...A...A.AG...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 495 0 1 ..C..A.CGT...T...T.AA...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 508 0 1 ..G..C.CAG...T...C.CT...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 554 0 1 ..A..G.AGA...G...T.TC...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 567 0 1 ..C..C.GTT...C...G.AC...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 613 0 1 ..G..A.TAT...C...G.AT...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 622 0 1 ..T..C.AGT...C...A.CT...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 627 0 1 ..A..T.GAC...T...A.GC...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 684 0 1 ..T..T.AGA...C...A.AG...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 874 0 1 ..A..A.GCC...G...T.TA...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 931 0 1 ..T..G.GAT...G...C.TT...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 994 0 1 ..A..T.GAT...T...G.TT...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1013 0 1 ..C..T.CAG...C...A.GT...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1153 0 1 ..T..T.TGG...T...C.TC...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1184 0 1 ..A..G.TCG...A...T.CA...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1241 0 1 ..A..G.TGG...T...C.TG...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1282 0 1 ..A..A.GGG...T...G.AG...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1320 0 1 ..A..T.AGT...G...G.TA...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1391 0 1 ..G..T.TAA...A...T.AT...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1684 0 1 ..G..A.GGT...G...T.TC...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1733 0 1 ..A..G.GTC...T...T.AG...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1770 0 1 ..C..T.CTG...G...G.CA...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1906 0 1 ..T..C.ATA...C...T.CT...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1954 0 1 .AGA.T.CTT...G...G.AG...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1247 0 1 .CCAGC.TTT...T...T.CT...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 18 0 1 .ATCAG.CTG...A...T.GT..AA..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1521 0 1 .AACAA.ATT...T...A.TA..TA..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 264 0 1 .AACTG.AAT...C...A.CA..CT..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1815 0 1 .ATGAAAATA...T...TAAAT.AT..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1379 0 1 .AATATAATT...T...TTAGA.TT..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 2011 0 1 .ACAGCTGGCA..T...AGAGC.AG.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1372 0 1 .ACATTTTTTAG.T.A.TTGTT.AC.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 55 0 1 .TTTATGTCCTT.A.AACTTAG.AGTT... DNX[[WRTXXBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 517 0 1 .TCATAAAACATCA.TATTGGAAAGGA... DMVTY[XXXTVWBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 965 0 1 .ACTAATCTTCCGC.CATATCCCCAAA... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 535 0 1 .GCCCAAGTATTGA.TATGTGCTCTAA... DMTXXYVPWVYXSODOYYTQTXXBBBBBBB 0
-SL-XAQ 505091110 7 1 1 72 0 1 .ACACACATATCAC.CACATCATACAC... DMMSWUXUZTYUZMDHSXZZZXBBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1886 0 1 .ACATATGCATACATATATAATAGATA... DMXYZ[QPVZYXXXZ[ZZ[[[ZZBBBBBBB 1
-SL-XAQ 505091110 7 1 2 1932 0 1 .AGCGATCCTCCCGCCTCTGCCTCCCA... DKPTSTTSPSTTBBBBBBBBBBBBBBBBBB 1
-SL-XAQ 505091110 7 1 2 1706 0 1 .GATATGTGGATACAGCTCACAAAGAG... DKXXYUNTUUXXXNVBBBBBBBBBBBBBBB 1
-SL-XAQ 505091110 7 1 2 363 0 1 .ATATTCTTTTTTTTTATTTATCAGAT... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 605 0 1 .GCATTGAGCAGACGTGGCATCCAGAT... DHOWTQQQNTTSTRBBBBBBBBBBBBBBBB 1
-SL-XAQ 505091110 7 1 2 449 0 1 .ATTCTAATTCTAGGAAATTAACAATC... DMXRPT[XRUXVODOBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1782 0 1 .ACCAAGTGTTTGGAGTATGCTGCCTA... DOYYYUUWWWTLTRRTNWTBBBBBBBBBBB 1
-SL-XAQ 505091110 7 1 2 246 0 1 .GGAGGTTTCATTTAGCCGATATTGTG... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 307 0 1 .GGATGAACAGAAACTAAAATAACACA... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 150 0 1 .AAGACTTGATTATATCCCTTGTATGA... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 546 0 1 .GGTTGTGTCTCTCTCAGCCTTTGGGATC. DKSUWWWSSSUWTLRTBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1727 0 1 .TATTGAAGGACTTTTGTATCCTCCTTAT. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1946 0 1 .ATCTTCTGGAATTTCTAACAGCTTGGAA. DOTPTMKMRT[XXVBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1275 0 1 .AGTGAAATAAGCCAGACACAGAAAGACA. DNTQOSYXXXVPVVRKSSVTTLRXVPVBBB 1
-SL-XAQ 505091110 7 1 2 786 0 1 .TAAACAATAATCTGATGATTTATAATCC. DOX[[[[Z[Z[W[XZ[X[Z[YY[[YYBBBB 1
-SL-XAQ 505091110 7 1 2 747 0 1 .AACAACAGCGGAAAATAATAAAAAAAAA. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 25 0 1 .GCTTTGGCAAGACAAATCTCCCGTCTGG. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1722 0 1 .AAAGAAAATTAAAGAAAAATATACACGT. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1301 0 1 .AGTAGACTGCATTAATTAATTGGAAGAG. DORVOHOQSQURPSSYSWZZBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1592 0 1 .GAAAACTGGCACAAGACAAGGATGCCCTC DKUVVWUWUPKRSUUGWSWTWUWUSWTWRB 1
-SL-XAQ 505091110 7 1 2 943 0 1 .AATACCAATAAACCTAGAATGTCTCATAC DOW[XUSU[URVWVSSVVSYPOOTVXX[SB 1
-SL-XAQ 505091110 7 1 2 974 0 1 .GATCAATGATCACATCTTTGGATATGTAT DNXXVX[XXYXXXYYXZZYVTPP[[[VV[[ 1
-SL-XAQ 505091110 7 1 2 858 0 1 .AAACGTTGCTGATCTTCTGTTTTAAACTA DNZVLQQQQUTRUULUXVVORTYYYZUQUZ 1
-SL-XAQ 505091110 7 1 2 209 0 1 .GACTCAACTCCTGGGCTCCCTACGACCAT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 988 0 1 .AAAGGAATGTTCAGCTCTGTGAGTTGAAC DNXQNOSYQLQVWTLRWVTNSOSRUQLPUQ 1
-SL-XAQ 505091110 7 1 2 1453 0 1 .ATATCTTATTTTCTTTTCTTTCAGGCTCT DMYVKKRXTQTTBBBBBBBBBBBBBBBBBB 1
-SL-XAQ 505091110 7 1 2 69 0 1 .TCAGTCTGCTGTTTTAAAAAAATACTGTG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1158 0 1 .GGGTCCTTCATAGTTTTTTTCTACTTTCC DOVVVUSUZOXXYYYXTZZZUWWYYXXBBB 1
-SL-XAQ 505091110 7 1 2 1753 0 1 .GTTCACACAAGGATAATATTTTTGATTAT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1238 0 1 .TCCTTATATTCAATTATTAATATTTTTAC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1827 0 1 .AACCGAGGATGTACACTGTCCCTGTGAAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAQ 505091110 7 1 2 309 0 1 .AATGGCCATGCTGCCCAAAGTATTTTATA DMVOTUXXYTLQQVVTXXXUVPVYYYXYXY 1
-SL-XAQ 505091110 7 1 2 1889 0 1 .GAAATGTATCAAGGTTTGTATAATTGCTG DLV[[YYY[QYYYWYS[[YOVTSVVUTXVW 1
-SL-XAQ 505091110 7 1 2 1878 0 1 .AATACTGAGATGTATTTAAGGCTGACACT DMXYXTVNRVUVOVXYYYVYTNTVYYXXXX 1
-SL-XAQ 505091110 7 1 2 658 0 1 .GATGCTTCTGTCCTAAGAAGCTTGAGACA DDQURQWWVSPQPOVVTRTUOTTTTSQQTT 1
-SL-XAQ 505091110 7 1 2 119 0 1 .GATTGGAATCAACCCGAGTGGAATGGAAT DOUYVTTVVVWUVSQLULUUNNNQWWTPVB 1
-SL-XAQ 505091110 7 1 2 1417 0 1 .ATTCCATTCGATGATTCCATTCGAGTCCA DLYYTUVZXRLTPOVWWOPSYWTRWPQQBB 1
-SL-XAQ 505091110 7 1 2 1895 0 1 .AAAACTTCTAAGTAATCATGAAGCTCTGC DMVZXYYYYY[WSYXXXWXY[UVW[YUVVU 1
-SL-XAQ 505091110 7 1 2 52 0 1 .AAGTATAATGTAGAGACGCTTGTATTGTC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 85 0 1 .GATAAAGTACAATGCTAATCACTTAAGAT DMTQRTROSUWVSJFOPXXXXVTZYXQTTZ 0
-SL-XAQ 505091110 7 1 2 63 0 1 .GAGTGGAATGGAATGGAGTGGAATGGCTT DKNUUWPWUWQWPPTTRTRUTQTWVTUWUB 1
-SL-XAQ 505091110 7 1 2 737 0 1 .AAAACAATTAAAATAAATGCTTAAAATCA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 802 0 1 .AAGTTAATTGTGTATTATTAACATCATTC DNUQV[[[[SSSRTW[[YYYYXWXXTVXVQ 1
-SL-XAQ 505091110 7 1 2 1465 0 1 .TTGTATTTCTGAAACCCCGAAGGGCATGG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1507 0 1 .GGCTTGGAAAGTGTAGGAGGGAGAGTCAC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAQ 505091110 7 1 2 950 0 1 .GTGTGTGTTTTTAGAGATGCCTTTTAGAA DLVSURWPVXXX[XXXXXWWVUXXXZUTVX 1
-SL-XAQ 505091110 7 1 2 358 0 1 .TCTGTTGTTATTTCCCTGTTACTTTTGGT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1336 0 1 .AAGTCTAAAATTATCTTGAAGTAAAAAGT DMVTVXTYWX[[[[SLVYYTWTVX[[[WMV 1
-SL-XAQ 505091110 7 1 2 190 0 1 .ATAAGTGTATATTTATTTGTACCATGACA DLZWUXSVVVYWZZX[Y[[[[XXXXWYXXU 1
-SL-XAQ 505091110 7 1 2 1995 0 1 .ATTTCCTGAACACAGCACAGGGAAGAGGA DNVWVVVVRWVVVYWWVVVWUVVUWTWQQT 1
-SL-XAQ 505091110 7 1 2 425 0 1 .AATATATGCAAGACTCCTGTTATTAGAAA DOXXYXXOTTYVQU[[X[XXVVYYXYYY[[ 1
-SL-XAQ 505091110 7 1 2 455 0 1 .GCTTGAACTCAGGATTCACAATTTCAACC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 11 0 1 .AAATGAAAAAAGAAATGCATTGTCAGGTG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 2 636 0 1 .GATCATTTACTGTTGTCAACTACCAAAAT DNVQFJVUXUQPTPRLPLTURQOQRTUTTV 0
-SL-XAQ 505091110 7 1 3 1488 0 1 .ATTCTGAGTAGCATGCTGGATCCCACCCC DLSSTOPSKSQNPUUUSQRBBBBBBBBBBB 1
-SL-XAQ 505091110 7 1 3 795 0 1 .GTAATGGAAGTCCTAGTACTAAAAATTAG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 3 1406 0 1 .AAAATGCCAGATAAATTTTATGTAAAACC DP[[XVQQVSUVYYVVGVZZZTOR[XYXVQ 0
-SL-XAQ 505091110 7 1 3 1861 0 1 .GATTAATGAATAGAGTGAATAGTGTCTGA DLOVYYYTMR[[VVWWTQXY[[TROYXUSU 1
-SL-XAQ 505091110 7 1 3 389 0 1 .GATGTTCAAACATGCATAACTCTAAGTAT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 3 683 0 1 .AAGTTTTTATTTATACGTAGAATTTATAC DMUPP[[YZ[XWZ[[[XRXXRVWX[Z[ZXY 1
-SL-XAQ 505091110 7 1 3 273 0 1 .AATTGACATAAATCAATATTGTTAAAATG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 3 277 0 1 .GATGGGAAGGCCCCGGCCTGGGGAGGTGG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 3 301 0 1 .TACGTGTGTGGCTGGATAGTCTGGACCAT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 3 347 0 1 .GTGGTGTGAGGTGTATCTGGGTCAGCAGG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 3 579 0 1 .GAAAAATGACCACACTTGCCTCCTGAGAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 3 608 0 1 .TGTGCTTCAATGATGCTATCAGGTGTGTT DMXUVTYVSVYVUUTTRYYXYVPPXYYWYY 1
-SL-XAQ 505091110 7 1 3 699 0 1 .TGTCTTCTTACACTATTTTTTTTAAAATC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 3 959 0 1 .AAAGTTTCCTGTGAGAAGGCGCATGGCAT DMTQLSWVWSWWUUVTVBBBBBBBBBBBBB 1
-SL-XAQ 505091110 7 1 3 1155 0 1 .CAGCGAAAGAAGTACCAGGGTATGGGAAG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 3 1233 0 1 .AACCAATTTCTTTACATACCAAATACGCC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 3 1348 0 1 .ATATTGATTCTTCCTACCCATGAGTATGG DPZZVWMJRWXXXXWWWZZWXPPWZVZWBB 1
-SL-XAQ 505091110 7 1 3 1358 0 1 .TCCTTCCTCAAGGGGACCCCGCCTCCCCT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 3 1450 0 1 .GATTCGATTAGAATCATCGAATGGACTCG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 3 1574 0 1 .TTATTCCTTAGGAAATTTTAAATTCTGTA DOXTTRTVXXXXXXYXXYYXXPOQYYXYRY 1
-SL-XAQ 505091110 7 1 3 1688 0 1 .CCTTCTTTACACACTGAGGAACTTAACCT DMMXXXXXYXYVVTRTUSLRTVVOWYXVVV 1
-SL-XAQ 505091110 7 1 3 1717 0 1 .AAACAGACTTGTTTCTTGTAATAATTATG DNZZWXUWXYXXX[VUYWRXXYXYYYYYBB 1
-SL-XAQ 505091110 7 1 3 1764 0 1 .TCTATGGGGTGTGTATCTGTTTCTGGACT DOXYYWSTGSTWUNUUUUWWSZWWTPMRPS 0
-SL-XAQ 505091110 7 1 3 1973 0 1 .CTTTTATTGAATTAGCTTCTGTGGAAACC DM[VVS[[PSTZPOT[[YU[V[YWWZBBBB 1
-SL-XAQ 505091110 7 1 3 1981 0 1 AGCCTGTCTGTAGAAAAAATACAAAAATTA _RZ\ZWN_\YWaW\aaaaaYa^aa`aa^Ya 1
-SL-XAQ 505091110 7 1 3 198 0 1 TATAATTTAATGGTTTTTATATATTCAGAG aab\aabb`\_\W[ababaa`aaba\aa[X 1
-SL-XAQ 505091110 7 1 3 1927 0 1 CACATCACCTTCTACTACATTTGAAATTCT ab`b`Wa]b\a`^bWabYFW\LT_H_\O\a 0
-SL-XAQ 505091110 7 1 3 162 0 1 AATGAAGGCCACAGAGTGGTCCAAATAGCC ^__T___]]`[O^Z\OWRXYQ[```a`\BB 1
-SL-XAQ 505091110 7 1 3 751 0 1 CACTTTTATTCTTAAGTACCACCTTCTGGA U`\bbbbabbb```^^_bbW__bbabY]H_ 1
-SL-XAQ 505091110 7 1 3 918 0 1 TTTTCATTCCTAGTCATCCACCCCATCAGA OGH_`\YQ]RY]GNGG[QQ`]YOGQOY_H_ 0
-SL-XAQ 505091110 7 1 3 1760 0 1 ACAAGAGACCCTAACATTAGGTAGGAATAT `Y__T`[a[SW_a_\]^`^YZY^T]`a^__ 1
-SL-XAQ 505091110 7 1 3 1222 0 1 TGGCATCCAGCTTTGTACTCATGAAAATTG `^\_ba`_\V`_]_X_aa`^]a\Z[\_^a_ 1
-SL-XAQ 505091110 7 1 3 1677 0 1 AGTGCAGTGGCGTGATCTTGGCTCACTGCA `^Vaaa_^XXUX`VaVZ_ZP]XYF\VZV_a 1
-SL-XAQ 505091110 7 1 3 890 0 1 TGCTTCTGTTTCCGTTAGCTAGATAAAGTT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 3 405 0 1 AAAAAACATAGAACGGGGTCAATATTTTAT G^`]WGVa^[GYFH^_HWGYGIY[WYO]F] 0
-SL-XAQ 505091110 7 1 3 1544 0 1 CGTGGATGGTTTTGATGAGTCCCACTGCAC \_\[HI_QQRVT`X_^RUGVUW_YFWXV[B 0
-SL-XAQ 505091110 7 1 3 1219 0 1 AGTTACTTATAGTGAATGGTTATTACTCCA a`]aaaaaa`_^Y^``ZZ[W_aX\XV]X]` 1
-SL-XAQ 505091110 7 1 3 1294 0 1 TGTAACTTTACTTTAGTTGCTTATTTGTAG a`BBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 3 1867 0 1 AGAAGCATTCTCAGAAACTTATTTGTGATG aa]WP]aa^L]^ZOV]SZa_a`aa^Y[_\Y 1
-SL-XAQ 505091110 7 1 3 1341 0 1 TGAAGAGTTTCTGGCACATAGGCACTCAAC aV``baZ]bV`^^S`a[a]aYFY_b````a 1
-SL-XAQ 505091110 7 1 3 676 0 1 ATAAGAAAATGCCAACCCATTTACAGTTTT ^FYVDUW]^[GMX`VG\YUW]`\Q]GX_^^ 0
-SL-XAQ 505091110 7 1 3 131 0 1 TAAAATAAAGTAAAAAGAAAGCAAGGTCCT aaaabbbaa`[bbbb`[[bab]aab\`b\b 1
-SL-XAQ 505091110 7 1 3 1311 0 1 AGACATAAAACCAGAGAGAAGATAGTGGGT ___aaaaba`Z]a]`aaaaaaaa`^ZXYR] 1
-SL-XAQ 505091110 7 1 3 900 0 1 TGAATCTTTGTTCAACACAGATTATTCCAG H]_JTI[aPFYGTKQR`]TH_YHGN]Y\BB 0
-SL-XAQ 505091110 7 1 3 2027 0 1 AATGTATTATGTTTCATAAGAAAACAAAAG a`VNL_W\_SKIP\]^Y`_Y]a_aaba_WB 1
-SL-XAQ 505091110 7 1 3 996 0 1 AAGGGAATTCTTGGACTTGATTAAATTGGT \bX^U^aaa^UZU]Z]`^a`^_Q[_aaYBB 1
-SL-XAQ 505091110 7 1 3 289 0 1 ATAGTGCTACAATAAACATGGGAGTGCAGA aa\Z]``aa_aaaaaa_`ba`]]a`ZX_^` 1
-SL-XAQ 505091110 7 1 3 33 0 1 CGGGCGCGGTGGATTCCGCCTTTAATCCTA VP_\]R^a`BBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 3 905 0 1 TGTTATGTTTAATTTTCTTTAGCACCCTTC ]V]^`YL[a`_O]_Y_W\`ZTDVZX^\YX_ 0
-SL-XAQ 505091110 7 1 3 1525 0 1 AGAAAATATCTGCATAGATGTGTTGAAGTC aaaaaa``__^[R[Ya\^a__`_a```_\` 1
-SL-XAQ 505091110 7 1 3 583 0 1 GGCTTACACAGTCAAACTGGAGAGAAGTAG GTU\bbbb\aWa`aaab_Y\aa```^K_`[ 1
-SL-XAQ 505091110 7 1 3 2037 0 1 CATCCTGTAACAAAGTGTTTATAGTTTTCA Y_X_aU[^`]G]`a_[IH\[ba`Y]TPYV` 0
-SL-XAQ 505091110 7 1 3 1319 0 1 TAAATGATTGCCTTCCACAGTATACATGTG a```[YY\a_VYWXH]\]aJHa_a_\BBBB 0
-SL-XAQ 505091110 7 1 3 1513 0 1 CACGCCACTGCGCCTGCAGCCTGGGCAATA a\TT_``U_\Z]Z]NZ__X_[]TQ[^_`a` 1
-SL-XAQ 505091110 7 1 3 1188 0 1 GCGAATGCCATTATTTCATTCCTTTTCATG \_b`b`^``abbbbbbbb`a^^bababbaa 1
-SL-XAQ 505091110 7 1 3 673 0 1 TCCTCAAAAACAAGATAAAACGGTTGAAAT ]GH]HFFWTaab^BBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 1 3 471 0 1 AGAAAAAGACAAGCAGGCCTCTCACAGAGC _\a]ba_^Waaa`[a[_`aa```\[_]]R[ 1
-SL-XAQ 505091110 7 1 3 1328 0 1 GCTACCAACCCCACTCCTAGATGAAAGACC OUWK\_H\``WQ_b_WZZ_RZWN[[BBBBB 0
-SL-XAQ 505091110 7 1 3 985 0 1 AGGTTTAATTGGTTCCAGGAGGTCACACTG ^WXW_aaa^_U[Z_]ZaYY]YLVXa`_`_Y 1
-SL-XAQ 505091110 7 1 3 176 0 1 ATATTTCATGAAAGACATAAATTTACAGTT aaabba_aaa`aaaa^`aaaaaaaa`aa_a 1
-SL-XAQ 505091110 7 1 3 880 0 1 ATGAGTGAGAAATAGAAGTCCTAAGTAGAT a_\ZNVT]H]^a_\R]_\[MQ\a_Q_]SXa 0
-SL-XAQ 505091110 7 1 3 695 0 1 TGATACTGCCTTTGCAAAAATTATAACAGT Z]`aabb[^`bbaaabbbbaa`ba``aa[` 1
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_1_0002_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_1_0002_qseq.txt
deleted file mode 100644
index 2969923..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_1_0002_qseq.txt
+++ /dev/null
@@ -1,200 +0,0 @@
-SL-XAQ 505091110 7 2 0 135 0 1 ........A...........G......... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 1547 0 1 ........C...........G...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 87 0 1 ........G........A..T...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 205 0 1 ........A........T..C...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 50 0 1 ........T........T..G...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 1620 0 1 ........CA.......A..C...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 1278 0 1 ........TA...T...C..A...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 186 0 1 ........CC...A...T..T...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 287 0 1 ........CC...C...T..A...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 441 0 1 ........TT...A...A..T...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 766 0 1 ........TG...A...A..T...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 1598 0 1 ........AT...T...A..G...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 382 0 1 ........CA...T...T..A...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 740 0 1 ........TT...A...T..A...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 501 0 1 .....G..AG...A...C.CT...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 1135 0 1 .....G..GT...A...T.TA...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 73 0 1 .....A.CAT...G...A.AC...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 1668 0 1 .....A.ATA...A...G.TG...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 1198 0 1 .....T.CTA...T...C.CA...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 0 1073 0 1 .....A.CAC...C...C.CA...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1351 0 1 .....C.ATA...T...A.AA...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1987 0 1 ..AT.G.ACA...C...T.GT...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1755 0 1 ..GT.A.TCT...C...C.TG...G.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1950 0 1 ..TT.A.AAA...C...T.CA...T.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 8 0 1 ..TGCG.TGG...C...AGGC..TT.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 56 0 1 ..GCCA.GGT...A...TCAC..GG.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 211 0 1 ..CTGA.ACA...G...TGCA..AC.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 242 0 1 ..GCTC.AGC...A...ATAT..TT.G... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 262 0 1 ..ATTG.AAT...C...TTCC..AT.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 298 0 1 ..TCAA.TTG...T...CTGC..TT.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 312 0 1 ..TTGC.AGA...A...AACT..TG.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 370 0 1 ..CTGG.AGC...T...CATA..AA.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 377 0 1 ..AGAA.GTG...T...AAAT..AA.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 414 0 1 ..TAGA.AGC...A...TCAG..AC.G... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 421 0 1 ..GTTA.TTC...A...CGTG..AT.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 555 0 1 ..CAAT.TCT...G...TACA..CT.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 569 0 1 ..AGGC.AGT...G...GTCC..GT.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 699 0 1 ..AATT.TTG...T...ATTT..GA.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 722 0 1 ..CCTC.CTG...C...CTGT..TG.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 749 0 1 ..AGTG.TAC...T...CTTG..CT.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 833 0 1 ..GAGC.CCT...A...CTCC..GA.G... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 848 0 1 ..TACT.AGT...G...TGTT..GC.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 998 0 1 ..ATGT.TGC...A...TATA..GG.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1159 0 1 ..ACTT.TAG...G...AAAT..CC.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1168 0 1 ..TCTA.CTT...T...ATTG..TT.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1180 0 1 ..ATGG.CTT...C...AGAA..TC.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1306 0 1 ..ACAT.AAA...T...AACA..GT.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1424 0 1 ..TCAT.TAG...C...ATGG..GT.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1521 0 1 ..ACAC.AAA...G...ATCT..TT.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1543 0 1 ..TTGA.ATC...A...AATA..TA.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1617 0 1 ..CCAT.ATC...G...CCAG..GT.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1627 0 1 ..TGGT.AGA...C...AAAA..CA.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1653 0 1 ..AATT.AAA...T...ATCT..AG.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1682 0 1 ..TCTT.TTT...G...AAAA..AA.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1731 0 1 ..TATA.GAA...T...TGCT..AG.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1812 0 1 ..TTGC.CAC...C...CCAT..AA.G... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1853 0 1 ..ATCT.TTC...A...AGTG..AT.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1919 0 1 ..AATT.AAA...A...AGAA..AG.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 2006 0 1 ..GTAT.TGA...G...CCTT..AG.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 64 0 1 .ATTAATCTT...T..GCACAATTCATT.. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1646 0 1 .TTAATTATA...A..TAAACATTCTAA.. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 37 0 1 .TGTAAACGA...C..TTCCTGTTCAGC.. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1515 0 1 .ATTAAATAT.A.A..GTAATAATAATA.. DNXBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 466 0 1 .ACACTCACA.C.A..TGTTTGGAATGA.. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 558 0 1 .AAAATATCA.T.A..AATAAATAATCA.. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 714 0 1 .ATTAACTTA.A.T..ACCACAACCTAA.. DMYBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1933 0 1 .AGGGTACAT.T.C..AATGTGCGGGTT.. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 628 0 1 .AGTATGCCC.C.C..ACCACTCCTATT.. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 44 0 1 .ACTACCTCA.G.A..AAGCAGGTTCTAA. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 428 0 1 .ATGTGAATA.T.A..TAGTTGGGATTCA. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1924 0 1 .ATATTCTGAAG.A..CCAATGAACCAAA. DPPU[XTVX[VBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 234 0 1 .AAGCCTGTGGG.A..CCCAGTGGGAGCG. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1004 0 1 .ATTTATCACTA.A.ATCCGCAAACCCTCC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1214 0 1 .AAAAAAAAAAA.A.TATAAGAAAGAATCA DORTYBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1034 0 1 .ATCATTTTCAT.C.TTTCACTGATACATT DMVRVYWWVSVPDLDPYWTTTTSTZUXUYY 0
-SL-XAQ 505091110 7 2 1 1536 0 1 .AGCAAAGACTT.G.ACCAACCCAAATGTT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 684 0 1 .AAAAATCAAATGA.CATAATTTTATAAAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 893 0 1 .GAGACAGAGTCTC.CTCTGTTCCCTAGCC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 604 0 1 .ATGATGAAACTCT.TCTCTACTAAAAATA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 760 0 1 .GTCTGTTTTATGT.AAATATTTTGTTTAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1452 0 1 .GAAATTTGTAAAA.CACCTGCAGAATACT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1959 0 1 .GACACATTCCTAC.ACAGAGAAAAATTTA DIVVZZ[Z[[Y[ZKDMYYZYUYXYY[SSWW 0
-SL-XAQ 505091110 7 2 1 1938 0 1 .AGTCCAGTGTCTCTGCTTCCGCAGGGACA DNWPWWUTNOTWWTWUSSWUUSTVUSUUUW 1
-SL-XAQ 505091110 7 2 1 1221 0 1 .GGTCACACTCACATAGTGTTCAGAGCACT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 1 363 0 1 .GAAAGGTTTTGCAGCATGTGCAAACTCAC DLTTUTUVWYWPVVUTUTORTPQNRVVWTU 1
-SL-XAQ 505091110 7 2 1 170 0 1 .AGAAGAAATGGGATCCTGCTGTGGCCAGT DNWWWWUTQWSPUWWUUVUVUURGUWVSNT 1
-SL-XAQ 505091110 7 2 2 463 0 1 .GTGCTTGGGGGCGTCTGTGTTGATGCGTG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 1636 0 1 .GTGTAAAAGTAGGGAAATACTATAGCAAG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 828 0 1 .TCAAGTCAATTTGGGACTTGAAACAGCTC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 220 0 1 .AATAAACCTCTTTCTTTGATAAATTACCC DMTYVWRRTTUVYTQT[VRUYXWUWZWBBB 1
-SL-XAQ 505091110 7 2 2 101 0 1 .GTTAATTTAGGGAAATTTGTTTGTATTTT DKRYXUXZ[TQVPWZ[[[VUWZYYXZXXXZ 1
-SL-XAQ 505091110 7 2 2 351 0 1 .GGGGTTGAGGTGTAAATAGAACATTTGTA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 1559 0 1 .ACAGAAGGGAAAAGGTCACAGACTAAAGA DNNUZZZWWSXZYXPKRTYYVTVYSYZYXY 1
-SL-XAQ 505091110 7 2 2 1671 0 1 .GGGAATTACATGGAAAATGATCAAAGGAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 0 0 1 .ATTCCTT.A.................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 61 0 1 .TTTCGATGGTGTTTCCATTTGATTCATTC DOZYXYZVXXYWYXVVVXY[UVX[XVVZYY 1
-SL-XAQ 505091110 7 2 2 1842 0 1 .GGTGGATCCCCTGAGGTCAGGAGTTCAAG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 12 0 1 .ATGCATTGTAATTTAATAGAGTGAAATGG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 599 0 1 .AAACAAAAAAGCTGATGGCCTGGCGGGGT DMWRUWSSVTPTWRKRWLHNWURWBBBBBB 0
-SL-XAQ 505091110 7 2 2 115 0 1 .GATGTGCTACACACTTTCAAACAAACAGA DOYTOOENXXZUXVQVYYXXTRPRRVSSWS 0
-SL-XAQ 505091110 7 2 2 255 0 1 .GGGTCCAAATAAGAGAAGGAGAAAAACAG DOOSPQORUWXROTVTTSPUVSUTZXWXVV 1
-SL-XAQ 505091110 7 2 2 1298 0 1 .GATTCCATTCAATGAATCCATTCGATTCC DMQRTJQQXVUBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 775 0 1 .GTTTATAATTGTGAGTTAAAAATCTAAAA DKLVWYWYXUWYSTTQS[[URUZ[Y[[[[[ 1
-SL-XAQ 505091110 7 2 2 131 0 1 .ATATATTGACAGCAGTCATGTTGTTGAAG DO[[[Y[XTXWVSSXQYXUXXXXUXYVVWS 1
-SL-XAQ 505091110 7 2 2 904 0 1 .TTAGACACCATGAAGGTAACTTCCTACTC DOYUQUUVXXXNEMUOTWYYTXVWSWXRUU 0
-SL-XAQ 505091110 7 2 2 1038 0 1 .ATGGAATCAACCTGAGTGGAATGAAATGG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 669 0 1 .GGCTGAAGCAGGAGGGTCACTTGAGCCAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 488 0 1 .TGGGAAACTAAACCCCATGAGGGCAGAGC DNQNPTUUUUVWTSSTQTTTTPNPQTSTNS 1
-SL-XAQ 505091110 7 2 2 953 0 1 .GTTTAGTACATACTAGGTTTCACCAAATT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 1723 0 1 .GAAGCTGACATTACAGGTTTCAGACACCA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 1944 0 1 .ATTAAATATATATTTTATTCTGAACATAA DOXYY[[[[[ZY[[[YXX[[X[[Z[Z[Y[[ 1
-SL-XAQ 505091110 7 2 2 1567 0 1 .AGACAGCAGTAACCTCTGCAGACTTAAAC DKUVYVQOTSSZSUUVYUQLTUUVYYUWVV 1
-SL-XAQ 505091110 7 2 2 679 0 1 .CTCTGTCTCAAAAAATAAAAATAAAAATA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 1985 0 1 .GACTATCACTCTAGGGCCTCCACCCTTGC DDQQUUSUUUUVPWUGUUBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 1402 0 1 .GGATGGCTTCCAGTATGGGAACCTTTTCA DMTSWSLNWTWWUTNVWNGNUQFNWWUTTT 0
-SL-XAQ 505091110 7 2 2 1874 0 1 .GGCATATATCCTTTTACATACCCAACACA DKOPRVYXSXUXXZXZWWVXWVWXVPVXXU 1
-SL-XAQ 505091110 7 2 2 611 0 1 .GGAACCAGGCAGGGCCACACACAGGTAGC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 1974 0 1 .ACGCCAATACAAAAATGTTGAAGCTAGCT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 1012 0 1 .AGAAATACCATTTGACCCACCAATCCCAT DOUUYYYXURUXURTUVVVWYYWWWXTLTW 1
-SL-XAQ 505091110 7 2 2 303 0 1 .AGATCTTGTCTTTCAATCTTTTTAAATTC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 1365 0 1 .ATAAAGATTATCCGTGAATGGCGCCTCCA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 184 0 1 .GAAACGTTTTTCGGTTGAGGAAACTTTTT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 646 0 1 .GAATCTAAGAAGACACAAAACTAAGGAAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 2 1662 0 1 .ACTAAAGACCTTATTCATGTAGCCAAATA DMQTTURRPHDOVXVXXYYXYVPWTT[WWY 0
-SL-XAQ 505091110 7 2 2 1745 0 1 .GGGAGCTAAGTAACTGGAACAAGTTTTTG DLTQRVVWXXXXYWWWUUWXYXYXTUXWWV 1
-SL-XAQ 505091110 7 2 3 1952 0 1 .ATAGATGATAAAAACATTTGACAGTGAAA DMWVRVWUWYYY[Z[ZXZXXVXYYXWTWZZ 1
-SL-XAQ 505091110 7 2 3 112 0 1 .ATGGAGTCTTGCTCTATTGCCCAGGCTGG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAQ 505091110 7 2 3 386 0 1 .TGAATAAATAAATATCTGTATTATTCCTA DPTUZXXYXXXYTVVRKSLTVXVRWTPMSW 0
-SL-XAQ 505091110 7 2 3 490 0 1 .CTAATTGATGGGTAAGAGGCAAAGCATGA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 495 0 1 .TCCGTTTTTATAACTGTAAATTTATCACT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 577 0 1 .TTCAACTCTGGGAGTTGAATGCAAACATC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 695 0 1 .CAACTCCAAGACACATAATTGTCAGATTC DNYYYXTTVWTWXXUXYYYZUTTXVSWZWQ 1
-SL-XAQ 505091110 7 2 3 808 0 1 .GAGTGTAATACAATGGTATGGATTTTAAC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 862 0 1 .CTTTAAGAAATCATTCATTCTGCAAACAC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 889 0 1 .TTTTTATAACACCTCAGGCATCGTCAAAC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 1025 0 1 .AATGGAAAGGAGTCCAATGGAAGGGAATC DNSUQUWWTLJRLRVVVYTRQTVORPRWRV 1
-SL-XAQ 505091110 7 2 3 1053 0 1 .TTTGATCATGATTCCATTCGAGACCATTC DMZZBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 1123 0 1 .CCTCTTCCACAACTTCCTTCTTCTCCTTT DMQRHVSVTVVUWVUSWUYZUVRSWWUVYW 0
-SL-XAQ 505091110 7 2 3 1209 0 1 .TTGAGGATGTTACTACATTATTATACAAA DNRRVONOPOMTTBBBBBBBBBBBBBBBBB 1
-SL-XAQ 505091110 7 2 3 1290 0 1 .TCACCTGAATCCACGTTAGCTGGGGAAGA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 1387 0 1 .CGATTATGACTCTGAGAGAAAGTAGGGCA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 1529 0 1 .TTATATGAATAGATAAATAAATAATCAAT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 1576 0 1 .GAAACCACGTGCCCATTTTCAGTTCTGGT DINDMTTUURPPVWUWVWWVWVNVUTBBBB 0
-SL-XAQ 505091110 7 2 3 1581 0 1 .ATAGGCAGGGAGCAAACCTCAATAAAAAG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 1733 0 1 .TTAAATGAGTGTAAATATTCAATTATGCA DKYUYYQNTZRXR[[XY[ZXPX[XVBBBBB 1
-SL-XAQ 505091110 7 2 3 1775 0 1 .AATCCGACAATTATGTGTCTTGGAGTTGC DMQQROPSXXXWWWUUSTUQTOIMSQSXTT 1
-SL-XAQ 505091110 7 2 3 1807 0 1 .GCATACTTCTTTCTTTCTTATTTTTCTTT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 1844 0 1 .GGACTACAAGCGCACGCCACATGCTCAGC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 1898 0 1 .TTGAATTGCTGGACTTCAATGTGTGTGGG DOWWUWYUSUWOJOLTYWVUTQTTUSVTQQ 0
-SL-XAQ 505091110 7 2 3 1917 0 1 .TCCACAAAAAAAAAAAAAATTAGTTGGGT DIU[VRV[SVTUBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 1970 0 1 .TAATACTCTTTGAGAAAGGACTGAGGGAA DMYVVTTWYUWWUQMRZWSTTYOOTVTRTZ 1
-SL-XAQ 505091110 7 2 3 2004 0 1 .AAGACTACCTTGCTGAAATAGGGCATTTA DMYWVTSTXZSLVSRGQXZZTPRXQUUBBB 0
-SL-XAQ 505091110 7 2 3 2038 0 1 .A.AGATAGATAGATAGATAGATAGATAGA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 317 0 1 AGAGAGAAATGTGGCATATGAGTATCACCT _S]aaa^`ab`a_]]`baa^a[``aabaaa 1
-SL-XAQ 505091110 7 2 3 1941 0 1 TGTACTCGTGTAGCCTTTCACAGGCACAGC a[M`baaaQZXb]_T`aaababa`abbbTa 1
-SL-XAQ 505091110 7 2 3 157 0 1 TGGGTGGTTCAAACTAAGCAGTCCAACTGC a`bb_aa`aaaabaabaaaaaa^``a^a^` 1
-SL-XAQ 505091110 7 2 3 99 0 1 CATATCTGTGTTATTTTAGCATAAATTTGA P_J_RP^GFSG`ZVR]H^VRHH_HH_b^BB 0
-SL-XAQ 505091110 7 2 3 143 0 1 AAAATCAATTCTGAAATGATTACATATTTT aaa`baa`ba\a^aaaabaabaaaaaabaa 1
-SL-XAQ 505091110 7 2 3 328 0 1 AGCTTAATATAGCATAGCAGATAAGATTTG GYIW]\KRYHH[H^`[GW]BBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 932 0 1 AGAAAGACAGACAGACAAACTGACTCTCAG _]_b_S`\^Q_a_M]`a`aaaa]\`YZ]_B 1
-SL-XAQ 505091110 7 2 3 1484 0 1 CATCAACCTGTCACAAAATGACAAAACCTA \`_T_ba^aT_^a__aaaa^`abbab_`aa 1
-SL-XAQ 505091110 7 2 3 875 0 1 AGGCAGTAGTCTAATCCCGAGGATCCCAAG YKVR\_^[M\_Z^^_YYR^WHT[\XDY^]V 0
-SL-XAQ 505091110 7 2 3 1016 0 1 TGGCTCTGTCCTAATATCTTATTCTTACAA [R\_aa`^_[\aabb_]U]aaaaa_a^_`b 1
-SL-XAQ 505091110 7 2 3 198 0 1 TGTCATTTTCTTTGCCTTAATTGTTCTTCT T_baaVLI[\BBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 470 0 1 TGTGGATTCCATTCGAATTCATTCGATTAT aabaa`bb_bbbb]H_ba`]_ba^abbbbb 1
-SL-XAQ 505091110 7 2 3 1094 0 1 CATATGGTATCACCACTCAGATACATAAAG ``aa[Y\Pbaabab_^``_H]bbaabba^\ 1
-SL-XAQ 505091110 7 2 3 782 0 1 AGCCATGGGCATATAGAATCACTGTAAACA a_aaaa]VZababaa_aaa^aa]Y\a`a_a 1
-SL-XAQ 505091110 7 2 3 991 0 1 TGGAAGCCAGCCAAAGATACACTCTTGGCA a`ab]Uaabaaaab```_a`ba[[^a`aaa 1
-SL-XAQ 505091110 7 2 3 1962 0 1 ACTAAATCCAAGAGCACATCAAAATGTTAA aTZaaa__W_a`aX]aaa`a`ba__aZ_aa 1
-SL-XAQ 505091110 7 2 3 1101 0 1 AAGATTATATGAGTATAATGGAGCTATTTG a[RW]a\]]a\\RO`aa`WWUZ^Z```__] 1
-SL-XAQ 505091110 7 2 3 207 0 1 AGTTAGAAACAGAATACGGGTAATAATGTA aabbb`_a`_```ab_bb_``babaaabab 1
-SL-XAQ 505091110 7 2 3 1326 0 1 AGGAGGGAATGATGAACCAGTAGGTTAAGG a]\[QWJ[aTDXYNZ`VW]JN\`BBBBBBB 0
-SL-XAQ 505091110 7 2 3 728 0 1 TGCCTCCTTGGAGAGGGCCGCAAAGCCAGG \]\V^`^VFTO]NXXUYZ[J]``_VJWaUV 0
-SL-XAQ 505091110 7 2 3 691 0 1 ATTTTCAAATCATAAATATGGATTGCTGTG aaa`a`baa`_`aaaaaaaVQV`aWJZaTT 1
-SL-XAQ 505091110 7 2 3 1352 0 1 AAAGTGGCCCTTTCTGCATAATTCTTCTTG _a_]QY__Y]a_```Y``]^a^]Y\[P\[B 1
-SL-XAQ 505091110 7 2 3 1389 0 1 TATCGATCTCCTGACCTCGTGATCCACCCA `bababa^baa_U`aba_Ha]baabb_SZT 1
-SL-XAQ 505091110 7 2 3 987 0 1 AAGAGCAATATTTTCTTTCACTATATTATT I_[__^`_OHVSSWH^b_H_SHXY_BBBBB 0
-SL-XAQ 505091110 7 2 3 1133 0 1 AGAAGCTTTCTATTCTGATCCCCAAGGAGT a`ba`]aa\PZ^a`^^T`]Y_QT[\MSRZ^ 1
-SL-XAQ 505091110 7 2 3 399 0 1 AGGGTATGTAAACCGAGTTTTGCGGGGGAT `___]aaaaa``]_Z^a^aa``]_Y_Y^`a 1
-SL-XAQ 505091110 7 2 3 16 0 1 AGCTGGGCATGGTGATGCGCCCCTGTAATC `Z^Z[[^_X^____S\RHP_TX^^X[TM[Q 1
-SL-XAQ 505091110 7 2 3 2013 0 1 AGCAGAAGCCTGCTGTGGGAACACTCAGTC a^aBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 898 0 1 TAACATTCCCACAGTGCTTGCCACAGAGCC `bbbbbb_b__a_HZ]Zaabb\_ab^a_Z] 1
-SL-XAQ 505091110 7 2 3 1712 0 1 AGTGCTGTGGCCTGGATGGATGTCAGGATT ]XPY^TY\TYVV]ROT]NZ\]PY[aXUXSZ 1
-SL-XAQ 505091110 7 2 3 179 0 1 CATTATTGTTAGACTGATTTTTTATAATCT a_HPOSMMIOL`G__G[`X`[GJXHL\UGa 0
-SL-XAQ 505091110 7 2 3 151 0 1 AGAGAACAGATAGGTCTGTCAGGGCTGACC ^]\XXa]a`^a]H^ZT`aZWXZ\U^^[VR] 1
-SL-XAQ 505091110 7 2 3 983 0 1 TGTTTTTTATTTTAACAGATGAAGTACCAA a\abbbbbbbbbbb`]``bbabb_`b_]ab 1
-SL-XAQ 505091110 7 2 3 567 0 1 TATCTTCACATAAAAACTACACAAAGCATT aba[`baa_abbaaba[aa[_Z^aa]\aaa 1
-SL-XAQ 505091110 7 2 3 72 0 1 CTAGTCTTTGACTTATATCAATTCAGTATT aab^`bbbbba_bbbbbbbabbbbb`_abb 1
-SL-XAQ 505091110 7 2 3 922 0 1 ATTTCTGTCTGACTTTTCCAAATGTGCTAT ``aa_]]]_]X_]````]Z_aa__TRZaaa 1
-SL-XAQ 505091110 7 2 3 584 0 1 AAAGTCCTGGGATTACAGGCATGAGCCACT `abQ[_\]WZU\]^]R]LR[]aX_N\X`Z[ 1
-SL-XAQ 505091110 7 2 3 274 0 1 AGTGAAGTGCTTAGCACCTGGGCCAGCAGC YTVMY__]XU\_XV]_\Z\]Z_Z_\_X\XZ 1
-SL-XAQ 505091110 7 2 3 1602 0 1 AATTCATGAATACTTTTCAGTCTTTAAAAA aba```aaaaa^[_a`a^``\^aaaaaaaa 1
-SL-XAQ 505091110 7 2 3 4 0 1 AGAGGCAATAAGTTTTAA............ `]a`_Xa`aR``BBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 663 0 1 AAAAGCATGTTGCTCAGTAAAAGCAAATAG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 80 0 1 AGGCAGGATGAAATTTTGTCTATTTATTCA _XYa_a_^a_`a`aaaa^^V``aaaaaa^` 1
-SL-XAQ 505091110 7 2 3 1179 0 1 ATTTAATAAATAAAGCAACCTGACAACTGA _PTZFWW^`_PNR\FPOUNX`VMIYNOWBB 0
-SL-XAQ 505091110 7 2 3 589 0 1 TGAATGCAGGTGCCAGGGAGACGTGACTTC \W`baa^^]_\^[`baX[Z^`]^^Z`[]^R 1
-SL-XAQ 505091110 7 2 3 640 0 1 AGATTAAAAAAAAATGACGTGACAAATTAA \Ubab_b`abaabab_]_\_`aabbaaabb 1
-SL-XAQ 505091110 7 2 3 2030 0 1 CGAGATAATTTTTTAAAAAAAGTCCAAAAA GG_ZGH_\\IV[GT`_[b]BBBBBBBBBBB 0
-SL-XAQ 505091110 7 2 3 247 0 1 TGTACATGACCAGGTAATTTGGTTATGTGA [_TXURTRZH]_`V\YK`OFU]BBBBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_2_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_2_0001_qseq.txt
deleted file mode 100644
index b539a57..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_2_0001_qseq.txt
+++ /dev/null
@@ -1,200 +0,0 @@
-SL-XAQ 505091110 7 1 0 1434 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 464 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 113 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1703 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 879 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 841 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1291 0 2 .....G.. BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1940 0 2 .....C.. BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 586 0 2 .....C.. BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1690 0 2 .....A.. BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 37 0 2 .....G.. BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 324 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 205 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1307 0 2 .....TA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1193 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1475 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 275 0 2 .....AT. BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 2001 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1093 0 2 .....TG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 0 1038 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 173 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1836 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1513 0 2 .....CT. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1917 0 2 .....AC. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1696 0 2 .....CT. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 812 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 2 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1555 0 2 .....CA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1243 0 2 .....TG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 30 0 2 .....AC. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 41 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 59 0 2 .....AC. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 111 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 132 0 2 .....TG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 140 0 2 .....CA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 155 0 2 .....CA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 164 0 2 .....TT. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 170 0 2 .....AC. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 184 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 195 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 240 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 262 0 2 .....CA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 299 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 353 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 367 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 416 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 483 0 2 .....TA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 486 0 2 .....TG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 495 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 508 0 2 .....CT. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 554 0 2 .....TA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 567 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 613 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 622 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 627 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 684 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 874 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 931 0 2 .....CA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 994 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1013 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1153 0 2 .....CT. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1184 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1241 0 2 .....CT. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1282 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1320 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1391 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1684 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1733 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1770 0 2 .....TC. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1906 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1954 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1247 0 2 .....AC. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 18 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1521 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 264 0 2 .....CGA BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1815 0 2 ...T.GAC BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1379 0 2 ...C.GAT BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 2011 0 2 ...G.TAG BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1372 0 2 ...G.TTA BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 55 0 2 ...G.TTA BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 517 0 2 ...C.AGA BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 965 0 2 ...T.TAA BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 535 0 2 ...C.CGA BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 72 0 2 ...T.GAC BBBBBBBB 0
-SL-XAQ 505091110 7 1 1 1886 0 2 ...G.GCC BBBBBBBB 1
-SL-XAQ 505091110 7 1 2 1932 0 2 ...C.AGA BBBBBBBB 1
-SL-XAQ 505091110 7 1 2 1706 0 2 ...C.GAT BBBBBBBB 1
-SL-XAQ 505091110 7 1 2 363 0 2 ...T.CTT BBBBBBBB 0
-SL-XAQ 505091110 7 1 2 605 0 2 ...T.GAC BBBBBBBB 1
-SL-XAQ 505091110 7 1 2 449 0 2 ...G.TGT BBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1782 0 2 ...T.AGC BBBBBBBB 1
-SL-XAQ 505091110 7 1 2 246 0 2 ...A.TTC BBBBBBBB 0
-SL-XAQ 505091110 7 1 2 307 0 2 ...T.GAC BBBBBBBB 0
-SL-XAQ 505091110 7 1 2 150 0 2 ...A.CCT BBBBBBBB 0
-SL-XAQ 505091110 7 1 2 546 0 2 ...A.GTT BBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1727 0 2 ...T.CTT BBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1946 0 2 ...T.GAC BBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1275 0 2 ...A.CTG BBBBBBBB 1
-SL-XAQ 505091110 7 1 2 786 0 2 ...GATGT BBBBBBBB 1
-SL-XAQ 505091110 7 1 2 747 0 2 ...CCAGG BBBBBBBB 0
-SL-XAQ 505091110 7 1 2 25 0 2 ...GATGA BBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1722 0 2 ...TCGAC BBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1301 0 2 ...TAACA BBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1592 0 2 ...GAGCC BBBBBBBB 1
-SL-XAQ 505091110 7 1 2 943 0 2 ..ACCAGG BBBBBBBB 1
-SL-XAQ 505091110 7 1 2 974 0 2 ..TATGTT DDOYYYY[ 1
-SL-XAQ 505091110 7 1 2 858 0 2 ..ACATCT DDNTVVXX 1
-SL-XAQ 505091110 7 1 2 209 0 2 ..CATTTC BBBBBBBB 0
-SL-XAQ 505091110 7 1 2 988 0 2 ..TGGCGA BBBBBBBB 1
-SL-XAQ 505091110 7 1 2 1453 0 2 ..ACCAGG BBBBBBBB 1
-SL-XAQ 505091110 7 1 2 69 0 2 ..GGAGCC BBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1158 0 2 ..CTTAGC BBBBBBBB 1
-SL-XAQ 505091110 7 1 2 1753 0 2 ..TGCTTA BBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1238 0 2 ..CTAAGC BBBBBBBB 0
-SL-XAQ 505091110 7 1 2 1827 0 2 ..CAACTG BBBBBBBB 1
-SL-XAQ 505091110 7 1 2 309 0 2 .TCGCTGA BBBBBBBB 1
-SL-XAQ 505091110 7 1 2 1889 0 2 .AGGATGT DMSUYZZX 1
-SL-XAQ 505091110 7 1 2 1878 0 2 CAGGAGCC a[WP[\VZ 1
-SL-XAQ 505091110 7 1 2 658 0 2 AGCAATTC _V\___\Z 1
-SL-XAQ 505091110 7 1 2 119 0 2 CATAGCGA ^_]\Z[ba 1
-SL-XAQ 505091110 7 1 2 1417 0 2 AAGGATGT a^T^^ab^ 1
-SL-XAQ 505091110 7 1 2 1895 0 2 CATAGCGA ^_bb_]ab 1
-SL-XAQ 505091110 7 1 2 52 0 2 TGCTCGAC YZZZYZ\Z 0
-SL-XAQ 505091110 7 1 2 85 0 2 TACTTAGC a]G]a\aQ 0
-SL-XAQ 505091110 7 1 2 63 0 2 TTCGCTGA V_\a[b_B 1
-SL-XAQ 505091110 7 1 2 737 0 2 TACTTAGC abbbabaa 0
-SL-XAQ 505091110 7 1 2 802 0 2 CAGGAGCC \]O]^V]B 1
-SL-XAQ 505091110 7 1 2 1465 0 2 CACATCCT [Y_\aa__ 0
-SL-XAQ 505091110 7 1 2 1507 0 2 AGCAATTC ^Q\_X`[] 1
-SL-XAQ 505091110 7 1 2 950 0 2 TGTCGGAT __\`Y``` 1
-SL-XAQ 505091110 7 1 2 358 0 2 AACTTGAC `^ZUTPVR 0
-SL-XAQ 505091110 7 1 2 1336 0 2 CAGGAGCC V_X\a\V_ 1
-SL-XAQ 505091110 7 1 2 190 0 2 CATAGCGA ``bb\\_a 1
-SL-XAQ 505091110 7 1 2 1995 0 2 CTACCAGG a\``^aa` 1
-SL-XAQ 505091110 7 1 2 425 0 2 CAGGAGCC ``__\XZ[ 1
-SL-XAQ 505091110 7 1 2 455 0 2 GTATAACT K_BBBBBB 0
-SL-XAQ 505091110 7 1 2 11 0 2 GTATAAGA _V\\_VBB 0
-SL-XAQ 505091110 7 1 2 636 0 2 CCTACCAT UR[_`^a\ 0
-SL-XAQ 505091110 7 1 3 1488 0 2 GTATAACA HV[Xaaaa 1
-SL-XAQ 505091110 7 1 3 795 0 2 ACCAACTG ]WW_`]BB 0
-SL-XAQ 505091110 7 1 3 1406 0 2 TCTGGCGA ``\ZT_\_ 0
-SL-XAQ 505091110 7 1 3 1861 0 2 AGTTGCTT aX_][`[b 1
-SL-XAQ 505091110 7 1 3 389 0 2 GCACATCT [Y___TUZ 0
-SL-XAQ 505091110 7 1 3 683 0 2 CACATCCT a_W_a^ba 1
-SL-XAQ 505091110 7 1 3 273 0 2 AAGGATGT RW\TJ`bV 0
-SL-XAQ 505091110 7 1 3 277 0 2 CATAGCGA a`^ZR]a\ 0
-SL-XAQ 505091110 7 1 3 301 0 2 GCACACGA BBBBBBBB 0
-SL-XAQ 505091110 7 1 3 347 0 2 ATTATGTT S`]^_HU[ 0
-SL-XAQ 505091110 7 1 3 579 0 2 AATCATGT VRBBBBBB 0
-SL-XAQ 505091110 7 1 3 608 0 2 AAGGATGT ``Ta^aa_ 1
-SL-XAQ 505091110 7 1 3 699 0 2 AGTTGCTT XW^]W]BB 0
-SL-XAQ 505091110 7 1 3 959 0 2 GCACACGA R^Z`a^\[ 1
-SL-XAQ 505091110 7 1 3 1155 0 2 TTGAGCCT BBBBBBBB 0
-SL-XAQ 505091110 7 1 3 1233 0 2 CCAACAGG BBBBBBBB 0
-SL-XAQ 505091110 7 1 3 1348 0 2 TGCTCGAC aX^^_V_T 1
-SL-XAQ 505091110 7 1 3 1358 0 2 CTACAAGG UQaaBBBB 0
-SL-XAQ 505091110 7 1 3 1450 0 2 AACTTGAC abPF[V`B 0
-SL-XAQ 505091110 7 1 3 1574 0 2 TACTTAGC _`baab_` 1
-SL-XAQ 505091110 7 1 3 1688 0 2 CCAGTTAG ]_\\Zb`\ 1
-SL-XAQ 505091110 7 1 3 1717 0 2 TCTGGCGA `a\PPZ`_ 1
-SL-XAQ 505091110 7 1 3 1764 0 2 AAGGATGT aa^aa_Y` 0
-SL-XAQ 505091110 7 1 3 1973 0 2 GTATAACA VZb`bbab 1
-SL-XAQ 505091110 7 1 3 1981 0 2 TGCTCGAC \I_PZ_aa 1
-SL-XAQ 505091110 7 1 3 198 0 2 CTACCAGG `aaa``^_ 1
-SL-XAQ 505091110 7 1 3 1927 0 2 CAGGAGCC a_[__\_^ 0
-SL-XAQ 505091110 7 1 3 162 0 2 AACTTGAC aaab_T]^ 1
-SL-XAQ 505091110 7 1 3 751 0 2 CACATCCT X_b`bbbb 1
-SL-XAQ 505091110 7 1 3 918 0 2 ACTACCTT H^Sa]BBB 0
-SL-XAQ 505091110 7 1 3 1760 0 2 AACTTGAC a`aa`a`` 1
-SL-XAQ 505091110 7 1 3 1222 0 2 AACTTGAC _bb\__]a 1
-SL-XAQ 505091110 7 1 3 1677 0 2 AACTTGAC ab`]\S\a 1
-SL-XAQ 505091110 7 1 3 890 0 2 GTCACCAT BBBBBBBB 0
-SL-XAQ 505091110 7 1 3 405 0 2 ACACAAGA OG][\BBB 0
-SL-XAQ 505091110 7 1 3 1544 0 2 GCACACGA GG[MZZPZ 0
-SL-XAQ 505091110 7 1 3 1219 0 2 ACCAACTG a^__`^^X 1
-SL-XAQ 505091110 7 1 3 1294 0 2 TCACAATG IRV[[_T[ 0
-SL-XAQ 505091110 7 1 3 1867 0 2 ATTATGTT aa`_VX]a 1
-SL-XAQ 505091110 7 1 3 1341 0 2 AGATGCTT aBBBBBBB 1
-SL-XAQ 505091110 7 1 3 676 0 2 GATCCAGA YGM[GGY_ 0
-SL-XAQ 505091110 7 1 3 131 0 2 GTATAACA SWbb`b`b 1
-SL-XAQ 505091110 7 1 3 1311 0 2 GCACACGA [^a``_`a 1
-SL-XAQ 505091110 7 1 3 900 0 2 CTCCCAGG GGGM`_WT 0
-SL-XAQ 505091110 7 1 3 2027 0 2 AAGGATGT a]VL[YYB 1
-SL-XAQ 505091110 7 1 3 996 0 2 CCAGTTAG `_T\]b[B 1
-SL-XAQ 505091110 7 1 3 289 0 2 GTATAACA ]abbbba] 1
-SL-XAQ 505091110 7 1 3 33 0 2 GGTCCAGA PV\ZKF__ 0
-SL-XAQ 505091110 7 1 3 905 0 2 ACATCCTA ``VWN[YB 0
-SL-XAQ 505091110 7 1 3 1525 0 2 CATGCTTA aaaZaaaa 1
-SL-XAQ 505091110 7 1 3 583 0 2 CCAGTTAG \]XRZb`] 1
-SL-XAQ 505091110 7 1 3 2037 0 2 TCGGAATG ^[HY\_\_ 0
-SL-XAQ 505091110 7 1 3 1319 0 2 ACCAACTG ^^W_`]WY 0
-SL-XAQ 505091110 7 1 3 1513 0 2 CATAGCGA T_a\RV_a 1
-SL-XAQ 505091110 7 1 3 1188 0 2 GTATAACA aaababba 1
-SL-XAQ 505091110 7 1 3 673 0 2 TGCCCAAA G[BBBBBB 0
-SL-XAQ 505091110 7 1 3 471 0 2 GGTCCAGA [`\_a\^_ 1
-SL-XAQ 505091110 7 1 3 1328 0 2 TCGGAATG `__Q\^WR 0
-SL-XAQ 505091110 7 1 3 985 0 2 AACTTGAC aaaa_]_a 1
-SL-XAQ 505091110 7 1 3 176 0 2 CTACCAGG `aaa^`aa 1
-SL-XAQ 505091110 7 1 3 880 0 2 TTCGCTGA ]_UQZ`\\ 0
-SL-XAQ 505091110 7 1 3 695 0 2 TCGGAATG a^Zaaa\^ 1
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_2_0002_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_2_0002_qseq.txt
deleted file mode 100644
index 24936ef..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_7_2_0002_qseq.txt
+++ /dev/null
@@ -1,200 +0,0 @@
-SL-XAQ 505091110 7 2 0 135 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 1547 0 2 .....CA. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 87 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 205 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 50 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 1620 0 2 .....TG. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 1278 0 2 .....TA. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 186 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 287 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 441 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 766 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 1598 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 382 0 2 .....TA. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 740 0 2 .....GG. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 501 0 2 .....TA. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 1135 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 73 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 1668 0 2 .....CT. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 1198 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 7 2 0 1073 0 2 .....CA. BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1351 0 2 .....TT. BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1987 0 2 .....TA. BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1755 0 2 .....CA. BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1950 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 8 0 2 ...A.... BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 56 0 2 ...T.AGC BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 211 0 2 ...G.TGT BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 242 0 2 ...C.CGC BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 262 0 2 ...C.AGG BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 298 0 2 ...G.TAG BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 312 0 2 ...A.GTT BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 370 0 2 ...A.CAT BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 377 0 2 ...C.TCT BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 414 0 2 ...G.TTA BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 421 0 2 ...A.CCT BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 555 0 2 ...C.GAT BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 569 0 2 ...A.CTG BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 699 0 2 ...C.CGA BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 722 0 2 ...C.AGG BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 749 0 2 ...T.GAC BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 833 0 2 ...A.CCT BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 848 0 2 ...A.CGA BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 998 0 2 ...A.GTT BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1159 0 2 ...T.GAC BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1168 0 2 ...G.TAG BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1180 0 2 ...T.AGC BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1306 0 2 ...A.CTG BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1424 0 2 ...C.TCT BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1521 0 2 ...C.AGG BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1543 0 2 ...A.TTC BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1617 0 2 ...C.AGG BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1627 0 2 ...A.CTG BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1653 0 2 ...G.TGT BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1682 0 2 ...G.GCC BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1731 0 2 ...T.AGC BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1812 0 2 ...C.TAT BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1853 0 2 ...C.CGA BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1919 0 2 ...A.CTG BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 2006 0 2 ...G.GCC BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 64 0 2 ...A.GTT BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1646 0 2 ...T.GAC BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 37 0 2 ...G.CGA BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1515 0 2 ...G.ATG BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 466 0 2 ...T.ACA BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 558 0 2 ...A.CGA BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 714 0 2 ...AGCGA BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1933 0 2 ...TTAGC BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 628 0 2 ...TAACA BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 44 0 2 ...AGCGA BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 428 0 2 ...ATGTT BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1924 0 2 ...AACTG BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 234 0 2 ...GCTTA BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1004 0 2 ...GCCGA BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1214 0 2 ...CATGA BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1034 0 2 ...AGCCT BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1536 0 2 ..ACATCT BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 684 0 2 ..AAACGA BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 893 0 2 ..CAATTC BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 604 0 2 ..CAACTG BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 760 0 2 ..ACAACA BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1452 0 2 ..AGATCC BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1959 0 2 ..TGCTTA BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 1938 0 2 ..CTCGAC BBBBBBBB 1
-SL-XAQ 505091110 7 2 1 1221 0 2 ..GGATGT BBBBBBBB 0
-SL-XAQ 505091110 7 2 1 363 0 2 ..TATGTT DDMXXXXX 1
-SL-XAQ 505091110 7 2 1 170 0 2 ..GAGCCT BBBBBBBB 1
-SL-XAQ 505091110 7 2 2 463 0 2 C.TAGCGA YDXWMG]X 0
-SL-XAQ 505091110 7 2 2 1636 0 2 ATCAACCC RUW^BBBB 0
-SL-XAQ 505091110 7 2 2 828 0 2 TATATCGA BBBBBBBB 0
-SL-XAQ 505091110 7 2 2 220 0 2 TCGGAATG a`\\__^Z 1
-SL-XAQ 505091110 7 2 2 101 0 2 TACTTAGC aa\bbbb^ 1
-SL-XAQ 505091110 7 2 2 351 0 2 TGATAGAA BBBBBBBB 0
-SL-XAQ 505091110 7 2 2 1559 0 2 TTGAGCCT `_T__Sab 1
-SL-XAQ 505091110 7 2 2 1671 0 2 CCAGTTAG _]]aZa`X 0
-SL-XAQ 505091110 7 2 2 0 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 7 2 2 61 0 2 GTATAACA [`abaaXa 1
-SL-XAQ 505091110 7 2 2 1842 0 2 AAGGATGT _YPZRXa] 0
-SL-XAQ 505091110 7 2 2 12 0 2 TACTTAGC `WDX[\BB 0
-SL-XAQ 505091110 7 2 2 599 0 2 AGCAATTC YLWa`aa^ 0
-SL-XAQ 505091110 7 2 2 115 0 2 TGCTCGAC a`\]\__\ 0
-SL-XAQ 505091110 7 2 2 255 0 2 CCAGTTAG `[^b``_Z 1
-SL-XAQ 505091110 7 2 2 1298 0 2 ACCAACTG `V][[DZ[ 0
-SL-XAQ 505091110 7 2 2 775 0 2 TTCGCTGA abbU`aab 1
-SL-XAQ 505091110 7 2 2 131 0 2 CACAATCC ``bbab`_ 1
-SL-XAQ 505091110 7 2 2 904 0 2 ACCAACTG `^`aa^ZV 0
-SL-XAQ 505091110 7 2 2 1038 0 2 GGTCCAGA \V\^^a__ 0
-SL-XAQ 505091110 7 2 2 669 0 2 TTCGCTGA a]aa_aaX 0
-SL-XAQ 505091110 7 2 2 488 0 2 TTGAGCCT _]\__Z_` 1
-SL-XAQ 505091110 7 2 2 953 0 2 CAGGAACC TGYXZFZZ 0
-SL-XAQ 505091110 7 2 2 1723 0 2 CCAATTAG _`BBBBBB 0
-SL-XAQ 505091110 7 2 2 1944 0 2 AAGGATGT aaXaa`YB 1
-SL-XAQ 505091110 7 2 2 1567 0 2 GCACATCT _a\Z_a^_ 1
-SL-XAQ 505091110 7 2 2 679 0 2 CATGCTTA T^_^^W[_ 0
-SL-XAQ 505091110 7 2 2 1985 0 2 AAGGATGT ab^V]Q[W 0
-SL-XAQ 505091110 7 2 2 1402 0 2 CACATCCT \__a`aba 0
-SL-XAQ 505091110 7 2 2 1874 0 2 ACCAACTG a]]]^W_\ 1
-SL-XAQ 505091110 7 2 2 611 0 2 CATAGCGA W_bba\Z_ 0
-SL-XAQ 505091110 7 2 2 1974 0 2 AGCAATCT ]BBBBBBB 0
-SL-XAQ 505091110 7 2 2 1012 0 2 CACATCCT aa^a`aaa 1
-SL-XAQ 505091110 7 2 2 303 0 2 CAGGAGCC `]I__XBB 0
-SL-XAQ 505091110 7 2 2 1365 0 2 AACTTGAC ab`a]]`a 0
-SL-XAQ 505091110 7 2 2 184 0 2 GCACACGA ]Z[_`__R 0
-SL-XAQ 505091110 7 2 2 646 0 2 ATCAATTA GG]SNSOU 0
-SL-XAQ 505091110 7 2 2 1662 0 2 GTATAACA WQa`_``a 0
-SL-XAQ 505091110 7 2 2 1745 0 2 ACCAACTG a`]aa`aa 1
-SL-XAQ 505091110 7 2 3 1952 0 2 AAGGATGT aa^aa_a[ 1
-SL-XAQ 505091110 7 2 3 112 0 2 CCAGTTAG a_[b`b_U 1
-SL-XAQ 505091110 7 2 3 386 0 2 GGTCCAGA X__XX__X 0
-SL-XAQ 505091110 7 2 3 490 0 2 AAGGATGT ^BBBBBBB 0
-SL-XAQ 505091110 7 2 3 495 0 2 GCACACGA TZT[`_\Z 0
-SL-XAQ 505091110 7 2 3 577 0 2 ACCAACTG a^YS[`^^ 0
-SL-XAQ 505091110 7 2 3 695 0 2 TCTGGCGA ``^]X\_` 1
-SL-XAQ 505091110 7 2 3 808 0 2 AGCAATTC ]QTYX^BB 0
-SL-XAQ 505091110 7 2 3 862 0 2 TAACAAGA SH\UXH\_ 0
-SL-XAQ 505091110 7 2 3 889 0 2 ATTATGTT O`U\`[J` 0
-SL-XAQ 505091110 7 2 3 1025 0 2 GCACACGA _\`a`___ 1
-SL-XAQ 505091110 7 2 3 1053 0 2 GCACATCT U[^a^b_S 0
-SL-XAQ 505091110 7 2 3 1123 0 2 TTGAGCCT a_UVGM`` 0
-SL-XAQ 505091110 7 2 3 1209 0 2 AACTTGAC R^_^XQZa 1
-SL-XAQ 505091110 7 2 3 1290 0 2 GCACACGA HTZ\_[GZ 0
-SL-XAQ 505091110 7 2 3 1387 0 2 CCAGTTAG ZJaKQRQ` 0
-SL-XAQ 505091110 7 2 3 1529 0 2 TAGAACCT XH_VR^a\ 0
-SL-XAQ 505091110 7 2 3 1576 0 2 CCAGTTAG Ya^\b`b` 0
-SL-XAQ 505091110 7 2 3 1581 0 2 GTATAACA YS[a```b 0
-SL-XAQ 505091110 7 2 3 1733 0 2 GGTCCAGA N]aaa``\ 1
-SL-XAQ 505091110 7 2 3 1775 0 2 CATGCTTA Z[RX[Z__ 1
-SL-XAQ 505091110 7 2 3 1807 0 2 AACTTGAC a^S\a_][ 0
-SL-XAQ 505091110 7 2 3 1844 0 2 TACTTAGC a^ab]Y__ 0
-SL-XAQ 505091110 7 2 3 1898 0 2 CATAGCGA aaba_\a_ 0
-SL-XAQ 505091110 7 2 3 1917 0 2 GCACACGA NTZ_\ZaX 0
-SL-XAQ 505091110 7 2 3 1970 0 2 CTACCAGG a`aaa`a_ 1
-SL-XAQ 505091110 7 2 3 2004 0 2 TCTGGCGA _^]N]aaa 0
-SL-XAQ 505091110 7 2 3 2038 0 2 AACTTGAC a`_ZGP]a 0
-SL-XAQ 505091110 7 2 3 317 0 2 TGCTCGAC a``aa`[\ 1
-SL-XAQ 505091110 7 2 3 1941 0 2 AACTTGAC abaaaaaa 1
-SL-XAQ 505091110 7 2 3 157 0 2 AGCAATTC aaa^^ba` 1
-SL-XAQ 505091110 7 2 3 99 0 2 CAGGAGCG GPZ`ZBBB 0
-SL-XAQ 505091110 7 2 3 143 0 2 TGTCGGAT `]`a^^\a 1
-SL-XAQ 505091110 7 2 3 328 0 2 CAAATCCT R[HHY[G[ 0
-SL-XAQ 505091110 7 2 3 932 0 2 CATGCTTA \b_``bba 1
-SL-XAQ 505091110 7 2 3 1484 0 2 CCAGTTAG ]a```b_[ 1
-SL-XAQ 505091110 7 2 3 875 0 2 CCTACCAT Z\___W_a 0
-SL-XAQ 505091110 7 2 3 1016 0 2 CATAGCGA ]_b__P_b 1
-SL-XAQ 505091110 7 2 3 198 0 2 CAGGATCT THOI_VWQ 0
-SL-XAQ 505091110 7 2 3 470 0 2 AAGGATGT a_UYY\aY 1
-SL-XAQ 505091110 7 2 3 1094 0 2 CACATCCT `abab]Ya 1
-SL-XAQ 505091110 7 2 3 782 0 2 TTGAGCCT a```[Za^ 1
-SL-XAQ 505091110 7 2 3 991 0 2 AGCAATTC aa`a_aa[ 1
-SL-XAQ 505091110 7 2 3 1962 0 2 AGTTGCTT `VU_W\O\ 1
-SL-XAQ 505091110 7 2 3 1101 0 2 TTGAGCCT V_TV[IT\ 1
-SL-XAQ 505091110 7 2 3 207 0 2 ACCAACTG a`ZU_^^_ 1
-SL-XAQ 505091110 7 2 3 1326 0 2 AACTTGAC abaaaRaa 0
-SL-XAQ 505091110 7 2 3 728 0 2 TACTTAGC aab`]aVB 0
-SL-XAQ 505091110 7 2 3 691 0 2 AGTTGCTT _\W_]_^` 1
-SL-XAQ 505091110 7 2 3 1352 0 2 GGTCCAGA OH[OZ___ 1
-SL-XAQ 505091110 7 2 3 1389 0 2 TGTCGGAT ^Q`b`_a[ 1
-SL-XAQ 505091110 7 2 3 987 0 2 TCTCGCGA O[GMGZP_ 0
-SL-XAQ 505091110 7 2 3 1133 0 2 AGCAATTC ^^X_T`aZ 1
-SL-XAQ 505091110 7 2 3 399 0 2 CATAGCGA \aa_\\`_ 1
-SL-XAQ 505091110 7 2 3 16 0 2 CACATCCT [[S__\F_ 1
-SL-XAQ 505091110 7 2 3 2013 0 2 CATAGCGA Vaba[_^[ 0
-SL-XAQ 505091110 7 2 3 898 0 2 TGTCGGAT ]W]`_\[_ 1
-SL-XAQ 505091110 7 2 3 1712 0 2 CACATCCT aa]__^\] 1
-SL-XAQ 505091110 7 2 3 179 0 2 GTTTATTA BBBBBBBB 0
-SL-XAQ 505091110 7 2 3 151 0 2 CAGGAGCC _`WNZ`\\ 1
-SL-XAQ 505091110 7 2 3 983 0 2 CATAGCGA `bbb_^`^ 1
-SL-XAQ 505091110 7 2 3 567 0 2 TCGGAATG _^_^`a_[ 1
-SL-XAQ 505091110 7 2 3 72 0 2 AGTTGCTT abab`]aa 1
-SL-XAQ 505091110 7 2 3 922 0 2 TCGGAATG a`[`ab^Z 1
-SL-XAQ 505091110 7 2 3 584 0 2 CATGCTTA ]`^^[bbb 1
-SL-XAQ 505091110 7 2 3 274 0 2 AGTTGCTT __^^[^ab 1
-SL-XAQ 505091110 7 2 3 1602 0 2 AGCAATTC ^U[`_a]W 1
-SL-XAQ 505091110 7 2 3 4 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 7 2 3 663 0 2 TCGGAATG \[QR[b\W 0
-SL-XAQ 505091110 7 2 3 80 0 2 TACTTAGC a_X`a`_W 1
-SL-XAQ 505091110 7 2 3 1179 0 2 CCAGTTAG HZZX__ZB 0
-SL-XAQ 505091110 7 2 3 589 0 2 AAGGATGT ^aaXaa_X 1
-SL-XAQ 505091110 7 2 3 640 0 2 AGTTGCTT `\aaaZ[` 1
-SL-XAQ 505091110 7 2 3 2030 0 2 GATCAAGA GGG]G[_[ 0
-SL-XAQ 505091110 7 2 3 247 0 2 CGGTAGCT BBBBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_8_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_8_1_0001_qseq.txt
deleted file mode 100644
index 1cf09df..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_8_1_0001_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 8 1 1793 1420 0 1 G... \DDD 0
-SL-XBA 1 8 1 1793 1441 0 1 C... GDDD 0
-SL-XBA 1 8 1 1793 1483 0 1 G... YDDD 0
-SL-XBA 1 8 1 1793 1495 0 1 G... VDDD 0
-SL-XBA 1 8 1 1793 1527 0 1 G... MDDD 0
-SL-XBA 1 8 1 1793 1545 0 1 C... HDDD 0
-SL-XBA 1 8 1 1793 1583 0 1 G... YDDD 0
-SL-XBA 1 8 1 1793 1596 0 1 G... TDDD 0
-SL-XBA 1 8 1 1793 1658 0 1 C... GDDD 0
-SL-XBA 1 8 1 1793 1718 0 1 G... YDDD 0
-SL-XBA 1 8 1 1793 1745 0 1 C... PDDD 0
-SL-XBA 1 8 1 1793 1777 0 1 G... YDDD 0
-SL-XBA 1 8 1 1793 1813 0 1 G... VDDD 0
-SL-XBA 1 8 1 1793 1916 0 1 G... [DDD 0
-SL-XBA 1 8 1 1793 1959 0 1 G... [DDD 0
-SL-XBA 1 8 1 1793 808 0 1 T... YDDD 0
-SL-XBA 1 8 1 1793 602 0 1 T... [DDD 0
-SL-XBA 1 8 1 1793 1602 0 1 C... [DDD 0
-SL-XBA 1 8 1 1793 1681 0 1 C... ^DDD 0
-SL-XBA 1 8 1 1793 1011 0 1 A... GDDD 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_8_2_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_8_2_0001_qseq.txt
deleted file mode 100644
index 79498d7..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_8_2_0001_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 8 1 1793 1420 0 2 C... ^DDD 0
-SL-XBA 1 8 1 1793 1441 0 2 C... [DDD 0
-SL-XBA 1 8 1 1793 1483 0 2 G... [DDD 0
-SL-XBA 1 8 1 1793 1495 0 2 A... HDDD 0
-SL-XBA 1 8 1 1793 1527 0 2 C... YDDD 0
-SL-XBA 1 8 1 1793 1545 0 2 C... TDDD 0
-SL-XBA 1 8 1 1793 1583 0 2 C... [DDD 0
-SL-XBA 1 8 1 1793 1596 0 2 C... [DDD 0
-SL-XBA 1 8 1 1793 1658 0 2 T... YDDD 0
-SL-XBA 1 8 1 1793 1718 0 2 A... GDDD 0
-SL-XBA 1 8 1 1793 1745 0 2 A... GDDD 0
-SL-XBA 1 8 1 1793 1777 0 2 A... HDDD 0
-SL-XBA 1 8 1 1793 1813 0 2 C... [DDD 0
-SL-XBA 1 8 1 1793 1916 0 2 C... GDDD 0
-SL-XBA 1 8 1 1793 1959 0 2 A... PDDD 0
-SL-XBA 1 8 1 1793 808 0 2 C... [DDD 0
-SL-XBA 1 8 1 1793 602 0 2 C... ^DDD 0
-SL-XBA 1 8 1 1793 1602 0 2 C... ZDDD 0
-SL-XBA 1 8 1 1793 1681 0 2 A... HDDD 0
-SL-XBA 1 8 1 1793 1011 0 2 A... RDDD 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_0001_barcode.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_0001_barcode.txt
deleted file mode 100644
index addca9d..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_0001_barcode.txt
+++ /dev/null
@@ -1,200 +0,0 @@
-................ N
-................ N
-................ N
-................ N
-................ N
-................ N
-.....G.......... N
-.....C.......C.. N
-.....C.......... N
-.....A.......... N
-.....G.......G.. N
-.....GT......... N
-.....CG......... N
-.....TA......... N
-.....GT......GT. N
-.....CC......C.. N
-.....AT......... N
-.....GA......... N
-.....TG......... N
-.....GT......... N
-.....CC......... N
-.....GT......GT. N
-.....CT......... N
-.....AC......AC. N
-.....CT......CT. N
-.....GA......GA. N
-................ N
-.....CA......C.. N
-.....TG......TG. N
-.....AC......... N
-.....GA......... N
-.....AC......A.. N
-.....CG......... N
-.....TG......T.. N
-.....CA......... N
-.....CA......... N
-.....TT......... N
-.....AC......AC. N
-.....GT......GT. N
-.....CG......... N
-.....GA......... N
-.....CA......C.. N
-.....CG......CG. N
-.....CG......... N
-.....AG......A.. N
-.....GA......... N
-.....TA......TA. N
-.....TG......... N
-.....GA......... N
-.....CT......C.. N
-.....TA......TA. N
-.....CC......... N
-.....AG......... N
-.....AG......... N
-.....GA......GA. N
-.....GA......GA. N
-.....GT......... N
-.....CA......C.. N
-.....CG......... N
-.....GA......... N
-.....CT......... N
-.....AG......... N
-.....CT......C.. N
-.....CC......C.. N
-.....CG......... N
-.....AG......... N
-.....CG......... N
-.....GA......GA. N
-.....TC......... N
-.....CG......... N
-.....CC......C.. N
-.....AC......A.. N
-.....CG......... N
-.....CC......CC. N
-.....CGA........ N
-...T.GAC...T.... N
-...C.GAT........ N
-...G.TAG........ N
-...G.TTA...G.... N
-...G.TTA........ N
-...C.AGA.....AG. N
-...T.TAA...T.... N
-...C.CGA...C.... N
-...T.GAC........ N
-...G.GCC...G.... N
-...C.AGA...C.... N
-...C.GAT...C.... N
-...T.CTT........ N
-...T.GAC...T.... N
-...G.TGT...G.... N
-...T.AGC........ N
-...A.TTC........ N
-...T.GAC...T.... N
-...A.CCT...A.... N
-...A.GTT.....G.. N
-...T.CTT...T.... N
-...T.GAC.....G.. N
-...A.CTG...A.... N
-...GATGT...G.... N
-...CCAGG........ N
-...GATGA...G.... N
-...TCGAC........ N
-...TAACA...TA... N
-...GAGCC...GA... N
-..ACCAGG...CC... N
-..TATGTT...AT... N
-..ACATCT....AT.. N
-..CATTTC...AT... N
-..TGGCGA...GG... N
-..ACCAGG........ N
-..GGAGCC....AG.. N
-..CTTAGC....TA.. N
-..TGCTTA........ N
-..CTAAGC.....AG. N
-..CAACTG....AC.. N
-.TCGCTGAAAGGATGT Y TTCGCTGAAAGGATGT
-.AGGATGTTTCGCTGA Y AAGGATGTTTCGCTGA
-CAGGAGCCGTATAACA Y CAGGAGCCGTATAACA
-AGCAATTCTGCTCGAC Y AGCAATTCTGCTCGAC
-CATAGCGAGGTCCAGA Y CATAGCGAGGTCCAGA
-AAGGATGTTTCGCTGA Y AAGGATGTTTCGCTGA
-CATAGCGAGGTCCAGA Y CATAGCGAGGTCCAGA
-TGCTCGACAGCAATTC Y TGCTCGACAGCAATTC
-TACTTAGCCACATCCT Y TACTTAGCCACATCCT
-TTCGCTGAAAGGATGT Y TTCGCTGAAAGGATGT
-TACTTAGCCACATCCT Y TACTTAGCCACATCCT
-CAGGAGCCGTATAACA Y CAGGAGCCGTATAACA
-CACATCCTTACTTAGC Y CACATCCTTACTTAGC
-AGCAATTCTGCTCGAC Y AGCAATTCTGCTCGAC
-TGTCGGATACCAACTG Y TGTCGGATACCAACTG
-AACTTGACTTGAGCCT Y AACTTGACTTGAGCCT
-CAGGAGCCGTATAACA Y CAGGAGCCGTATAACA
-CATAGCGAGGTCCAGA Y CATAGCGAGGTCCAGA
-CTACCAGGCCTACCAT Y CTACCAGGCCTACCAT
-CAGGAGCCGTATAACA Y CAGGAGCCGTATAACA
-GTATAACTCAGGAGCC Y GTATAACACAGGAGCC
-GTATAAGACAGGAGCC Y GTATAACACAGGAGCC
-CCTACCATCTACCAGG Y CCTACCATCTACCAGG
-GTATAACACAGGAGCC Y GTATAACACAGGAGCC
-ACCAACTGTGTCGGAT Y ACCAACTGTGTCGGAT
-TCTGGCGAAGTTGCTT Y TCTGGCGAAGTTGCTT
-AGTTGCTTTCTGGCGA Y AGTTGCTTTCTGGCGA
-GCACATCTCATGCTTA Y GCACATCTCATGCTTA
-CACATCCTTACTTAGC Y CACATCCTTACTTAGC
-AAGGATGTTTCGCTGA Y AAGGATGTTTCGCTGA
-CATAGCGAGGTCCAGA Y CATAGCGAGGTCCAGA
-GCACACGACCAGTTAG Y GCACACGACCAGTTAG
-ATTATGTTTCGGAATG Y ATTATGTTTCGGAATG
-AATCATGT....AT.. N
-AAGGATGTTTCGCTGA Y AAGGATGTTTCGCTGA
-AGTTGCTTTCTGGCGA Y AGTTGCTTTCTGGCGA
-GCACACGACCAGTTAG Y GCACACGACCAGTTAG
-TTGAGCCTAACTTGAC Y TTGAGCCTAACTTGAC
-CCAACAGG...AC... N
-TGCTCGACAGCAATTC Y TGCTCGACAGCAATTC
-CTACAAGGCCTACCAT Y CTACCAGGCCTACCAT
-AACTTGACTTGAGCCT Y AACTTGACTTGAGCCT
-TACTTAGCCACATCCT Y TACTTAGCCACATCCT
-CCAGTTAGGCACACGA Y CCAGTTAGGCACACGA
-TCTGGCGAAGTTGCTT Y TCTGGCGAAGTTGCTT
-AAGGATGTTTCGCTGA Y AAGGATGTTTCGCTGA
-GTATAACACAGGAGCC Y GTATAACACAGGAGCC
-TGCTCGACAGCAATTC Y TGCTCGACAGCAATTC
-CTACCAGGCCTACCAT Y CTACCAGGCCTACCAT
-CAGGAGCCGTATAACA Y CAGGAGCCGTATAACA
-AACTTGACTTGAGCCT Y AACTTGACTTGAGCCT
-CACATCCTTACTTAGC Y CACATCCTTACTTAGC
-ACTACCTT.....CT. N
-AACTTGACTTGAGCCT Y AACTTGACTTGAGCCT
-AACTTGACTTGAGCCT Y AACTTGACTTGAGCCT
-AACTTGACTTGAGCCT Y AACTTGACTTGAGCCT
-GTCACCAT..CA.... N
-ACACAAGA.....AG. N
-GCACACGACCAGTTAG Y GCACACGACCAGTTAG
-ACCAACTGTGTCGGAT Y ACCAACTGTGTCGGAT
-TCACAATGTC...... N
-ATTATGTTTCGGAATG Y ATTATGTTTCGGAATG
-AGATGCTTTCTGGCGA Y AGTTGCTTTCTGGCGA
-GATCCAGACATAGCGA Y GGTCCAGACATAGCGA
-GTATAACACAGGAGCC Y GTATAACACAGGAGCC
-GCACACGACCAGTTAG Y GCACACGACCAGTTAG
-CTCCCAGGCCTACCAT Y CTACCAGGCCTACCAT
-AAGGATGTTTCGCTGA Y AAGGATGTTTCGCTGA
-CCAGTTAGGCACACGA Y CCAGTTAGGCACACGA
-GTATAACACAGGAGCC Y GTATAACACAGGAGCC
-GGTCCAGACATAGCGA Y GGTCCAGACATAGCGA
-ACATCCTAAC...... N
-CATGCTTAGCACATCT Y CATGCTTAGCACATCT
-CCAGTTAGGCACACGA Y CCAGTTAGGCACACGA
-TCGGAATGATTATGTT Y TCGGAATGATTATGTT
-ACCAACTGTGTCGGAT Y ACCAACTGTGTCGGAT
-CATAGCGAGGTCCAGA Y CATAGCGAGGTCCAGA
-GTATAACACAGGAGCC Y GTATAACACAGGAGCC
-TGCCCAAA...CC... N
-GGTCCAGACATAGCGA Y GGTCCAGACATAGCGA
-TCGGAATGATTATGTT Y TCGGAATGATTATGTT
-AACTTGACTTGAGCCT Y AACTTGACTTGAGCCT
-CTACCAGGCCTACCAT Y CTACCAGGCCTACCAT
-TTCGCTGAAAGGATGT Y TTCGCTGAAAGGATGT
-TCGGAATGATTATGTT Y TCGGAATGATTATGTT
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_0002_barcode.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_0002_barcode.txt
deleted file mode 100644
index 7e7d7ab..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_0002_barcode.txt
+++ /dev/null
@@ -1,200 +0,0 @@
-.....CG......C.. N
-.....CA......... N
-.....CG......... N
-.....AG......... N
-.....GA......... N
-.....TG......... N
-.....TA......... N
-.....CC......... N
-.....GA......... N
-.....AG......AG. N
-.....CC......CC. N
-.....AG......... N
-.....TA......T.. N
-.....GG......... N
-.....TA......... N
-.....AG......... N
-.....CG......C.. N
-.....CT......... N
-.....CC......CC. N
-.....CA......... N
-.....TT......T.. N
-.....TA......... N
-.....CA......... N
-.....GT......... N
-...A............ N
-...T.AGC.....A.. N
-...G.TGT.....TG. N
-...C.CGC...C.... N
-...C.AGG...C.... N
-...G.TAG...G.... N
-...A.GTT........ N
-...A.CAT...A.... N
-...C.TCT.....T.. N
-...G.TTA...G.... N
-...A.CCT...A.... N
-...C.GAT...C.... N
-...A.CTG........ N
-...C.CGA...C.... N
-...C.AGG........ N
-...T.GAC.....G.. N
-...A.CCT.....CC. N
-...A.CGA...A.... N
-...A.GTT.....G.. N
-...T.GAC...T.... N
-...G.TAG........ N
-...T.AGC.....AG. N
-...A.CTG.....C.. N
-...C.TCT...C.... N
-...C.AGG........ N
-...A.TTC...A.... N
-...C.AGG........ N
-...A.CTG...A.... N
-...G.TGT........ N
-...G.GCC.....G.. N
-...T.AGC.....AG. N
-...C.TAT...C.... N
-...C.CGA........ N
-...A.CTG...A.... N
-...G.GCC........ N
-...A.GTT.....GT. N
-...T.GAC...T.... N
-...G.CGA...G.... N
-...G.ATG.....A.. N
-...T.ACA...T.... N
-...A.CGA........ N
-...AGCGA........ N
-...TTAGC...T.... N
-...TAACA........ N
-...AGCGA...AG... N
-...ATGTT...A.... N
-...AACTG...AA... N
-...GCTTA....CT.. N
-...GCCGA.....CG. N
-...CATGA........ N
-...AGCCT........ N
-..ACATCT..A..... N
-..AAACGA..AA.... N
-..CAATTC...AA... N
-..CAACTG..C..... N
-..ACAACA....AA.. N
-..AGATCC....AT.. N
-..TGCTTA....CT.. N
-..CTCGAC..CT.... N
-..GGATGT.....TG. N
-..TATGTT..T..... N
-..GAGCCT...AG... N
-C.TAGCGAGGTCCAGA Y CATAGCGAGGTCCAGA
-ATCAACCC...AA... N
-TATATCGA.....CG. N
-TCGGAATGATTATGTT Y TCGGAATGATTATGTT
-TACTTAGCCACATCCT Y TACTTAGCCACATCCT
-TGATAGAA.....GA. N
-TTGAGCCTAACTTGAC Y TTGAGCCTAACTTGAC
-CCAGTTAGGCACACGA Y CCAGTTAGGCACACGA
-................ N
-GTATAACACAGGAGCC Y GTATAACACAGGAGCC
-AAGGATGTTTCGCTGA Y AAGGATGTTTCGCTGA
-TACTTAGCCACATCCT Y TACTTAGCCACATCCT
-AGCAATTCTGCTCGAC Y AGCAATTCTGCTCGAC
-TGCTCGACAGCAATTC Y TGCTCGACAGCAATTC
-CCAGTTAGGCACACGA Y CCAGTTAGGCACACGA
-ACCAACTGTGTCGGAT Y ACCAACTGTGTCGGAT
-TTCGCTGAAAGGATGT Y TTCGCTGAAAGGATGT
-CACAATCC...AA... N
-ACCAACTGTGTCGGAT Y ACCAACTGTGTCGGAT
-GGTCCAGACATAGCGA Y GGTCCAGACATAGCGA
-TTCGCTGAAAGGATGT Y TTCGCTGAAAGGATGT
-TTGAGCCTAACTTGAC Y TTGAGCCTAACTTGAC
-CAGGAACCGTATAACA Y CAGGAGCCGTATAACA
-CCAATTAGGCACACGA Y CCAGTTAGGCACACGA
-AAGGATGTTTCGCTGA Y AAGGATGTTTCGCTGA
-GCACATCTCATGCTTA Y GCACATCTCATGCTTA
-CATGCTTAGCACATCT Y CATGCTTAGCACATCT
-AAGGATGTTTCGCTGA Y AAGGATGTTTCGCTGA
-CACATCCTTACTTAGC Y CACATCCTTACTTAGC
-ACCAACTGTGTCGGAT Y ACCAACTGTGTCGGAT
-CATAGCGAGGTCCAGA Y CATAGCGAGGTCCAGA
-AGCAATCT.GC..... N
-CACATCCTTACTTAGC Y CACATCCTTACTTAGC
-CAGGAGCCGTATAACA Y CAGGAGCCGTATAACA
-AACTTGACTTGAGCCT Y AACTTGACTTGAGCCT
-GCACACGACCAGTTAG Y GCACACGACCAGTTAG
-ATCAATTA.TC..... N
-GTATAACACAGGAGCC Y GTATAACACAGGAGCC
-ACCAACTGTGTCGGAT Y ACCAACTGTGTCGGAT
-AAGGATGTTTCGCTGA Y AAGGATGTTTCGCTGA
-CCAGTTAGGCACACGA Y CCAGTTAGGCACACGA
-GGTCCAGACATAGCGA Y GGTCCAGACATAGCGA
-AAGGATGTTTCGCTGA Y AAGGATGTTTCGCTGA
-GCACACGACCAGTTAG Y GCACACGACCAGTTAG
-ACCAACTGTGTCGGAT Y ACCAACTGTGTCGGAT
-TCTGGCGAAGTTGCTT Y TCTGGCGAAGTTGCTT
-AGCAATTCTGCTCGAC Y AGCAATTCTGCTCGAC
-TAACAAGATA...... N
-ATTATGTTTCGGAATG Y ATTATGTTTCGGAATG
-GCACACGACCAGTTAG Y GCACACGACCAGTTAG
-GCACATCTCATGCTTA Y GCACATCTCATGCTTA
-TTGAGCCTAACTTGAC Y TTGAGCCTAACTTGAC
-AACTTGACTTGAGCCT Y AACTTGACTTGAGCCT
-GCACACGACCAGTTAG Y GCACACGACCAGTTAG
-CCAGTTAGGCACACGA Y CCAGTTAGGCACACGA
-TAGAACCT.AG..... N
-CCAGTTAGGCACACGA Y CCAGTTAGGCACACGA
-GTATAACACAGGAGCC Y GTATAACACAGGAGCC
-GGTCCAGACATAGCGA Y GGTCCAGACATAGCGA
-CATGCTTAGCACATCT Y CATGCTTAGCACATCT
-AACTTGACTTGAGCCT Y AACTTGACTTGAGCCT
-TACTTAGCCACATCCT Y TACTTAGCCACATCCT
-CATAGCGAGGTCCAGA Y CATAGCGAGGTCCAGA
-GCACACGACCAGTTAG Y GCACACGACCAGTTAG
-CTACCAGGCCTACCAT Y CTACCAGGCCTACCAT
-TCTGGCGAAGTTGCTT Y TCTGGCGAAGTTGCTT
-AACTTGACTTGAGCCT Y AACTTGACTTGAGCCT
-TGCTCGACAGCAATTC Y TGCTCGACAGCAATTC
-AACTTGACTTGAGCCT Y AACTTGACTTGAGCCT
-AGCAATTCTGCTCGAC Y AGCAATTCTGCTCGAC
-CAGGAGCGGTATAACA Y CAGGAGCCGTATAACA
-TGTCGGATACCAACTG Y TGTCGGATACCAACTG
-CAAATCCTTACTTAGC Y CACATCCTTACTTAGC
-CATGCTTAGCACATCT Y CATGCTTAGCACATCT
-CCAGTTAGGCACACGA Y CCAGTTAGGCACACGA
-CCTACCATCTACCAGG Y CCTACCATCTACCAGG
-CATAGCGAGGTCCAGA Y CATAGCGAGGTCCAGA
-CAGGATCT.....TC. N
-AAGGATGTTTCGCTGA Y AAGGATGTTTCGCTGA
-CACATCCTTACTTAGC Y CACATCCTTACTTAGC
-TTGAGCCTAACTTGAC Y TTGAGCCTAACTTGAC
-AGCAATTCTGCTCGAC Y AGCAATTCTGCTCGAC
-AGTTGCTTTCTGGCGA Y AGTTGCTTTCTGGCGA
-TTGAGCCTAACTTGAC Y TTGAGCCTAACTTGAC
-ACCAACTGTGTCGGAT Y ACCAACTGTGTCGGAT
-AACTTGACTTGAGCCT Y AACTTGACTTGAGCCT
-TACTTAGCCACATCCT Y TACTTAGCCACATCCT
-AGTTGCTTTCTGGCGA Y AGTTGCTTTCTGGCGA
-GGTCCAGACATAGCGA Y GGTCCAGACATAGCGA
-TGTCGGATACCAACTG Y TGTCGGATACCAACTG
-TCTCGCGAAGTTGCTT Y TCTGGCGAAGTTGCTT
-AGCAATTCTGCTCGAC Y AGCAATTCTGCTCGAC
-CATAGCGAGGTCCAGA Y CATAGCGAGGTCCAGA
-CACATCCTTACTTAGC Y CACATCCTTACTTAGC
-CATAGCGAGGTCCAGA Y CATAGCGAGGTCCAGA
-TGTCGGATACCAACTG Y TGTCGGATACCAACTG
-CACATCCTTACTTAGC Y CACATCCTTACTTAGC
-GTTTATTA...TA... N
-CAGGAGCCGTATAACA Y CAGGAGCCGTATAACA
-CATAGCGAGGTCCAGA Y CATAGCGAGGTCCAGA
-TCGGAATGATTATGTT Y TCGGAATGATTATGTT
-AGTTGCTTTCTGGCGA Y AGTTGCTTTCTGGCGA
-TCGGAATGATTATGTT Y TCGGAATGATTATGTT
-CATGCTTAGCACATCT Y CATGCTTAGCACATCT
-AGTTGCTTTCTGGCGA Y AGTTGCTTTCTGGCGA
-AGCAATTCTGCTCGAC Y AGCAATTCTGCTCGAC
-................ N
-TCGGAATGATTATGTT Y TCGGAATGATTATGTT
-TACTTAGCCACATCCT Y TACTTAGCCACATCCT
-CCAGTTAGGCACACGA Y CCAGTTAGGCACACGA
-AAGGATGTTTCGCTGA Y AAGGATGTTTCGCTGA
-AGTTGCTTTCTGGCGA Y AGTTGCTTTCTGGCGA
-GATCAAGA...CA... N
-CGGTAGCTCG...... N
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_1_0001_qseq.txt
deleted file mode 100644
index 1073f1e..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_1_0001_qseq.txt
+++ /dev/null
@@ -1,200 +0,0 @@
-SL-XAQ 505091110 9 1 0 1434 0 1 .............................. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 464 0 1 .............................. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 113 0 1 ........G...........A......... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1703 0 1 ........A...........A......... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 879 0 1 ........T...........T......... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 841 0 1 ........C...........T......... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1291 0 1 ........A........A..T......... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1940 0 1 ........C........T..T......... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 586 0 1 ........C........C..C...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1690 0 1 ........A........G..C...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 37 0 1 ........A........C..T...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 324 0 1 ........T........T..A...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 205 0 1 ........A........A..T...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1307 0 1 ........C....A...T..T...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1193 0 1 ........T....T...T..T...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1475 0 1 .....G..A....A...A..A...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 275 0 1 .....A..CA...T...G.CC...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 2001 0 1 .....A..TG...G...A.GC...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1093 0 1 .....C..GT...A...G.AA...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1038 0 1 .....C..CA...C...C.CC...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 173 0 1 .....A..AT...T...C.TT...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1836 0 1 .....G..TA...G...T.CT...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1513 0 1 .....A..TT...A...A.AA...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1917 0 1 .....T..GA...C...A.AA...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1696 0 1 ..A..G..GC...G...A.AC...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 812 0 1 ..A..C.AAG...T...A.TC...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 2 0 1 ..A..G.GAA...C................ BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1555 0 1 ..T..G.AGA...A...C.TA...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1243 0 1 ..A..A.GGA...A...C.TA...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 30 0 1 ..A..A.TTT...T...G.TC...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 41 0 1 ..A..C.AAA...G...T.CA...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 59 0 1 ..A..G.TGC...T...T.AC...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 111 0 1 ..C..T.GCG...T...A.CT...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 132 0 1 ..A..G.GGG...G...G.GG...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 140 0 1 ..A..T.TAA...G...C.TT...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 155 0 1 ..G..C.AGT...C...A.TT...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 164 0 1 ..A..A.TAA...T...T.AT...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 170 0 1 ..T..C.CAC...G...G.TC...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 184 0 1 ..C..T.TAA...A...T.AT...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 195 0 1 ..A..G.GTG...G...C.AT...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 240 0 1 ..G..A.GTA...T...T.CC...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 262 0 1 ..C..G.CAT...A...C.TG...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 299 0 1 ..C..T.GCA...A...C.AA...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 353 0 1 ..A..T.TAG...A...T.AT...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 367 0 1 ..A..T.AGC...G...A.GT...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 416 0 1 ..A..C.AAT...G...G.AC...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 483 0 1 ..G..G.GGG...G...G.TT...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 486 0 1 ..A..A.TTT...A...A.AG...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 495 0 1 ..C..A.CGT...T...T.AA...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 508 0 1 ..G..C.CAG...T...C.CT...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 554 0 1 ..A..G.AGA...G...T.TC...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 567 0 1 ..C..C.GTT...C...G.AC...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 613 0 1 ..G..A.TAT...C...G.AT...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 622 0 1 ..T..C.AGT...C...A.CT...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 627 0 1 ..A..T.GAC...T...A.GC...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 684 0 1 ..T..T.AGA...C...A.AG...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 874 0 1 ..A..A.GCC...G...T.TA...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 931 0 1 ..T..G.GAT...G...C.TT...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 994 0 1 ..A..T.GAT...T...G.TT...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1013 0 1 ..C..T.CAG...C...A.GT...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1153 0 1 ..T..T.TGG...T...C.TC...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1184 0 1 ..A..G.TCG...A...T.CA...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1241 0 1 ..A..G.TGG...T...C.TG...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1282 0 1 ..A..A.GGG...T...G.AG...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1320 0 1 ..A..T.AGT...G...G.TA...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1391 0 1 ..G..T.TAA...A...T.AT...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1684 0 1 ..G..A.GGT...G...T.TC...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1733 0 1 ..A..G.GTC...T...T.AG...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1770 0 1 ..C..T.CTG...G...G.CA...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1906 0 1 ..T..C.ATA...C...T.CT...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1954 0 1 .AGA.T.CTT...G...G.AG...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1247 0 1 .CCAGC.TTT...T...T.CT...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 18 0 1 .ATCAG.CTG...A...T.GT..AA..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1521 0 1 .AACAA.ATT...T...A.TA..TA..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 264 0 1 .AACTG.AAT...C...A.CA..CT..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1815 0 1 .ATGAAAATA...T...TAAAT.AT..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1379 0 1 .AATATAATT...T...TTAGA.TT..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 2011 0 1 .ACAGCTGGCA..T...AGAGC.AG.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1372 0 1 .ACATTTTTTAG.T.A.TTGTT.AC.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 55 0 1 .TTTATGTCCTT.A.AACTTAG.AGTT... DNX[[WRTXXBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 517 0 1 .TCATAAAACATCA.TATTGGAAAGGA... DMVTY[XXXTVWBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 965 0 1 .ACTAATCTTCCGC.CATATCCCCAAA... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 535 0 1 .GCCCAAGTATTGA.TATGTGCTCTAA... DMTXXYVPWVYXSODOYYTQTXXBBBBBBB 0
-SL-XAQ 505091110 9 1 1 72 0 1 .ACACACATATCAC.CACATCATACAC... DMMSWUXUZTYUZMDHSXZZZXBBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1886 0 1 .ACATATGCATACATATATAATAGATA... DMXYZ[QPVZYXXXZ[ZZ[[[ZZBBBBBBB 1
-SL-XAQ 505091110 9 1 2 1932 0 1 .AGCGATCCTCCCGCCTCTGCCTCCCA... DKPTSTTSPSTTBBBBBBBBBBBBBBBBBB 1
-SL-XAQ 505091110 9 1 2 1706 0 1 .GATATGTGGATACAGCTCACAAAGAG... DKXXYUNTUUXXXNVBBBBBBBBBBBBBBB 1
-SL-XAQ 505091110 9 1 2 363 0 1 .ATATTCTTTTTTTTTATTTATCAGAT... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 605 0 1 .GCATTGAGCAGACGTGGCATCCAGAT... DHOWTQQQNTTSTRBBBBBBBBBBBBBBBB 1
-SL-XAQ 505091110 9 1 2 449 0 1 .ATTCTAATTCTAGGAAATTAACAATC... DMXRPT[XRUXVODOBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1782 0 1 .ACCAAGTGTTTGGAGTATGCTGCCTA... DOYYYUUWWWTLTRRTNWTBBBBBBBBBBB 1
-SL-XAQ 505091110 9 1 2 246 0 1 .GGAGGTTTCATTTAGCCGATATTGTG... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 307 0 1 .GGATGAACAGAAACTAAAATAACACA... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 150 0 1 .AAGACTTGATTATATCCCTTGTATGA... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 546 0 1 .GGTTGTGTCTCTCTCAGCCTTTGGGATC. DKSUWWWSSSUWTLRTBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1727 0 1 .TATTGAAGGACTTTTGTATCCTCCTTAT. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1946 0 1 .ATCTTCTGGAATTTCTAACAGCTTGGAA. DOTPTMKMRT[XXVBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1275 0 1 .AGTGAAATAAGCCAGACACAGAAAGACA. DNTQOSYXXXVPVVRKSSVTTLRXVPVBBB 1
-SL-XAQ 505091110 9 1 2 786 0 1 .TAAACAATAATCTGATGATTTATAATCC. DOX[[[[Z[Z[W[XZ[X[Z[YY[[YYBBBB 1
-SL-XAQ 505091110 9 1 2 747 0 1 .AACAACAGCGGAAAATAATAAAAAAAAA. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 25 0 1 .GCTTTGGCAAGACAAATCTCCCGTCTGG. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1722 0 1 .AAAGAAAATTAAAGAAAAATATACACGT. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1301 0 1 .AGTAGACTGCATTAATTAATTGGAAGAG. DORVOHOQSQURPSSYSWZZBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1592 0 1 .GAAAACTGGCACAAGACAAGGATGCCCTC DKUVVWUWUPKRSUUGWSWTWUWUSWTWRB 1
-SL-XAQ 505091110 9 1 2 943 0 1 .AATACCAATAAACCTAGAATGTCTCATAC DOW[XUSU[URVWVSSVVSYPOOTVXX[SB 1
-SL-XAQ 505091110 9 1 2 974 0 1 .GATCAATGATCACATCTTTGGATATGTAT DNXXVX[XXYXXXYYXZZYVTPP[[[VV[[ 1
-SL-XAQ 505091110 9 1 2 858 0 1 .AAACGTTGCTGATCTTCTGTTTTAAACTA DNZVLQQQQUTRUULUXVVORTYYYZUQUZ 1
-SL-XAQ 505091110 9 1 2 209 0 1 .GACTCAACTCCTGGGCTCCCTACGACCAT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 988 0 1 .AAAGGAATGTTCAGCTCTGTGAGTTGAAC DNXQNOSYQLQVWTLRWVTNSOSRUQLPUQ 1
-SL-XAQ 505091110 9 1 2 1453 0 1 .ATATCTTATTTTCTTTTCTTTCAGGCTCT DMYVKKRXTQTTBBBBBBBBBBBBBBBBBB 1
-SL-XAQ 505091110 9 1 2 69 0 1 .TCAGTCTGCTGTTTTAAAAAAATACTGTG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1158 0 1 .GGGTCCTTCATAGTTTTTTTCTACTTTCC DOVVVUSUZOXXYYYXTZZZUWWYYXXBBB 1
-SL-XAQ 505091110 9 1 2 1753 0 1 .GTTCACACAAGGATAATATTTTTGATTAT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1238 0 1 .TCCTTATATTCAATTATTAATATTTTTAC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1827 0 1 .AACCGAGGATGTACACTGTCCCTGTGAAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAQ 505091110 9 1 2 309 0 1 .AATGGCCATGCTGCCCAAAGTATTTTATA DMVOTUXXYTLQQVVTXXXUVPVYYYXYXY 1
-SL-XAQ 505091110 9 1 2 1889 0 1 .GAAATGTATCAAGGTTTGTATAATTGCTG DLV[[YYY[QYYYWYS[[YOVTSVVUTXVW 1
-SL-XAQ 505091110 9 1 2 1878 0 1 .AATACTGAGATGTATTTAAGGCTGACACT DMXYXTVNRVUVOVXYYYVYTNTVYYXXXX 1
-SL-XAQ 505091110 9 1 2 658 0 1 .GATGCTTCTGTCCTAAGAAGCTTGAGACA DDQURQWWVSPQPOVVTRTUOTTTTSQQTT 1
-SL-XAQ 505091110 9 1 2 119 0 1 .GATTGGAATCAACCCGAGTGGAATGGAAT DOUYVTTVVVWUVSQLULUUNNNQWWTPVB 1
-SL-XAQ 505091110 9 1 2 1417 0 1 .ATTCCATTCGATGATTCCATTCGAGTCCA DLYYTUVZXRLTPOVWWOPSYWTRWPQQBB 1
-SL-XAQ 505091110 9 1 2 1895 0 1 .AAAACTTCTAAGTAATCATGAAGCTCTGC DMVZXYYYYY[WSYXXXWXY[UVW[YUVVU 1
-SL-XAQ 505091110 9 1 2 52 0 1 .AAGTATAATGTAGAGACGCTTGTATTGTC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 85 0 1 .GATAAAGTACAATGCTAATCACTTAAGAT DMTQRTROSUWVSJFOPXXXXVTZYXQTTZ 0
-SL-XAQ 505091110 9 1 2 63 0 1 .GAGTGGAATGGAATGGAGTGGAATGGCTT DKNUUWPWUWQWPPTTRTRUTQTWVTUWUB 1
-SL-XAQ 505091110 9 1 2 737 0 1 .AAAACAATTAAAATAAATGCTTAAAATCA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 802 0 1 .AAGTTAATTGTGTATTATTAACATCATTC DNUQV[[[[SSSRTW[[YYYYXWXXTVXVQ 1
-SL-XAQ 505091110 9 1 2 1465 0 1 .TTGTATTTCTGAAACCCCGAAGGGCATGG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1507 0 1 .GGCTTGGAAAGTGTAGGAGGGAGAGTCAC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAQ 505091110 9 1 2 950 0 1 .GTGTGTGTTTTTAGAGATGCCTTTTAGAA DLVSURWPVXXX[XXXXXWWVUXXXZUTVX 1
-SL-XAQ 505091110 9 1 2 358 0 1 .TCTGTTGTTATTTCCCTGTTACTTTTGGT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1336 0 1 .AAGTCTAAAATTATCTTGAAGTAAAAAGT DMVTVXTYWX[[[[SLVYYTWTVX[[[WMV 1
-SL-XAQ 505091110 9 1 2 190 0 1 .ATAAGTGTATATTTATTTGTACCATGACA DLZWUXSVVVYWZZX[Y[[[[XXXXWYXXU 1
-SL-XAQ 505091110 9 1 2 1995 0 1 .ATTTCCTGAACACAGCACAGGGAAGAGGA DNVWVVVVRWVVVYWWVVVWUVVUWTWQQT 1
-SL-XAQ 505091110 9 1 2 425 0 1 .AATATATGCAAGACTCCTGTTATTAGAAA DOXXYXXOTTYVQU[[X[XXVVYYXYYY[[ 1
-SL-XAQ 505091110 9 1 2 455 0 1 .GCTTGAACTCAGGATTCACAATTTCAACC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 11 0 1 .AAATGAAAAAAGAAATGCATTGTCAGGTG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 2 636 0 1 .GATCATTTACTGTTGTCAACTACCAAAAT DNVQFJVUXUQPTPRLPLTURQOQRTUTTV 0
-SL-XAQ 505091110 9 1 3 1488 0 1 .ATTCTGAGTAGCATGCTGGATCCCACCCC DLSSTOPSKSQNPUUUSQRBBBBBBBBBBB 1
-SL-XAQ 505091110 9 1 3 795 0 1 .GTAATGGAAGTCCTAGTACTAAAAATTAG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 3 1406 0 1 .AAAATGCCAGATAAATTTTATGTAAAACC DP[[XVQQVSUVYYVVGVZZZTOR[XYXVQ 0
-SL-XAQ 505091110 9 1 3 1861 0 1 .GATTAATGAATAGAGTGAATAGTGTCTGA DLOVYYYTMR[[VVWWTQXY[[TROYXUSU 1
-SL-XAQ 505091110 9 1 3 389 0 1 .GATGTTCAAACATGCATAACTCTAAGTAT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 3 683 0 1 .AAGTTTTTATTTATACGTAGAATTTATAC DMUPP[[YZ[XWZ[[[XRXXRVWX[Z[ZXY 1
-SL-XAQ 505091110 9 1 3 273 0 1 .AATTGACATAAATCAATATTGTTAAAATG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 3 277 0 1 .GATGGGAAGGCCCCGGCCTGGGGAGGTGG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 3 301 0 1 .TACGTGTGTGGCTGGATAGTCTGGACCAT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 3 347 0 1 .GTGGTGTGAGGTGTATCTGGGTCAGCAGG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 3 579 0 1 .GAAAAATGACCACACTTGCCTCCTGAGAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 3 608 0 1 .TGTGCTTCAATGATGCTATCAGGTGTGTT DMXUVTYVSVYVUUTTRYYXYVPPXYYWYY 1
-SL-XAQ 505091110 9 1 3 699 0 1 .TGTCTTCTTACACTATTTTTTTTAAAATC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 3 959 0 1 .AAAGTTTCCTGTGAGAAGGCGCATGGCAT DMTQLSWVWSWWUUVTVBBBBBBBBBBBBB 1
-SL-XAQ 505091110 9 1 3 1155 0 1 .CAGCGAAAGAAGTACCAGGGTATGGGAAG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 3 1233 0 1 .AACCAATTTCTTTACATACCAAATACGCC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 3 1348 0 1 .ATATTGATTCTTCCTACCCATGAGTATGG DPZZVWMJRWXXXXWWWZZWXPPWZVZWBB 1
-SL-XAQ 505091110 9 1 3 1358 0 1 .TCCTTCCTCAAGGGGACCCCGCCTCCCCT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 3 1450 0 1 .GATTCGATTAGAATCATCGAATGGACTCG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 3 1574 0 1 .TTATTCCTTAGGAAATTTTAAATTCTGTA DOXTTRTVXXXXXXYXXYYXXPOQYYXYRY 1
-SL-XAQ 505091110 9 1 3 1688 0 1 .CCTTCTTTACACACTGAGGAACTTAACCT DMMXXXXXYXYVVTRTUSLRTVVOWYXVVV 1
-SL-XAQ 505091110 9 1 3 1717 0 1 .AAACAGACTTGTTTCTTGTAATAATTATG DNZZWXUWXYXXX[VUYWRXXYXYYYYYBB 1
-SL-XAQ 505091110 9 1 3 1764 0 1 .TCTATGGGGTGTGTATCTGTTTCTGGACT DOXYYWSTGSTWUNUUUUWWSZWWTPMRPS 0
-SL-XAQ 505091110 9 1 3 1973 0 1 .CTTTTATTGAATTAGCTTCTGTGGAAACC DM[VVS[[PSTZPOT[[YU[V[YWWZBBBB 1
-SL-XAQ 505091110 9 1 3 1981 0 1 AGCCTGTCTGTAGAAAAAATACAAAAATTA _RZ\ZWN_\YWaW\aaaaaYa^aa`aa^Ya 1
-SL-XAQ 505091110 9 1 3 198 0 1 TATAATTTAATGGTTTTTATATATTCAGAG aab\aabb`\_\W[ababaa`aaba\aa[X 1
-SL-XAQ 505091110 9 1 3 1927 0 1 CACATCACCTTCTACTACATTTGAAATTCT ab`b`Wa]b\a`^bWabYFW\LT_H_\O\a 0
-SL-XAQ 505091110 9 1 3 162 0 1 AATGAAGGCCACAGAGTGGTCCAAATAGCC ^__T___]]`[O^Z\OWRXYQ[```a`\BB 1
-SL-XAQ 505091110 9 1 3 751 0 1 CACTTTTATTCTTAAGTACCACCTTCTGGA U`\bbbbabbb```^^_bbW__bbabY]H_ 1
-SL-XAQ 505091110 9 1 3 918 0 1 TTTTCATTCCTAGTCATCCACCCCATCAGA OGH_`\YQ]RY]GNGG[QQ`]YOGQOY_H_ 0
-SL-XAQ 505091110 9 1 3 1760 0 1 ACAAGAGACCCTAACATTAGGTAGGAATAT `Y__T`[a[SW_a_\]^`^YZY^T]`a^__ 1
-SL-XAQ 505091110 9 1 3 1222 0 1 TGGCATCCAGCTTTGTACTCATGAAAATTG `^\_ba`_\V`_]_X_aa`^]a\Z[\_^a_ 1
-SL-XAQ 505091110 9 1 3 1677 0 1 AGTGCAGTGGCGTGATCTTGGCTCACTGCA `^Vaaa_^XXUX`VaVZ_ZP]XYF\VZV_a 1
-SL-XAQ 505091110 9 1 3 890 0 1 TGCTTCTGTTTCCGTTAGCTAGATAAAGTT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 3 405 0 1 AAAAAACATAGAACGGGGTCAATATTTTAT G^`]WGVa^[GYFH^_HWGYGIY[WYO]F] 0
-SL-XAQ 505091110 9 1 3 1544 0 1 CGTGGATGGTTTTGATGAGTCCCACTGCAC \_\[HI_QQRVT`X_^RUGVUW_YFWXV[B 0
-SL-XAQ 505091110 9 1 3 1219 0 1 AGTTACTTATAGTGAATGGTTATTACTCCA a`]aaaaaa`_^Y^``ZZ[W_aX\XV]X]` 1
-SL-XAQ 505091110 9 1 3 1294 0 1 TGTAACTTTACTTTAGTTGCTTATTTGTAG a`BBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 3 1867 0 1 AGAAGCATTCTCAGAAACTTATTTGTGATG aa]WP]aa^L]^ZOV]SZa_a`aa^Y[_\Y 1
-SL-XAQ 505091110 9 1 3 1341 0 1 TGAAGAGTTTCTGGCACATAGGCACTCAAC aV``baZ]bV`^^S`a[a]aYFY_b````a 1
-SL-XAQ 505091110 9 1 3 676 0 1 ATAAGAAAATGCCAACCCATTTACAGTTTT ^FYVDUW]^[GMX`VG\YUW]`\Q]GX_^^ 0
-SL-XAQ 505091110 9 1 3 131 0 1 TAAAATAAAGTAAAAAGAAAGCAAGGTCCT aaaabbbaa`[bbbb`[[bab]aab\`b\b 1
-SL-XAQ 505091110 9 1 3 1311 0 1 AGACATAAAACCAGAGAGAAGATAGTGGGT ___aaaaba`Z]a]`aaaaaaaa`^ZXYR] 1
-SL-XAQ 505091110 9 1 3 900 0 1 TGAATCTTTGTTCAACACAGATTATTCCAG H]_JTI[aPFYGTKQR`]TH_YHGN]Y\BB 0
-SL-XAQ 505091110 9 1 3 2027 0 1 AATGTATTATGTTTCATAAGAAAACAAAAG a`VNL_W\_SKIP\]^Y`_Y]a_aaba_WB 1
-SL-XAQ 505091110 9 1 3 996 0 1 AAGGGAATTCTTGGACTTGATTAAATTGGT \bX^U^aaa^UZU]Z]`^a`^_Q[_aaYBB 1
-SL-XAQ 505091110 9 1 3 289 0 1 ATAGTGCTACAATAAACATGGGAGTGCAGA aa\Z]``aa_aaaaaa_`ba`]]a`ZX_^` 1
-SL-XAQ 505091110 9 1 3 33 0 1 CGGGCGCGGTGGATTCCGCCTTTAATCCTA VP_\]R^a`BBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 3 905 0 1 TGTTATGTTTAATTTTCTTTAGCACCCTTC ]V]^`YL[a`_O]_Y_W\`ZTDVZX^\YX_ 0
-SL-XAQ 505091110 9 1 3 1525 0 1 AGAAAATATCTGCATAGATGTGTTGAAGTC aaaaaa``__^[R[Ya\^a__`_a```_\` 1
-SL-XAQ 505091110 9 1 3 583 0 1 GGCTTACACAGTCAAACTGGAGAGAAGTAG GTU\bbbb\aWa`aaab_Y\aa```^K_`[ 1
-SL-XAQ 505091110 9 1 3 2037 0 1 CATCCTGTAACAAAGTGTTTATAGTTTTCA Y_X_aU[^`]G]`a_[IH\[ba`Y]TPYV` 0
-SL-XAQ 505091110 9 1 3 1319 0 1 TAAATGATTGCCTTCCACAGTATACATGTG a```[YY\a_VYWXH]\]aJHa_a_\BBBB 0
-SL-XAQ 505091110 9 1 3 1513 0 1 CACGCCACTGCGCCTGCAGCCTGGGCAATA a\TT_``U_\Z]Z]NZ__X_[]TQ[^_`a` 1
-SL-XAQ 505091110 9 1 3 1188 0 1 GCGAATGCCATTATTTCATTCCTTTTCATG \_b`b`^``abbbbbbbb`a^^bababbaa 1
-SL-XAQ 505091110 9 1 3 673 0 1 TCCTCAAAAACAAGATAAAACGGTTGAAAT ]GH]HFFWTaab^BBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 1 3 471 0 1 AGAAAAAGACAAGCAGGCCTCTCACAGAGC _\a]ba_^Waaa`[a[_`aa```\[_]]R[ 1
-SL-XAQ 505091110 9 1 3 1328 0 1 GCTACCAACCCCACTCCTAGATGAAAGACC OUWK\_H\``WQ_b_WZZ_RZWN[[BBBBB 0
-SL-XAQ 505091110 9 1 3 985 0 1 AGGTTTAATTGGTTCCAGGAGGTCACACTG ^WXW_aaa^_U[Z_]ZaYY]YLVXa`_`_Y 1
-SL-XAQ 505091110 9 1 3 176 0 1 ATATTTCATGAAAGACATAAATTTACAGTT aaabba_aaa`aaaa^`aaaaaaaa`aa_a 1
-SL-XAQ 505091110 9 1 3 880 0 1 ATGAGTGAGAAATAGAAGTCCTAAGTAGAT a_\ZNVT]H]^a_\R]_\[MQ\a_Q_]SXa 0
-SL-XAQ 505091110 9 1 3 695 0 1 TGATACTGCCTTTGCAAAAATTATAACAGT Z]`aabb[^`bbaaabbbbaa`ba``aa[` 1
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_1_0002_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_1_0002_qseq.txt
deleted file mode 100644
index 7066e8e..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_1_0002_qseq.txt
+++ /dev/null
@@ -1,200 +0,0 @@
-SL-XAQ 505091110 9 2 0 135 0 1 ........A...........G......... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1547 0 1 ........C...........G...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 87 0 1 ........G........A..T...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 205 0 1 ........A........T..C...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 50 0 1 ........T........T..G...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1620 0 1 ........CA.......A..C...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1278 0 1 ........TA...T...C..A...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 186 0 1 ........CC...A...T..T...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 287 0 1 ........CC...C...T..A...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 441 0 1 ........TT...A...A..T...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 766 0 1 ........TG...A...A..T...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1598 0 1 ........AT...T...A..G...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 382 0 1 ........CA...T...T..A...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 740 0 1 ........TT...A...T..A...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 501 0 1 .....G..AG...A...C.CT...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1135 0 1 .....G..GT...A...T.TA...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 73 0 1 .....A.CAT...G...A.AC...G..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1668 0 1 .....A.ATA...A...G.TG...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1198 0 1 .....T.CTA...T...C.CA...A..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1073 0 1 .....A.CAC...C...C.CA...C..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1351 0 1 .....C.ATA...T...A.AA...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1987 0 1 ..AT.G.ACA...C...T.GT...T..... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1755 0 1 ..GT.A.TCT...C...C.TG...G.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1950 0 1 ..TT.A.AAA...C...T.CA...T.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 8 0 1 ..TGCG.TGG...C...AGGC..TT.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 56 0 1 ..GCCA.GGT...A...TCAC..GG.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 211 0 1 ..CTGA.ACA...G...TGCA..AC.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 242 0 1 ..GCTC.AGC...A...ATAT..TT.G... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 262 0 1 ..ATTG.AAT...C...TTCC..AT.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 298 0 1 ..TCAA.TTG...T...CTGC..TT.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 312 0 1 ..TTGC.AGA...A...AACT..TG.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 370 0 1 ..CTGG.AGC...T...CATA..AA.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 377 0 1 ..AGAA.GTG...T...AAAT..AA.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 414 0 1 ..TAGA.AGC...A...TCAG..AC.G... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 421 0 1 ..GTTA.TTC...A...CGTG..AT.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 555 0 1 ..CAAT.TCT...G...TACA..CT.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 569 0 1 ..AGGC.AGT...G...GTCC..GT.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 699 0 1 ..AATT.TTG...T...ATTT..GA.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 722 0 1 ..CCTC.CTG...C...CTGT..TG.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 749 0 1 ..AGTG.TAC...T...CTTG..CT.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 833 0 1 ..GAGC.CCT...A...CTCC..GA.G... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 848 0 1 ..TACT.AGT...G...TGTT..GC.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 998 0 1 ..ATGT.TGC...A...TATA..GG.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1159 0 1 ..ACTT.TAG...G...AAAT..CC.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1168 0 1 ..TCTA.CTT...T...ATTG..TT.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1180 0 1 ..ATGG.CTT...C...AGAA..TC.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1306 0 1 ..ACAT.AAA...T...AACA..GT.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1424 0 1 ..TCAT.TAG...C...ATGG..GT.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1521 0 1 ..ACAC.AAA...G...ATCT..TT.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1543 0 1 ..TTGA.ATC...A...AATA..TA.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1617 0 1 ..CCAT.ATC...G...CCAG..GT.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1627 0 1 ..TGGT.AGA...C...AAAA..CA.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1653 0 1 ..AATT.AAA...T...ATCT..AG.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1682 0 1 ..TCTT.TTT...G...AAAA..AA.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1731 0 1 ..TATA.GAA...T...TGCT..AG.T... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1812 0 1 ..TTGC.CAC...C...CCAT..AA.G... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1853 0 1 ..ATCT.TTC...A...AGTG..AT.C... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1919 0 1 ..AATT.AAA...A...AGAA..AG.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 2006 0 1 ..GTAT.TGA...G...CCTT..AG.A... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 64 0 1 .ATTAATCTT...T..GCACAATTCATT.. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1646 0 1 .TTAATTATA...A..TAAACATTCTAA.. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 37 0 1 .TGTAAACGA...C..TTCCTGTTCAGC.. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1515 0 1 .ATTAAATAT.A.A..GTAATAATAATA.. DNXBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 466 0 1 .ACACTCACA.C.A..TGTTTGGAATGA.. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 558 0 1 .AAAATATCA.T.A..AATAAATAATCA.. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 714 0 1 .ATTAACTTA.A.T..ACCACAACCTAA.. DMYBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1933 0 1 .AGGGTACAT.T.C..AATGTGCGGGTT.. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 628 0 1 .AGTATGCCC.C.C..ACCACTCCTATT.. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 44 0 1 .ACTACCTCA.G.A..AAGCAGGTTCTAA. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 428 0 1 .ATGTGAATA.T.A..TAGTTGGGATTCA. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1924 0 1 .ATATTCTGAAG.A..CCAATGAACCAAA. DPPU[XTVX[VBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 234 0 1 .AAGCCTGTGGG.A..CCCAGTGGGAGCG. BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1004 0 1 .ATTTATCACTA.A.ATCCGCAAACCCTCC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1214 0 1 .AAAAAAAAAAA.A.TATAAGAAAGAATCA DORTYBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1034 0 1 .ATCATTTTCAT.C.TTTCACTGATACATT DMVRVYWWVSVPDLDPYWTTTTSTZUXUYY 0
-SL-XAQ 505091110 9 2 1 1536 0 1 .AGCAAAGACTT.G.ACCAACCCAAATGTT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 684 0 1 .AAAAATCAAATGA.CATAATTTTATAAAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 893 0 1 .GAGACAGAGTCTC.CTCTGTTCCCTAGCC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 604 0 1 .ATGATGAAACTCT.TCTCTACTAAAAATA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 760 0 1 .GTCTGTTTTATGT.AAATATTTTGTTTAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1452 0 1 .GAAATTTGTAAAA.CACCTGCAGAATACT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1959 0 1 .GACACATTCCTAC.ACAGAGAAAAATTTA DIVVZZ[Z[[Y[ZKDMYYZYUYXYY[SSWW 0
-SL-XAQ 505091110 9 2 1 1938 0 1 .AGTCCAGTGTCTCTGCTTCCGCAGGGACA DNWPWWUTNOTWWTWUSSWUUSTVUSUUUW 1
-SL-XAQ 505091110 9 2 1 1221 0 1 .GGTCACACTCACATAGTGTTCAGAGCACT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 1 363 0 1 .GAAAGGTTTTGCAGCATGTGCAAACTCAC DLTTUTUVWYWPVVUTUTORTPQNRVVWTU 1
-SL-XAQ 505091110 9 2 1 170 0 1 .AGAAGAAATGGGATCCTGCTGTGGCCAGT DNWWWWUTQWSPUWWUUVUVUURGUWVSNT 1
-SL-XAQ 505091110 9 2 2 463 0 1 .GTGCTTGGGGGCGTCTGTGTTGATGCGTG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 1636 0 1 .GTGTAAAAGTAGGGAAATACTATAGCAAG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 828 0 1 .TCAAGTCAATTTGGGACTTGAAACAGCTC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 220 0 1 .AATAAACCTCTTTCTTTGATAAATTACCC DMTYVWRRTTUVYTQT[VRUYXWUWZWBBB 1
-SL-XAQ 505091110 9 2 2 101 0 1 .GTTAATTTAGGGAAATTTGTTTGTATTTT DKRYXUXZ[TQVPWZ[[[VUWZYYXZXXXZ 1
-SL-XAQ 505091110 9 2 2 351 0 1 .GGGGTTGAGGTGTAAATAGAACATTTGTA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 1559 0 1 .ACAGAAGGGAAAAGGTCACAGACTAAAGA DNNUZZZWWSXZYXPKRTYYVTVYSYZYXY 1
-SL-XAQ 505091110 9 2 2 1671 0 1 .GGGAATTACATGGAAAATGATCAAAGGAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 0 0 1 .ATTCCTT.A.................... BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 61 0 1 .TTTCGATGGTGTTTCCATTTGATTCATTC DOZYXYZVXXYWYXVVVXY[UVX[XVVZYY 1
-SL-XAQ 505091110 9 2 2 1842 0 1 .GGTGGATCCCCTGAGGTCAGGAGTTCAAG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 12 0 1 .ATGCATTGTAATTTAATAGAGTGAAATGG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 599 0 1 .AAACAAAAAAGCTGATGGCCTGGCGGGGT DMWRUWSSVTPTWRKRWLHNWURWBBBBBB 0
-SL-XAQ 505091110 9 2 2 115 0 1 .GATGTGCTACACACTTTCAAACAAACAGA DOYTOOENXXZUXVQVYYXXTRPRRVSSWS 0
-SL-XAQ 505091110 9 2 2 255 0 1 .GGGTCCAAATAAGAGAAGGAGAAAAACAG DOOSPQORUWXROTVTTSPUVSUTZXWXVV 1
-SL-XAQ 505091110 9 2 2 1298 0 1 .GATTCCATTCAATGAATCCATTCGATTCC DMQRTJQQXVUBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 775 0 1 .GTTTATAATTGTGAGTTAAAAATCTAAAA DKLVWYWYXUWYSTTQS[[URUZ[Y[[[[[ 1
-SL-XAQ 505091110 9 2 2 131 0 1 .ATATATTGACAGCAGTCATGTTGTTGAAG DO[[[Y[XTXWVSSXQYXUXXXXUXYVVWS 1
-SL-XAQ 505091110 9 2 2 904 0 1 .TTAGACACCATGAAGGTAACTTCCTACTC DOYUQUUVXXXNEMUOTWYYTXVWSWXRUU 0
-SL-XAQ 505091110 9 2 2 1038 0 1 .ATGGAATCAACCTGAGTGGAATGAAATGG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 669 0 1 .GGCTGAAGCAGGAGGGTCACTTGAGCCAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 488 0 1 .TGGGAAACTAAACCCCATGAGGGCAGAGC DNQNPTUUUUVWTSSTQTTTTPNPQTSTNS 1
-SL-XAQ 505091110 9 2 2 953 0 1 .GTTTAGTACATACTAGGTTTCACCAAATT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 1723 0 1 .GAAGCTGACATTACAGGTTTCAGACACCA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 1944 0 1 .ATTAAATATATATTTTATTCTGAACATAA DOXYY[[[[[ZY[[[YXX[[X[[Z[Z[Y[[ 1
-SL-XAQ 505091110 9 2 2 1567 0 1 .AGACAGCAGTAACCTCTGCAGACTTAAAC DKUVYVQOTSSZSUUVYUQLTUUVYYUWVV 1
-SL-XAQ 505091110 9 2 2 679 0 1 .CTCTGTCTCAAAAAATAAAAATAAAAATA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 1985 0 1 .GACTATCACTCTAGGGCCTCCACCCTTGC DDQQUUSUUUUVPWUGUUBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 1402 0 1 .GGATGGCTTCCAGTATGGGAACCTTTTCA DMTSWSLNWTWWUTNVWNGNUQFNWWUTTT 0
-SL-XAQ 505091110 9 2 2 1874 0 1 .GGCATATATCCTTTTACATACCCAACACA DKOPRVYXSXUXXZXZWWVXWVWXVPVXXU 1
-SL-XAQ 505091110 9 2 2 611 0 1 .GGAACCAGGCAGGGCCACACACAGGTAGC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 1974 0 1 .ACGCCAATACAAAAATGTTGAAGCTAGCT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 1012 0 1 .AGAAATACCATTTGACCCACCAATCCCAT DOUUYYYXURUXURTUVVVWYYWWWXTLTW 1
-SL-XAQ 505091110 9 2 2 303 0 1 .AGATCTTGTCTTTCAATCTTTTTAAATTC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 1365 0 1 .ATAAAGATTATCCGTGAATGGCGCCTCCA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 184 0 1 .GAAACGTTTTTCGGTTGAGGAAACTTTTT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 646 0 1 .GAATCTAAGAAGACACAAAACTAAGGAAA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 2 1662 0 1 .ACTAAAGACCTTATTCATGTAGCCAAATA DMQTTURRPHDOVXVXXYYXYVPWTT[WWY 0
-SL-XAQ 505091110 9 2 2 1745 0 1 .GGGAGCTAAGTAACTGGAACAAGTTTTTG DLTQRVVWXXXXYWWWUUWXYXYXTUXWWV 1
-SL-XAQ 505091110 9 2 3 1952 0 1 .ATAGATGATAAAAACATTTGACAGTGAAA DMWVRVWUWYYY[Z[ZXZXXVXYYXWTWZZ 1
-SL-XAQ 505091110 9 2 3 112 0 1 .ATGGAGTCTTGCTCTATTGCCCAGGCTGG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1
-SL-XAQ 505091110 9 2 3 386 0 1 .TGAATAAATAAATATCTGTATTATTCCTA DPTUZXXYXXXYTVVRKSLTVXVRWTPMSW 0
-SL-XAQ 505091110 9 2 3 490 0 1 .CTAATTGATGGGTAAGAGGCAAAGCATGA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 495 0 1 .TCCGTTTTTATAACTGTAAATTTATCACT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 577 0 1 .TTCAACTCTGGGAGTTGAATGCAAACATC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 695 0 1 .CAACTCCAAGACACATAATTGTCAGATTC DNYYYXTTVWTWXXUXYYYZUTTXVSWZWQ 1
-SL-XAQ 505091110 9 2 3 808 0 1 .GAGTGTAATACAATGGTATGGATTTTAAC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 862 0 1 .CTTTAAGAAATCATTCATTCTGCAAACAC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 889 0 1 .TTTTTATAACACCTCAGGCATCGTCAAAC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 1025 0 1 .AATGGAAAGGAGTCCAATGGAAGGGAATC DNSUQUWWTLJRLRVVVYTRQTVORPRWRV 1
-SL-XAQ 505091110 9 2 3 1053 0 1 .TTTGATCATGATTCCATTCGAGACCATTC DMZZBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 1123 0 1 .CCTCTTCCACAACTTCCTTCTTCTCCTTT DMQRHVSVTVVUWVUSWUYZUVRSWWUVYW 0
-SL-XAQ 505091110 9 2 3 1209 0 1 .TTGAGGATGTTACTACATTATTATACAAA DNRRVONOPOMTTBBBBBBBBBBBBBBBBB 1
-SL-XAQ 505091110 9 2 3 1290 0 1 .TCACCTGAATCCACGTTAGCTGGGGAAGA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 1387 0 1 .CGATTATGACTCTGAGAGAAAGTAGGGCA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 1529 0 1 .TTATATGAATAGATAAATAAATAATCAAT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 1576 0 1 .GAAACCACGTGCCCATTTTCAGTTCTGGT DINDMTTUURPPVWUWVWWVWVNVUTBBBB 0
-SL-XAQ 505091110 9 2 3 1581 0 1 .ATAGGCAGGGAGCAAACCTCAATAAAAAG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 1733 0 1 .TTAAATGAGTGTAAATATTCAATTATGCA DKYUYYQNTZRXR[[XY[ZXPX[XVBBBBB 1
-SL-XAQ 505091110 9 2 3 1775 0 1 .AATCCGACAATTATGTGTCTTGGAGTTGC DMQQROPSXXXWWWUUSTUQTOIMSQSXTT 1
-SL-XAQ 505091110 9 2 3 1807 0 1 .GCATACTTCTTTCTTTCTTATTTTTCTTT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 1844 0 1 .GGACTACAAGCGCACGCCACATGCTCAGC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 1898 0 1 .TTGAATTGCTGGACTTCAATGTGTGTGGG DOWWUWYUSUWOJOLTYWVUTQTTUSVTQQ 0
-SL-XAQ 505091110 9 2 3 1917 0 1 .TCCACAAAAAAAAAAAAAATTAGTTGGGT DIU[VRV[SVTUBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 1970 0 1 .TAATACTCTTTGAGAAAGGACTGAGGGAA DMYVVTTWYUWWUQMRZWSTTYOOTVTRTZ 1
-SL-XAQ 505091110 9 2 3 2004 0 1 .AAGACTACCTTGCTGAAATAGGGCATTTA DMYWVTSTXZSLVSRGQXZZTPRXQUUBBB 0
-SL-XAQ 505091110 9 2 3 2038 0 1 .A.AGATAGATAGATAGATAGATAGATAGA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 317 0 1 AGAGAGAAATGTGGCATATGAGTATCACCT _S]aaa^`ab`a_]]`baa^a[``aabaaa 1
-SL-XAQ 505091110 9 2 3 1941 0 1 TGTACTCGTGTAGCCTTTCACAGGCACAGC a[M`baaaQZXb]_T`aaababa`abbbTa 1
-SL-XAQ 505091110 9 2 3 157 0 1 TGGGTGGTTCAAACTAAGCAGTCCAACTGC a`bb_aa`aaaabaabaaaaaa^``a^a^` 1
-SL-XAQ 505091110 9 2 3 99 0 1 CATATCTGTGTTATTTTAGCATAAATTTGA P_J_RP^GFSG`ZVR]H^VRHH_HH_b^BB 0
-SL-XAQ 505091110 9 2 3 143 0 1 AAAATCAATTCTGAAATGATTACATATTTT aaa`baa`ba\a^aaaabaabaaaaaabaa 1
-SL-XAQ 505091110 9 2 3 328 0 1 AGCTTAATATAGCATAGCAGATAAGATTTG GYIW]\KRYHH[H^`[GW]BBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 932 0 1 AGAAAGACAGACAGACAAACTGACTCTCAG _]_b_S`\^Q_a_M]`a`aaaa]\`YZ]_B 1
-SL-XAQ 505091110 9 2 3 1484 0 1 CATCAACCTGTCACAAAATGACAAAACCTA \`_T_ba^aT_^a__aaaa^`abbab_`aa 1
-SL-XAQ 505091110 9 2 3 875 0 1 AGGCAGTAGTCTAATCCCGAGGATCCCAAG YKVR\_^[M\_Z^^_YYR^WHT[\XDY^]V 0
-SL-XAQ 505091110 9 2 3 1016 0 1 TGGCTCTGTCCTAATATCTTATTCTTACAA [R\_aa`^_[\aabb_]U]aaaaa_a^_`b 1
-SL-XAQ 505091110 9 2 3 198 0 1 TGTCATTTTCTTTGCCTTAATTGTTCTTCT T_baaVLI[\BBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 470 0 1 TGTGGATTCCATTCGAATTCATTCGATTAT aabaa`bb_bbbb]H_ba`]_ba^abbbbb 1
-SL-XAQ 505091110 9 2 3 1094 0 1 CATATGGTATCACCACTCAGATACATAAAG ``aa[Y\Pbaabab_^``_H]bbaabba^\ 1
-SL-XAQ 505091110 9 2 3 782 0 1 AGCCATGGGCATATAGAATCACTGTAAACA a_aaaa]VZababaa_aaa^aa]Y\a`a_a 1
-SL-XAQ 505091110 9 2 3 991 0 1 TGGAAGCCAGCCAAAGATACACTCTTGGCA a`ab]Uaabaaaab```_a`ba[[^a`aaa 1
-SL-XAQ 505091110 9 2 3 1962 0 1 ACTAAATCCAAGAGCACATCAAAATGTTAA aTZaaa__W_a`aX]aaa`a`ba__aZ_aa 1
-SL-XAQ 505091110 9 2 3 1101 0 1 AAGATTATATGAGTATAATGGAGCTATTTG a[RW]a\]]a\\RO`aa`WWUZ^Z```__] 1
-SL-XAQ 505091110 9 2 3 207 0 1 AGTTAGAAACAGAATACGGGTAATAATGTA aabbb`_a`_```ab_bb_``babaaabab 1
-SL-XAQ 505091110 9 2 3 1326 0 1 AGGAGGGAATGATGAACCAGTAGGTTAAGG a]\[QWJ[aTDXYNZ`VW]JN\`BBBBBBB 0
-SL-XAQ 505091110 9 2 3 728 0 1 TGCCTCCTTGGAGAGGGCCGCAAAGCCAGG \]\V^`^VFTO]NXXUYZ[J]``_VJWaUV 0
-SL-XAQ 505091110 9 2 3 691 0 1 ATTTTCAAATCATAAATATGGATTGCTGTG aaa`a`baa`_`aaaaaaaVQV`aWJZaTT 1
-SL-XAQ 505091110 9 2 3 1352 0 1 AAAGTGGCCCTTTCTGCATAATTCTTCTTG _a_]QY__Y]a_```Y``]^a^]Y\[P\[B 1
-SL-XAQ 505091110 9 2 3 1389 0 1 TATCGATCTCCTGACCTCGTGATCCACCCA `bababa^baa_U`aba_Ha]baabb_SZT 1
-SL-XAQ 505091110 9 2 3 987 0 1 AAGAGCAATATTTTCTTTCACTATATTATT I_[__^`_OHVSSWH^b_H_SHXY_BBBBB 0
-SL-XAQ 505091110 9 2 3 1133 0 1 AGAAGCTTTCTATTCTGATCCCCAAGGAGT a`ba`]aa\PZ^a`^^T`]Y_QT[\MSRZ^ 1
-SL-XAQ 505091110 9 2 3 399 0 1 AGGGTATGTAAACCGAGTTTTGCGGGGGAT `___]aaaaa``]_Z^a^aa``]_Y_Y^`a 1
-SL-XAQ 505091110 9 2 3 16 0 1 AGCTGGGCATGGTGATGCGCCCCTGTAATC `Z^Z[[^_X^____S\RHP_TX^^X[TM[Q 1
-SL-XAQ 505091110 9 2 3 2013 0 1 AGCAGAAGCCTGCTGTGGGAACACTCAGTC a^aBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 898 0 1 TAACATTCCCACAGTGCTTGCCACAGAGCC `bbbbbb_b__a_HZ]Zaabb\_ab^a_Z] 1
-SL-XAQ 505091110 9 2 3 1712 0 1 AGTGCTGTGGCCTGGATGGATGTCAGGATT ]XPY^TY\TYVV]ROT]NZ\]PY[aXUXSZ 1
-SL-XAQ 505091110 9 2 3 179 0 1 CATTATTGTTAGACTGATTTTTTATAATCT a_HPOSMMIOL`G__G[`X`[GJXHL\UGa 0
-SL-XAQ 505091110 9 2 3 151 0 1 AGAGAACAGATAGGTCTGTCAGGGCTGACC ^]\XXa]a`^a]H^ZT`aZWXZ\U^^[VR] 1
-SL-XAQ 505091110 9 2 3 983 0 1 TGTTTTTTATTTTAACAGATGAAGTACCAA a\abbbbbbbbbbb`]``bbabb_`b_]ab 1
-SL-XAQ 505091110 9 2 3 567 0 1 TATCTTCACATAAAAACTACACAAAGCATT aba[`baa_abbaaba[aa[_Z^aa]\aaa 1
-SL-XAQ 505091110 9 2 3 72 0 1 CTAGTCTTTGACTTATATCAATTCAGTATT aab^`bbbbba_bbbbbbbabbbbb`_abb 1
-SL-XAQ 505091110 9 2 3 922 0 1 ATTTCTGTCTGACTTTTCCAAATGTGCTAT ``aa_]]]_]X_]````]Z_aa__TRZaaa 1
-SL-XAQ 505091110 9 2 3 584 0 1 AAAGTCCTGGGATTACAGGCATGAGCCACT `abQ[_\]WZU\]^]R]LR[]aX_N\X`Z[ 1
-SL-XAQ 505091110 9 2 3 274 0 1 AGTGAAGTGCTTAGCACCTGGGCCAGCAGC YTVMY__]XU\_XV]_\Z\]Z_Z_\_X\XZ 1
-SL-XAQ 505091110 9 2 3 1602 0 1 AATTCATGAATACTTTTCAGTCTTTAAAAA aba```aaaaa^[_a`a^``\^aaaaaaaa 1
-SL-XAQ 505091110 9 2 3 4 0 1 AGAGGCAATAAGTTTTAA............ `]a`_Xa`aR``BBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 663 0 1 AAAAGCATGTTGCTCAGTAAAAGCAAATAG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 80 0 1 AGGCAGGATGAAATTTTGTCTATTTATTCA _XYa_a_^a_`a`aaaa^^V``aaaaaa^` 1
-SL-XAQ 505091110 9 2 3 1179 0 1 ATTTAATAAATAAAGCAACCTGACAACTGA _PTZFWW^`_PNR\FPOUNX`VMIYNOWBB 0
-SL-XAQ 505091110 9 2 3 589 0 1 TGAATGCAGGTGCCAGGGAGACGTGACTTC \W`baa^^]_\^[`baX[Z^`]^^Z`[]^R 1
-SL-XAQ 505091110 9 2 3 640 0 1 AGATTAAAAAAAAATGACGTGACAAATTAA \Ubab_b`abaabab_]_\_`aabbaaabb 1
-SL-XAQ 505091110 9 2 3 2030 0 1 CGAGATAATTTTTTAAAAAAAGTCCAAAAA GG_ZGH_\\IV[GT`_[b]BBBBBBBBBBB 0
-SL-XAQ 505091110 9 2 3 247 0 1 TGTACATGACCAGGTAATTTGGTTATGTGA [_TXURTRZH]_`V\YK`OFU]BBBBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_2_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_2_0001_qseq.txt
deleted file mode 100644
index 806ce3a..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_2_0001_qseq.txt
+++ /dev/null
@@ -1,200 +0,0 @@
-SL-XAQ 505091110 9 1 0 1434 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 464 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 113 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1703 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 879 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 841 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1291 0 2 .....G.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1940 0 2 .....C.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 586 0 2 .....C.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1690 0 2 .....A.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 37 0 2 .....G.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 324 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 205 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1307 0 2 .....TA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1193 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1475 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 275 0 2 .....AT. BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 2001 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1093 0 2 .....TG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1038 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 173 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1836 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1513 0 2 .....CT. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1917 0 2 .....AC. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1696 0 2 .....CT. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 812 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 2 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1555 0 2 .....CA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1243 0 2 .....TG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 30 0 2 .....AC. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 41 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 59 0 2 .....AC. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 111 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 132 0 2 .....TG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 140 0 2 .....CA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 155 0 2 .....CA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 164 0 2 .....TT. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 170 0 2 .....AC. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 184 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 195 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 240 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 262 0 2 .....CA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 299 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 353 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 367 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 416 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 483 0 2 .....TA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 486 0 2 .....TG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 495 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 508 0 2 .....CT. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 554 0 2 .....TA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 567 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 613 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 622 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 627 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 684 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 874 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 931 0 2 .....CA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 994 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1013 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1153 0 2 .....CT. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1184 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1241 0 2 .....CT. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1282 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1320 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1391 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1684 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1733 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1770 0 2 .....TC. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1906 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1954 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1247 0 2 .....AC. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 18 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1521 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 264 0 2 .....CGA BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1815 0 2 ...T.GAC BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1379 0 2 ...C.GAT BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 2011 0 2 ...G.TAG BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1372 0 2 ...G.TTA BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 55 0 2 ...G.TTA BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 517 0 2 ...C.AGA BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 965 0 2 ...T.TAA BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 535 0 2 ...C.CGA BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 72 0 2 ...T.GAC BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1886 0 2 ...G.GCC BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 1932 0 2 ...C.AGA BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 1706 0 2 ...C.GAT BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 363 0 2 ...T.CTT BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 605 0 2 ...T.GAC BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 449 0 2 ...G.TGT BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1782 0 2 ...T.AGC BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 246 0 2 ...A.TTC BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 307 0 2 ...T.GAC BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 150 0 2 ...A.CCT BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 546 0 2 ...A.GTT BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1727 0 2 ...T.CTT BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1946 0 2 ...T.GAC BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1275 0 2 ...A.CTG BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 786 0 2 ...GATGT BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 747 0 2 ...CCAGG BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 25 0 2 ...GATGA BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1722 0 2 ...TCGAC BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1301 0 2 ...TAACA BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1592 0 2 ...GAGCC BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 943 0 2 ..ACCAGG BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 974 0 2 ..TATGTT DDOYYYY[ 1
-SL-XAQ 505091110 9 1 2 858 0 2 ..ACATCT DDNTVVXX 1
-SL-XAQ 505091110 9 1 2 209 0 2 ..CATTTC BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 988 0 2 ..TGGCGA BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 1453 0 2 ..ACCAGG BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 69 0 2 ..GGAGCC BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1158 0 2 ..CTTAGC BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 1753 0 2 ..TGCTTA BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1238 0 2 ..CTAAGC BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1827 0 2 ..CAACTG BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 309 0 2 .TCGCTGA BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 1889 0 2 .AGGATGT DMSUYZZX 1
-SL-XAQ 505091110 9 1 2 1878 0 2 CAGGAGCC a[WP[\VZ 1
-SL-XAQ 505091110 9 1 2 658 0 2 AGCAATTC _V\___\Z 1
-SL-XAQ 505091110 9 1 2 119 0 2 CATAGCGA ^_]\Z[ba 1
-SL-XAQ 505091110 9 1 2 1417 0 2 AAGGATGT a^T^^ab^ 1
-SL-XAQ 505091110 9 1 2 1895 0 2 CATAGCGA ^_bb_]ab 1
-SL-XAQ 505091110 9 1 2 52 0 2 TGCTCGAC YZZZYZ\Z 0
-SL-XAQ 505091110 9 1 2 85 0 2 TACTTAGC a]G]a\aQ 0
-SL-XAQ 505091110 9 1 2 63 0 2 TTCGCTGA V_\a[b_B 1
-SL-XAQ 505091110 9 1 2 737 0 2 TACTTAGC abbbabaa 0
-SL-XAQ 505091110 9 1 2 802 0 2 CAGGAGCC \]O]^V]B 1
-SL-XAQ 505091110 9 1 2 1465 0 2 CACATCCT [Y_\aa__ 0
-SL-XAQ 505091110 9 1 2 1507 0 2 AGCAATTC ^Q\_X`[] 1
-SL-XAQ 505091110 9 1 2 950 0 2 TGTCGGAT __\`Y``` 1
-SL-XAQ 505091110 9 1 2 358 0 2 AACTTGAC `^ZUTPVR 0
-SL-XAQ 505091110 9 1 2 1336 0 2 CAGGAGCC V_X\a\V_ 1
-SL-XAQ 505091110 9 1 2 190 0 2 CATAGCGA ``bb\\_a 1
-SL-XAQ 505091110 9 1 2 1995 0 2 CTACCAGG a\``^aa` 1
-SL-XAQ 505091110 9 1 2 425 0 2 CAGGAGCC ``__\XZ[ 1
-SL-XAQ 505091110 9 1 2 455 0 2 GTATAACT K_BBBBBB 0
-SL-XAQ 505091110 9 1 2 11 0 2 GTATAAGA _V\\_VBB 0
-SL-XAQ 505091110 9 1 2 636 0 2 CCTACCAT UR[_`^a\ 0
-SL-XAQ 505091110 9 1 3 1488 0 2 GTATAACA HV[Xaaaa 1
-SL-XAQ 505091110 9 1 3 795 0 2 ACCAACTG ]WW_`]BB 0
-SL-XAQ 505091110 9 1 3 1406 0 2 TCTGGCGA ``\ZT_\_ 0
-SL-XAQ 505091110 9 1 3 1861 0 2 AGTTGCTT aX_][`[b 1
-SL-XAQ 505091110 9 1 3 389 0 2 GCACATCT [Y___TUZ 0
-SL-XAQ 505091110 9 1 3 683 0 2 CACATCCT a_W_a^ba 1
-SL-XAQ 505091110 9 1 3 273 0 2 AAGGATGT RW\TJ`bV 0
-SL-XAQ 505091110 9 1 3 277 0 2 CATAGCGA a`^ZR]a\ 0
-SL-XAQ 505091110 9 1 3 301 0 2 GCACACGA BBBBBBBB 0
-SL-XAQ 505091110 9 1 3 347 0 2 ATTATGTT S`]^_HU[ 0
-SL-XAQ 505091110 9 1 3 579 0 2 AATCATGT VRBBBBBB 0
-SL-XAQ 505091110 9 1 3 608 0 2 AAGGATGT ``Ta^aa_ 1
-SL-XAQ 505091110 9 1 3 699 0 2 AGTTGCTT XW^]W]BB 0
-SL-XAQ 505091110 9 1 3 959 0 2 GCACACGA R^Z`a^\[ 1
-SL-XAQ 505091110 9 1 3 1155 0 2 TTGAGCCT BBBBBBBB 0
-SL-XAQ 505091110 9 1 3 1233 0 2 CCAACAGG BBBBBBBB 0
-SL-XAQ 505091110 9 1 3 1348 0 2 TGCTCGAC aX^^_V_T 1
-SL-XAQ 505091110 9 1 3 1358 0 2 CTACAAGG UQaaBBBB 0
-SL-XAQ 505091110 9 1 3 1450 0 2 AACTTGAC abPF[V`B 0
-SL-XAQ 505091110 9 1 3 1574 0 2 TACTTAGC _`baab_` 1
-SL-XAQ 505091110 9 1 3 1688 0 2 CCAGTTAG ]_\\Zb`\ 1
-SL-XAQ 505091110 9 1 3 1717 0 2 TCTGGCGA `a\PPZ`_ 1
-SL-XAQ 505091110 9 1 3 1764 0 2 AAGGATGT aa^aa_Y` 0
-SL-XAQ 505091110 9 1 3 1973 0 2 GTATAACA VZb`bbab 1
-SL-XAQ 505091110 9 1 3 1981 0 2 TGCTCGAC \I_PZ_aa 1
-SL-XAQ 505091110 9 1 3 198 0 2 CTACCAGG `aaa``^_ 1
-SL-XAQ 505091110 9 1 3 1927 0 2 CAGGAGCC a_[__\_^ 0
-SL-XAQ 505091110 9 1 3 162 0 2 AACTTGAC aaab_T]^ 1
-SL-XAQ 505091110 9 1 3 751 0 2 CACATCCT X_b`bbbb 1
-SL-XAQ 505091110 9 1 3 918 0 2 ACTACCTT H^Sa]BBB 0
-SL-XAQ 505091110 9 1 3 1760 0 2 AACTTGAC a`aa`a`` 1
-SL-XAQ 505091110 9 1 3 1222 0 2 AACTTGAC _bb\__]a 1
-SL-XAQ 505091110 9 1 3 1677 0 2 AACTTGAC ab`]\S\a 1
-SL-XAQ 505091110 9 1 3 890 0 2 GTCACCAT BBBBBBBB 0
-SL-XAQ 505091110 9 1 3 405 0 2 ACACAAGA OG][\BBB 0
-SL-XAQ 505091110 9 1 3 1544 0 2 GCACACGA GG[MZZPZ 0
-SL-XAQ 505091110 9 1 3 1219 0 2 ACCAACTG a^__`^^X 1
-SL-XAQ 505091110 9 1 3 1294 0 2 TCACAATG IRV[[_T[ 0
-SL-XAQ 505091110 9 1 3 1867 0 2 ATTATGTT aa`_VX]a 1
-SL-XAQ 505091110 9 1 3 1341 0 2 AGATGCTT aBBBBBBB 1
-SL-XAQ 505091110 9 1 3 676 0 2 GATCCAGA YGM[GGY_ 0
-SL-XAQ 505091110 9 1 3 131 0 2 GTATAACA SWbb`b`b 1
-SL-XAQ 505091110 9 1 3 1311 0 2 GCACACGA [^a``_`a 1
-SL-XAQ 505091110 9 1 3 900 0 2 CTCCCAGG GGGM`_WT 0
-SL-XAQ 505091110 9 1 3 2027 0 2 AAGGATGT a]VL[YYB 1
-SL-XAQ 505091110 9 1 3 996 0 2 CCAGTTAG `_T\]b[B 1
-SL-XAQ 505091110 9 1 3 289 0 2 GTATAACA ]abbbba] 1
-SL-XAQ 505091110 9 1 3 33 0 2 GGTCCAGA PV\ZKF__ 0
-SL-XAQ 505091110 9 1 3 905 0 2 ACATCCTA ``VWN[YB 0
-SL-XAQ 505091110 9 1 3 1525 0 2 CATGCTTA aaaZaaaa 1
-SL-XAQ 505091110 9 1 3 583 0 2 CCAGTTAG \]XRZb`] 1
-SL-XAQ 505091110 9 1 3 2037 0 2 TCGGAATG ^[HY\_\_ 0
-SL-XAQ 505091110 9 1 3 1319 0 2 ACCAACTG ^^W_`]WY 0
-SL-XAQ 505091110 9 1 3 1513 0 2 CATAGCGA T_a\RV_a 1
-SL-XAQ 505091110 9 1 3 1188 0 2 GTATAACA aaababba 1
-SL-XAQ 505091110 9 1 3 673 0 2 TGCCCAAA G[BBBBBB 0
-SL-XAQ 505091110 9 1 3 471 0 2 GGTCCAGA [`\_a\^_ 1
-SL-XAQ 505091110 9 1 3 1328 0 2 TCGGAATG `__Q\^WR 0
-SL-XAQ 505091110 9 1 3 985 0 2 AACTTGAC aaaa_]_a 1
-SL-XAQ 505091110 9 1 3 176 0 2 CTACCAGG `aaa^`aa 1
-SL-XAQ 505091110 9 1 3 880 0 2 TTCGCTGA ]_UQZ`\\ 0
-SL-XAQ 505091110 9 1 3 695 0 2 TCGGAATG a^Zaaa\^ 1
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_2_0002_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_2_0002_qseq.txt
deleted file mode 100644
index ac4624c..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_2_0002_qseq.txt
+++ /dev/null
@@ -1,200 +0,0 @@
-SL-XAQ 505091110 9 2 0 135 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1547 0 2 .....CA. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 87 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 205 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 50 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1620 0 2 .....TG. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1278 0 2 .....TA. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 186 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 287 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 441 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 766 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1598 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 382 0 2 .....TA. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 740 0 2 .....GG. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 501 0 2 .....TA. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1135 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 73 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1668 0 2 .....CT. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1198 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1073 0 2 .....CA. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1351 0 2 .....TT. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1987 0 2 .....TA. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1755 0 2 .....CA. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1950 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 8 0 2 ...A.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 56 0 2 ...T.AGC BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 211 0 2 ...G.TGT BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 242 0 2 ...C.CGC BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 262 0 2 ...C.AGG BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 298 0 2 ...G.TAG BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 312 0 2 ...A.GTT BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 370 0 2 ...A.CAT BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 377 0 2 ...C.TCT BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 414 0 2 ...G.TTA BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 421 0 2 ...A.CCT BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 555 0 2 ...C.GAT BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 569 0 2 ...A.CTG BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 699 0 2 ...C.CGA BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 722 0 2 ...C.AGG BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 749 0 2 ...T.GAC BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 833 0 2 ...A.CCT BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 848 0 2 ...A.CGA BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 998 0 2 ...A.GTT BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1159 0 2 ...T.GAC BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1168 0 2 ...G.TAG BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1180 0 2 ...T.AGC BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1306 0 2 ...A.CTG BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1424 0 2 ...C.TCT BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1521 0 2 ...C.AGG BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1543 0 2 ...A.TTC BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1617 0 2 ...C.AGG BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1627 0 2 ...A.CTG BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1653 0 2 ...G.TGT BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1682 0 2 ...G.GCC BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1731 0 2 ...T.AGC BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1812 0 2 ...C.TAT BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1853 0 2 ...C.CGA BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1919 0 2 ...A.CTG BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 2006 0 2 ...G.GCC BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 64 0 2 ...A.GTT BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1646 0 2 ...T.GAC BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 37 0 2 ...G.CGA BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1515 0 2 ...G.ATG BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 466 0 2 ...T.ACA BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 558 0 2 ...A.CGA BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 714 0 2 ...AGCGA BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1933 0 2 ...TTAGC BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 628 0 2 ...TAACA BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 44 0 2 ...AGCGA BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 428 0 2 ...ATGTT BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1924 0 2 ...AACTG BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 234 0 2 ...GCTTA BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1004 0 2 ...GCCGA BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1214 0 2 ...CATGA BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1034 0 2 ...AGCCT BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1536 0 2 ..ACATCT BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 684 0 2 ..AAACGA BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 893 0 2 ..CAATTC BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 604 0 2 ..CAACTG BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 760 0 2 ..ACAACA BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1452 0 2 ..AGATCC BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1959 0 2 ..TGCTTA BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1938 0 2 ..CTCGAC BBBBBBBB 1
-SL-XAQ 505091110 9 2 1 1221 0 2 ..GGATGT BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 363 0 2 ..TATGTT DDMXXXXX 1
-SL-XAQ 505091110 9 2 1 170 0 2 ..GAGCCT BBBBBBBB 1
-SL-XAQ 505091110 9 2 2 463 0 2 C.TAGCGA YDXWMG]X 0
-SL-XAQ 505091110 9 2 2 1636 0 2 ATCAACCC RUW^BBBB 0
-SL-XAQ 505091110 9 2 2 828 0 2 TATATCGA BBBBBBBB 0
-SL-XAQ 505091110 9 2 2 220 0 2 TCGGAATG a`\\__^Z 1
-SL-XAQ 505091110 9 2 2 101 0 2 TACTTAGC aa\bbbb^ 1
-SL-XAQ 505091110 9 2 2 351 0 2 TGATAGAA BBBBBBBB 0
-SL-XAQ 505091110 9 2 2 1559 0 2 TTGAGCCT `_T__Sab 1
-SL-XAQ 505091110 9 2 2 1671 0 2 CCAGTTAG _]]aZa`X 0
-SL-XAQ 505091110 9 2 2 0 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 2 61 0 2 GTATAACA [`abaaXa 1
-SL-XAQ 505091110 9 2 2 1842 0 2 AAGGATGT _YPZRXa] 0
-SL-XAQ 505091110 9 2 2 12 0 2 TACTTAGC `WDX[\BB 0
-SL-XAQ 505091110 9 2 2 599 0 2 AGCAATTC YLWa`aa^ 0
-SL-XAQ 505091110 9 2 2 115 0 2 TGCTCGAC a`\]\__\ 0
-SL-XAQ 505091110 9 2 2 255 0 2 CCAGTTAG `[^b``_Z 1
-SL-XAQ 505091110 9 2 2 1298 0 2 ACCAACTG `V][[DZ[ 0
-SL-XAQ 505091110 9 2 2 775 0 2 TTCGCTGA abbU`aab 1
-SL-XAQ 505091110 9 2 2 131 0 2 CACAATCC ``bbab`_ 1
-SL-XAQ 505091110 9 2 2 904 0 2 ACCAACTG `^`aa^ZV 0
-SL-XAQ 505091110 9 2 2 1038 0 2 GGTCCAGA \V\^^a__ 0
-SL-XAQ 505091110 9 2 2 669 0 2 TTCGCTGA a]aa_aaX 0
-SL-XAQ 505091110 9 2 2 488 0 2 TTGAGCCT _]\__Z_` 1
-SL-XAQ 505091110 9 2 2 953 0 2 CAGGAACC TGYXZFZZ 0
-SL-XAQ 505091110 9 2 2 1723 0 2 CCAATTAG _`BBBBBB 0
-SL-XAQ 505091110 9 2 2 1944 0 2 AAGGATGT aaXaa`YB 1
-SL-XAQ 505091110 9 2 2 1567 0 2 GCACATCT _a\Z_a^_ 1
-SL-XAQ 505091110 9 2 2 679 0 2 CATGCTTA T^_^^W[_ 0
-SL-XAQ 505091110 9 2 2 1985 0 2 AAGGATGT ab^V]Q[W 0
-SL-XAQ 505091110 9 2 2 1402 0 2 CACATCCT \__a`aba 0
-SL-XAQ 505091110 9 2 2 1874 0 2 ACCAACTG a]]]^W_\ 1
-SL-XAQ 505091110 9 2 2 611 0 2 CATAGCGA W_bba\Z_ 0
-SL-XAQ 505091110 9 2 2 1974 0 2 AGCAATCT ]BBBBBBB 0
-SL-XAQ 505091110 9 2 2 1012 0 2 CACATCCT aa^a`aaa 1
-SL-XAQ 505091110 9 2 2 303 0 2 CAGGAGCC `]I__XBB 0
-SL-XAQ 505091110 9 2 2 1365 0 2 AACTTGAC ab`a]]`a 0
-SL-XAQ 505091110 9 2 2 184 0 2 GCACACGA ]Z[_`__R 0
-SL-XAQ 505091110 9 2 2 646 0 2 ATCAATTA GG]SNSOU 0
-SL-XAQ 505091110 9 2 2 1662 0 2 GTATAACA WQa`_``a 0
-SL-XAQ 505091110 9 2 2 1745 0 2 ACCAACTG a`]aa`aa 1
-SL-XAQ 505091110 9 2 3 1952 0 2 AAGGATGT aa^aa_a[ 1
-SL-XAQ 505091110 9 2 3 112 0 2 CCAGTTAG a_[b`b_U 1
-SL-XAQ 505091110 9 2 3 386 0 2 GGTCCAGA X__XX__X 0
-SL-XAQ 505091110 9 2 3 490 0 2 AAGGATGT ^BBBBBBB 0
-SL-XAQ 505091110 9 2 3 495 0 2 GCACACGA TZT[`_\Z 0
-SL-XAQ 505091110 9 2 3 577 0 2 ACCAACTG a^YS[`^^ 0
-SL-XAQ 505091110 9 2 3 695 0 2 TCTGGCGA ``^]X\_` 1
-SL-XAQ 505091110 9 2 3 808 0 2 AGCAATTC ]QTYX^BB 0
-SL-XAQ 505091110 9 2 3 862 0 2 TAACAAGA SH\UXH\_ 0
-SL-XAQ 505091110 9 2 3 889 0 2 ATTATGTT O`U\`[J` 0
-SL-XAQ 505091110 9 2 3 1025 0 2 GCACACGA _\`a`___ 1
-SL-XAQ 505091110 9 2 3 1053 0 2 GCACATCT U[^a^b_S 0
-SL-XAQ 505091110 9 2 3 1123 0 2 TTGAGCCT a_UVGM`` 0
-SL-XAQ 505091110 9 2 3 1209 0 2 AACTTGAC R^_^XQZa 1
-SL-XAQ 505091110 9 2 3 1290 0 2 GCACACGA HTZ\_[GZ 0
-SL-XAQ 505091110 9 2 3 1387 0 2 CCAGTTAG ZJaKQRQ` 0
-SL-XAQ 505091110 9 2 3 1529 0 2 TAGAACCT XH_VR^a\ 0
-SL-XAQ 505091110 9 2 3 1576 0 2 CCAGTTAG Ya^\b`b` 0
-SL-XAQ 505091110 9 2 3 1581 0 2 GTATAACA YS[a```b 0
-SL-XAQ 505091110 9 2 3 1733 0 2 GGTCCAGA N]aaa``\ 1
-SL-XAQ 505091110 9 2 3 1775 0 2 CATGCTTA Z[RX[Z__ 1
-SL-XAQ 505091110 9 2 3 1807 0 2 AACTTGAC a^S\a_][ 0
-SL-XAQ 505091110 9 2 3 1844 0 2 TACTTAGC a^ab]Y__ 0
-SL-XAQ 505091110 9 2 3 1898 0 2 CATAGCGA aaba_\a_ 0
-SL-XAQ 505091110 9 2 3 1917 0 2 GCACACGA NTZ_\ZaX 0
-SL-XAQ 505091110 9 2 3 1970 0 2 CTACCAGG a`aaa`a_ 1
-SL-XAQ 505091110 9 2 3 2004 0 2 TCTGGCGA _^]N]aaa 0
-SL-XAQ 505091110 9 2 3 2038 0 2 AACTTGAC a`_ZGP]a 0
-SL-XAQ 505091110 9 2 3 317 0 2 TGCTCGAC a``aa`[\ 1
-SL-XAQ 505091110 9 2 3 1941 0 2 AACTTGAC abaaaaaa 1
-SL-XAQ 505091110 9 2 3 157 0 2 AGCAATTC aaa^^ba` 1
-SL-XAQ 505091110 9 2 3 99 0 2 CAGGAGCG GPZ`ZBBB 0
-SL-XAQ 505091110 9 2 3 143 0 2 TGTCGGAT `]`a^^\a 1
-SL-XAQ 505091110 9 2 3 328 0 2 CAAATCCT R[HHY[G[ 0
-SL-XAQ 505091110 9 2 3 932 0 2 CATGCTTA \b_``bba 1
-SL-XAQ 505091110 9 2 3 1484 0 2 CCAGTTAG ]a```b_[ 1
-SL-XAQ 505091110 9 2 3 875 0 2 CCTACCAT Z\___W_a 0
-SL-XAQ 505091110 9 2 3 1016 0 2 CATAGCGA ]_b__P_b 1
-SL-XAQ 505091110 9 2 3 198 0 2 CAGGATCT THOI_VWQ 0
-SL-XAQ 505091110 9 2 3 470 0 2 AAGGATGT a_UYY\aY 1
-SL-XAQ 505091110 9 2 3 1094 0 2 CACATCCT `abab]Ya 1
-SL-XAQ 505091110 9 2 3 782 0 2 TTGAGCCT a```[Za^ 1
-SL-XAQ 505091110 9 2 3 991 0 2 AGCAATTC aa`a_aa[ 1
-SL-XAQ 505091110 9 2 3 1962 0 2 AGTTGCTT `VU_W\O\ 1
-SL-XAQ 505091110 9 2 3 1101 0 2 TTGAGCCT V_TV[IT\ 1
-SL-XAQ 505091110 9 2 3 207 0 2 ACCAACTG a`ZU_^^_ 1
-SL-XAQ 505091110 9 2 3 1326 0 2 AACTTGAC abaaaRaa 0
-SL-XAQ 505091110 9 2 3 728 0 2 TACTTAGC aab`]aVB 0
-SL-XAQ 505091110 9 2 3 691 0 2 AGTTGCTT _\W_]_^` 1
-SL-XAQ 505091110 9 2 3 1352 0 2 GGTCCAGA OH[OZ___ 1
-SL-XAQ 505091110 9 2 3 1389 0 2 TGTCGGAT ^Q`b`_a[ 1
-SL-XAQ 505091110 9 2 3 987 0 2 TCTCGCGA O[GMGZP_ 0
-SL-XAQ 505091110 9 2 3 1133 0 2 AGCAATTC ^^X_T`aZ 1
-SL-XAQ 505091110 9 2 3 399 0 2 CATAGCGA \aa_\\`_ 1
-SL-XAQ 505091110 9 2 3 16 0 2 CACATCCT [[S__\F_ 1
-SL-XAQ 505091110 9 2 3 2013 0 2 CATAGCGA Vaba[_^[ 0
-SL-XAQ 505091110 9 2 3 898 0 2 TGTCGGAT ]W]`_\[_ 1
-SL-XAQ 505091110 9 2 3 1712 0 2 CACATCCT aa]__^\] 1
-SL-XAQ 505091110 9 2 3 179 0 2 GTTTATTA BBBBBBBB 0
-SL-XAQ 505091110 9 2 3 151 0 2 CAGGAGCC _`WNZ`\\ 1
-SL-XAQ 505091110 9 2 3 983 0 2 CATAGCGA `bbb_^`^ 1
-SL-XAQ 505091110 9 2 3 567 0 2 TCGGAATG _^_^`a_[ 1
-SL-XAQ 505091110 9 2 3 72 0 2 AGTTGCTT abab`]aa 1
-SL-XAQ 505091110 9 2 3 922 0 2 TCGGAATG a`[`ab^Z 1
-SL-XAQ 505091110 9 2 3 584 0 2 CATGCTTA ]`^^[bbb 1
-SL-XAQ 505091110 9 2 3 274 0 2 AGTTGCTT __^^[^ab 1
-SL-XAQ 505091110 9 2 3 1602 0 2 AGCAATTC ^U[`_a]W 1
-SL-XAQ 505091110 9 2 3 4 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 3 663 0 2 TCGGAATG \[QR[b\W 0
-SL-XAQ 505091110 9 2 3 80 0 2 TACTTAGC a_X`a`_W 1
-SL-XAQ 505091110 9 2 3 1179 0 2 CCAGTTAG HZZX__ZB 0
-SL-XAQ 505091110 9 2 3 589 0 2 AAGGATGT ^aaXaa_X 1
-SL-XAQ 505091110 9 2 3 640 0 2 AGTTGCTT `\aaaZ[` 1
-SL-XAQ 505091110 9 2 3 2030 0 2 GATCAAGA GGG]G[_[ 0
-SL-XAQ 505091110 9 2 3 247 0 2 CGGTAGCT BBBBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_3_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_3_0001_qseq.txt
deleted file mode 100644
index cdb025a..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_3_0001_qseq.txt
+++ /dev/null
@@ -1,200 +0,0 @@
-SL-XAQ 505091110 9 1 0 1434 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 464 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 113 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1703 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 879 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 841 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1291 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1940 0 2 .....C.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 586 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1690 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 37 0 2 .....G.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 324 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 205 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1307 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1193 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1475 0 2 .....C.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 275 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 2001 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1093 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 0 1038 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 173 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1836 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1513 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1917 0 2 .....AC. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1696 0 2 .....CT. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 812 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 2 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1555 0 2 .....C.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1243 0 2 .....TG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 30 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 41 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 59 0 2 .....A.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 111 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 132 0 2 .....T.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 140 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 155 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 164 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 170 0 2 .....AC. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 184 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 195 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 240 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 262 0 2 .....C.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 299 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 353 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 367 0 2 .....A.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 416 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 483 0 2 .....TA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 486 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 495 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 508 0 2 .....C.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 554 0 2 .....TA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 567 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 613 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 622 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 627 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 684 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 874 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 931 0 2 .....C.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 994 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1013 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1153 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1184 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1241 0 2 .....C.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1282 0 2 .....C.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1320 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1391 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1684 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1733 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1770 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1906 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1954 0 2 .....C.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1247 0 2 .....A.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 18 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1521 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 264 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1815 0 2 ...T.... BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1379 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 2011 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1372 0 2 ...G.... BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 55 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 517 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 965 0 2 ...T.... BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 535 0 2 ...C.... BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 72 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 1 1886 0 2 ...G.... BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 1932 0 2 ...C.... BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 1706 0 2 ...C.... BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 363 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 605 0 2 ...T.... BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 449 0 2 ...G.... BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1782 0 2 ........ BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 246 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 307 0 2 ...T.... BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 150 0 2 ...A.... BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 546 0 2 .....G.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1727 0 2 ...T.... BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1946 0 2 .....G.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1275 0 2 ...A.... BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 786 0 2 ...G.... BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 747 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 25 0 2 ...G.... BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1722 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1301 0 2 ...TA... BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1592 0 2 ...GA... BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 943 0 2 ...CC... BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 974 0 2 ...AT... DDOYYYY[ 1
-SL-XAQ 505091110 9 1 2 858 0 2 ....AT.. DDNTVVXX 1
-SL-XAQ 505091110 9 1 2 209 0 2 ...AT... BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 988 0 2 ...GG... BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 1453 0 2 ........ BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 69 0 2 ....AG.. BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1158 0 2 ....TA.. BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 1753 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1238 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 9 1 2 1827 0 2 ....AC.. BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 309 0 2 AAGGATGT BBBBBBBB 1
-SL-XAQ 505091110 9 1 2 1889 0 2 TTCGCTGA DMSUYZZX 1
-SL-XAQ 505091110 9 1 2 1878 0 2 GTATAACA a[WP[\VZ 1
-SL-XAQ 505091110 9 1 2 658 0 2 TGCTCGAC _V\___\Z 1
-SL-XAQ 505091110 9 1 2 119 0 2 GGTCCAGA ^_]\Z[ba 1
-SL-XAQ 505091110 9 1 2 1417 0 2 TTCGCTGA a^T^^ab^ 1
-SL-XAQ 505091110 9 1 2 1895 0 2 GGTCCAGA ^_bb_]ab 1
-SL-XAQ 505091110 9 1 2 52 0 2 AGCAATTC YZZZYZ\Z 0
-SL-XAQ 505091110 9 1 2 85 0 2 CACATCCT a]G]a\aQ 0
-SL-XAQ 505091110 9 1 2 63 0 2 AAGGATGT V_\a[b_B 1
-SL-XAQ 505091110 9 1 2 737 0 2 CACATCCT abbbabaa 0
-SL-XAQ 505091110 9 1 2 802 0 2 GTATAACA \]O]^V]B 1
-SL-XAQ 505091110 9 1 2 1465 0 2 TACTTAGC [Y_\aa__ 0
-SL-XAQ 505091110 9 1 2 1507 0 2 TGCTCGAC ^Q\_X`[] 1
-SL-XAQ 505091110 9 1 2 950 0 2 ACCAACTG __\`Y``` 1
-SL-XAQ 505091110 9 1 2 358 0 2 TTGAGCCT `^ZUTPVR 0
-SL-XAQ 505091110 9 1 2 1336 0 2 GTATAACA V_X\a\V_ 1
-SL-XAQ 505091110 9 1 2 190 0 2 GGTCCAGA ``bb\\_a 1
-SL-XAQ 505091110 9 1 2 1995 0 2 CCTACCAT a\``^aa` 1
-SL-XAQ 505091110 9 1 2 425 0 2 GTATAACA ``__\XZ[ 1
-SL-XAQ 505091110 9 1 2 455 0 2 CAGGAGCC K_BBBBBB 0
-SL-XAQ 505091110 9 1 2 11 0 2 CAGGAGCC _V\\_VBB 0
-SL-XAQ 505091110 9 1 2 636 0 2 CTACCAGG UR[_`^a\ 0
-SL-XAQ 505091110 9 1 3 1488 0 2 CAGGAGCC HV[Xaaaa 1
-SL-XAQ 505091110 9 1 3 795 0 2 TGTCGGAT ]WW_`]BB 0
-SL-XAQ 505091110 9 1 3 1406 0 2 AGTTGCTT ``\ZT_\_ 0
-SL-XAQ 505091110 9 1 3 1861 0 2 TCTGGCGA aX_][`[b 1
-SL-XAQ 505091110 9 1 3 389 0 2 CATGCTTA [Y___TUZ 0
-SL-XAQ 505091110 9 1 3 683 0 2 TACTTAGC a_W_a^ba 1
-SL-XAQ 505091110 9 1 3 273 0 2 TTCGCTGA RW\TJ`bV 0
-SL-XAQ 505091110 9 1 3 277 0 2 GGTCCAGA a`^ZR]a\ 0
-SL-XAQ 505091110 9 1 3 301 0 2 CCAGTTAG BBBBBBBB 0
-SL-XAQ 505091110 9 1 3 347 0 2 TCGGAATG S`]^_HU[ 0
-SL-XAQ 505091110 9 1 3 579 0 2 ....AT.. VRBBBBBB 0
-SL-XAQ 505091110 9 1 3 608 0 2 TTCGCTGA ``Ta^aa_ 1
-SL-XAQ 505091110 9 1 3 699 0 2 TCTGGCGA XW^]W]BB 0
-SL-XAQ 505091110 9 1 3 959 0 2 CCAGTTAG R^Z`a^\[ 1
-SL-XAQ 505091110 9 1 3 1155 0 2 AACTTGAC BBBBBBBB 0
-SL-XAQ 505091110 9 1 3 1233 0 2 ...AC... BBBBBBBB 0
-SL-XAQ 505091110 9 1 3 1348 0 2 AGCAATTC aX^^_V_T 1
-SL-XAQ 505091110 9 1 3 1358 0 2 CCTACCAT UQaaBBBB 0
-SL-XAQ 505091110 9 1 3 1450 0 2 TTGAGCCT abPF[V`B 0
-SL-XAQ 505091110 9 1 3 1574 0 2 CACATCCT _`baab_` 1
-SL-XAQ 505091110 9 1 3 1688 0 2 GCACACGA ]_\\Zb`\ 1
-SL-XAQ 505091110 9 1 3 1717 0 2 AGTTGCTT `a\PPZ`_ 1
-SL-XAQ 505091110 9 1 3 1764 0 2 TTCGCTGA aa^aa_Y` 0
-SL-XAQ 505091110 9 1 3 1973 0 2 CAGGAGCC VZb`bbab 1
-SL-XAQ 505091110 9 1 3 1981 0 2 AGCAATTC \I_PZ_aa 1
-SL-XAQ 505091110 9 1 3 198 0 2 CCTACCAT `aaa``^_ 1
-SL-XAQ 505091110 9 1 3 1927 0 2 GTATAACA a_[__\_^ 0
-SL-XAQ 505091110 9 1 3 162 0 2 TTGAGCCT aaab_T]^ 1
-SL-XAQ 505091110 9 1 3 751 0 2 TACTTAGC X_b`bbbb 1
-SL-XAQ 505091110 9 1 3 918 0 2 .....CT. H^Sa]BBB 0
-SL-XAQ 505091110 9 1 3 1760 0 2 TTGAGCCT a`aa`a`` 1
-SL-XAQ 505091110 9 1 3 1222 0 2 TTGAGCCT _bb\__]a 1
-SL-XAQ 505091110 9 1 3 1677 0 2 TTGAGCCT ab`]\S\a 1
-SL-XAQ 505091110 9 1 3 890 0 2 ..CA.... BBBBBBBB 0
-SL-XAQ 505091110 9 1 3 405 0 2 .....AG. OG][\BBB 0
-SL-XAQ 505091110 9 1 3 1544 0 2 CCAGTTAG GG[MZZPZ 0
-SL-XAQ 505091110 9 1 3 1219 0 2 TGTCGGAT a^__`^^X 1
-SL-XAQ 505091110 9 1 3 1294 0 2 TC...... IRV[[_T[ 0
-SL-XAQ 505091110 9 1 3 1867 0 2 TCGGAATG aa`_VX]a 1
-SL-XAQ 505091110 9 1 3 1341 0 2 TCTGGCGA aBBBBBBB 1
-SL-XAQ 505091110 9 1 3 676 0 2 CATAGCGA YGM[GGY_ 0
-SL-XAQ 505091110 9 1 3 131 0 2 CAGGAGCC SWbb`b`b 1
-SL-XAQ 505091110 9 1 3 1311 0 2 CCAGTTAG [^a``_`a 1
-SL-XAQ 505091110 9 1 3 900 0 2 CCTACCAT GGGM`_WT 0
-SL-XAQ 505091110 9 1 3 2027 0 2 TTCGCTGA a]VL[YYB 1
-SL-XAQ 505091110 9 1 3 996 0 2 GCACACGA `_T\]b[B 1
-SL-XAQ 505091110 9 1 3 289 0 2 CAGGAGCC ]abbbba] 1
-SL-XAQ 505091110 9 1 3 33 0 2 CATAGCGA PV\ZKF__ 0
-SL-XAQ 505091110 9 1 3 905 0 2 AC...... ``VWN[YB 0
-SL-XAQ 505091110 9 1 3 1525 0 2 GCACATCT aaaZaaaa 1
-SL-XAQ 505091110 9 1 3 583 0 2 GCACACGA \]XRZb`] 1
-SL-XAQ 505091110 9 1 3 2037 0 2 ATTATGTT ^[HY\_\_ 0
-SL-XAQ 505091110 9 1 3 1319 0 2 TGTCGGAT ^^W_`]WY 0
-SL-XAQ 505091110 9 1 3 1513 0 2 GGTCCAGA T_a\RV_a 1
-SL-XAQ 505091110 9 1 3 1188 0 2 CAGGAGCC aaababba 1
-SL-XAQ 505091110 9 1 3 673 0 2 ...CC... G[BBBBBB 0
-SL-XAQ 505091110 9 1 3 471 0 2 CATAGCGA [`\_a\^_ 1
-SL-XAQ 505091110 9 1 3 1328 0 2 ATTATGTT `__Q\^WR 0
-SL-XAQ 505091110 9 1 3 985 0 2 TTGAGCCT aaaa_]_a 1
-SL-XAQ 505091110 9 1 3 176 0 2 CCTACCAT `aaa^`aa 1
-SL-XAQ 505091110 9 1 3 880 0 2 AAGGATGT ]_UQZ`\\ 0
-SL-XAQ 505091110 9 1 3 695 0 2 ATTATGTT a^Zaaa\^ 1
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_3_0002_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_3_0002_qseq.txt
deleted file mode 100644
index 32245a3..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/BasecallsDir/s_9_3_0002_qseq.txt
+++ /dev/null
@@ -1,200 +0,0 @@
-SL-XAQ 505091110 9 2 0 135 0 2 .....C.. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1547 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 87 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 205 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 50 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1620 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1278 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 186 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 287 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 441 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 766 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1598 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 382 0 2 .....T.. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 740 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 501 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1135 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 73 0 2 .....C.. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1668 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1198 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 9 2 0 1073 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1351 0 2 .....T.. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1987 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1755 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1950 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 8 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 56 0 2 .....A.. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 211 0 2 .....TG. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 242 0 2 ...C.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 262 0 2 ...C.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 298 0 2 ...G.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 312 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 370 0 2 ...A.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 377 0 2 .....T.. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 414 0 2 ...G.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 421 0 2 ...A.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 555 0 2 ...C.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 569 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 699 0 2 ...C.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 722 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 749 0 2 .....G.. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 833 0 2 .....CC. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 848 0 2 ...A.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 998 0 2 .....G.. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1159 0 2 ...T.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1168 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1180 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1306 0 2 .....C.. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1424 0 2 ...C.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1521 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1543 0 2 ...A.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1617 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1627 0 2 ...A.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1653 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1682 0 2 .....G.. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1731 0 2 .....AG. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1812 0 2 ...C.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1853 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1919 0 2 ...A.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 2006 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 64 0 2 .....GT. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1646 0 2 ...T.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 37 0 2 ...G.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1515 0 2 .....A.. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 466 0 2 ...T.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 558 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 714 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1933 0 2 ...T.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 628 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 44 0 2 ...AG... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 428 0 2 ...A.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1924 0 2 ...AA... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 234 0 2 ....CT.. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1004 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1214 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1034 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1536 0 2 ..A..... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 684 0 2 ..AA.... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 893 0 2 ...AA... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 604 0 2 ..C..... BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 760 0 2 ....AA.. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1452 0 2 ....AT.. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1959 0 2 ....CT.. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 1938 0 2 ..CT.... BBBBBBBB 1
-SL-XAQ 505091110 9 2 1 1221 0 2 .....TG. BBBBBBBB 0
-SL-XAQ 505091110 9 2 1 363 0 2 ..T..... DDMXXXXX 1
-SL-XAQ 505091110 9 2 1 170 0 2 ...AG... BBBBBBBB 1
-SL-XAQ 505091110 9 2 2 463 0 2 GGTCCAGA YDXWMG]X 0
-SL-XAQ 505091110 9 2 2 1636 0 2 ...AA... RUW^BBBB 0
-SL-XAQ 505091110 9 2 2 828 0 2 .....CG. BBBBBBBB 0
-SL-XAQ 505091110 9 2 2 220 0 2 ATTATGTT a`\\__^Z 1
-SL-XAQ 505091110 9 2 2 101 0 2 CACATCCT aa\bbbb^ 1
-SL-XAQ 505091110 9 2 2 351 0 2 .....GA. BBBBBBBB 0
-SL-XAQ 505091110 9 2 2 1559 0 2 AACTTGAC `_T__Sab 1
-SL-XAQ 505091110 9 2 2 1671 0 2 GCACACGA _]]aZa`X 0
-SL-XAQ 505091110 9 2 2 0 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 2 61 0 2 CAGGAGCC [`abaaXa 1
-SL-XAQ 505091110 9 2 2 1842 0 2 TTCGCTGA _YPZRXa] 0
-SL-XAQ 505091110 9 2 2 12 0 2 CACATCCT `WDX[\BB 0
-SL-XAQ 505091110 9 2 2 599 0 2 TGCTCGAC YLWa`aa^ 0
-SL-XAQ 505091110 9 2 2 115 0 2 AGCAATTC a`\]\__\ 0
-SL-XAQ 505091110 9 2 2 255 0 2 GCACACGA `[^b``_Z 1
-SL-XAQ 505091110 9 2 2 1298 0 2 TGTCGGAT `V][[DZ[ 0
-SL-XAQ 505091110 9 2 2 775 0 2 AAGGATGT abbU`aab 1
-SL-XAQ 505091110 9 2 2 131 0 2 ...AA... ``bbab`_ 1
-SL-XAQ 505091110 9 2 2 904 0 2 TGTCGGAT `^`aa^ZV 0
-SL-XAQ 505091110 9 2 2 1038 0 2 CATAGCGA \V\^^a__ 0
-SL-XAQ 505091110 9 2 2 669 0 2 AAGGATGT a]aa_aaX 0
-SL-XAQ 505091110 9 2 2 488 0 2 AACTTGAC _]\__Z_` 1
-SL-XAQ 505091110 9 2 2 953 0 2 GTATAACA TGYXZFZZ 0
-SL-XAQ 505091110 9 2 2 1723 0 2 GCACACGA _`BBBBBB 0
-SL-XAQ 505091110 9 2 2 1944 0 2 TTCGCTGA aaXaa`YB 1
-SL-XAQ 505091110 9 2 2 1567 0 2 CATGCTTA _a\Z_a^_ 1
-SL-XAQ 505091110 9 2 2 679 0 2 GCACATCT T^_^^W[_ 0
-SL-XAQ 505091110 9 2 2 1985 0 2 TTCGCTGA ab^V]Q[W 0
-SL-XAQ 505091110 9 2 2 1402 0 2 TACTTAGC \__a`aba 0
-SL-XAQ 505091110 9 2 2 1874 0 2 TGTCGGAT a]]]^W_\ 1
-SL-XAQ 505091110 9 2 2 611 0 2 GGTCCAGA W_bba\Z_ 0
-SL-XAQ 505091110 9 2 2 1974 0 2 .GC..... ]BBBBBBB 0
-SL-XAQ 505091110 9 2 2 1012 0 2 TACTTAGC aa^a`aaa 1
-SL-XAQ 505091110 9 2 2 303 0 2 GTATAACA `]I__XBB 0
-SL-XAQ 505091110 9 2 2 1365 0 2 TTGAGCCT ab`a]]`a 0
-SL-XAQ 505091110 9 2 2 184 0 2 CCAGTTAG ]Z[_`__R 0
-SL-XAQ 505091110 9 2 2 646 0 2 .TC..... GG]SNSOU 0
-SL-XAQ 505091110 9 2 2 1662 0 2 CAGGAGCC WQa`_``a 0
-SL-XAQ 505091110 9 2 2 1745 0 2 TGTCGGAT a`]aa`aa 1
-SL-XAQ 505091110 9 2 3 1952 0 2 TTCGCTGA aa^aa_a[ 1
-SL-XAQ 505091110 9 2 3 112 0 2 GCACACGA a_[b`b_U 1
-SL-XAQ 505091110 9 2 3 386 0 2 CATAGCGA X__XX__X 0
-SL-XAQ 505091110 9 2 3 490 0 2 TTCGCTGA ^BBBBBBB 0
-SL-XAQ 505091110 9 2 3 495 0 2 CCAGTTAG TZT[`_\Z 0
-SL-XAQ 505091110 9 2 3 577 0 2 TGTCGGAT a^YS[`^^ 0
-SL-XAQ 505091110 9 2 3 695 0 2 AGTTGCTT ``^]X\_` 1
-SL-XAQ 505091110 9 2 3 808 0 2 TGCTCGAC ]QTYX^BB 0
-SL-XAQ 505091110 9 2 3 862 0 2 TA...... SH\UXH\_ 0
-SL-XAQ 505091110 9 2 3 889 0 2 TCGGAATG O`U\`[J` 0
-SL-XAQ 505091110 9 2 3 1025 0 2 CCAGTTAG _\`a`___ 1
-SL-XAQ 505091110 9 2 3 1053 0 2 CATGCTTA U[^a^b_S 0
-SL-XAQ 505091110 9 2 3 1123 0 2 AACTTGAC a_UVGM`` 0
-SL-XAQ 505091110 9 2 3 1209 0 2 TTGAGCCT R^_^XQZa 1
-SL-XAQ 505091110 9 2 3 1290 0 2 CCAGTTAG HTZ\_[GZ 0
-SL-XAQ 505091110 9 2 3 1387 0 2 GCACACGA ZJaKQRQ` 0
-SL-XAQ 505091110 9 2 3 1529 0 2 .AG..... XH_VR^a\ 0
-SL-XAQ 505091110 9 2 3 1576 0 2 GCACACGA Ya^\b`b` 0
-SL-XAQ 505091110 9 2 3 1581 0 2 CAGGAGCC YS[a```b 0
-SL-XAQ 505091110 9 2 3 1733 0 2 CATAGCGA N]aaa``\ 1
-SL-XAQ 505091110 9 2 3 1775 0 2 GCACATCT Z[RX[Z__ 1
-SL-XAQ 505091110 9 2 3 1807 0 2 TTGAGCCT a^S\a_][ 0
-SL-XAQ 505091110 9 2 3 1844 0 2 CACATCCT a^ab]Y__ 0
-SL-XAQ 505091110 9 2 3 1898 0 2 GGTCCAGA aaba_\a_ 0
-SL-XAQ 505091110 9 2 3 1917 0 2 CCAGTTAG NTZ_\ZaX 0
-SL-XAQ 505091110 9 2 3 1970 0 2 CCTACCAT a`aaa`a_ 1
-SL-XAQ 505091110 9 2 3 2004 0 2 AGTTGCTT _^]N]aaa 0
-SL-XAQ 505091110 9 2 3 2038 0 2 TTGAGCCT a`_ZGP]a 0
-SL-XAQ 505091110 9 2 3 317 0 2 AGCAATTC a``aa`[\ 1
-SL-XAQ 505091110 9 2 3 1941 0 2 TTGAGCCT abaaaaaa 1
-SL-XAQ 505091110 9 2 3 157 0 2 TGCTCGAC aaa^^ba` 1
-SL-XAQ 505091110 9 2 3 99 0 2 GTATAACA GPZ`ZBBB 0
-SL-XAQ 505091110 9 2 3 143 0 2 ACCAACTG `]`a^^\a 1
-SL-XAQ 505091110 9 2 3 328 0 2 TACTTAGC R[HHY[G[ 0
-SL-XAQ 505091110 9 2 3 932 0 2 GCACATCT \b_``bba 1
-SL-XAQ 505091110 9 2 3 1484 0 2 GCACACGA ]a```b_[ 1
-SL-XAQ 505091110 9 2 3 875 0 2 CTACCAGG Z\___W_a 0
-SL-XAQ 505091110 9 2 3 1016 0 2 GGTCCAGA ]_b__P_b 1
-SL-XAQ 505091110 9 2 3 198 0 2 .....TC. THOI_VWQ 0
-SL-XAQ 505091110 9 2 3 470 0 2 TTCGCTGA a_UYY\aY 1
-SL-XAQ 505091110 9 2 3 1094 0 2 TACTTAGC `abab]Ya 1
-SL-XAQ 505091110 9 2 3 782 0 2 AACTTGAC a```[Za^ 1
-SL-XAQ 505091110 9 2 3 991 0 2 TGCTCGAC aa`a_aa[ 1
-SL-XAQ 505091110 9 2 3 1962 0 2 TCTGGCGA `VU_W\O\ 1
-SL-XAQ 505091110 9 2 3 1101 0 2 AACTTGAC V_TV[IT\ 1
-SL-XAQ 505091110 9 2 3 207 0 2 TGTCGGAT a`ZU_^^_ 1
-SL-XAQ 505091110 9 2 3 1326 0 2 TTGAGCCT abaaaRaa 0
-SL-XAQ 505091110 9 2 3 728 0 2 CACATCCT aab`]aVB 0
-SL-XAQ 505091110 9 2 3 691 0 2 TCTGGCGA _\W_]_^` 1
-SL-XAQ 505091110 9 2 3 1352 0 2 CATAGCGA OH[OZ___ 1
-SL-XAQ 505091110 9 2 3 1389 0 2 ACCAACTG ^Q`b`_a[ 1
-SL-XAQ 505091110 9 2 3 987 0 2 AGTTGCTT O[GMGZP_ 0
-SL-XAQ 505091110 9 2 3 1133 0 2 TGCTCGAC ^^X_T`aZ 1
-SL-XAQ 505091110 9 2 3 399 0 2 GGTCCAGA \aa_\\`_ 1
-SL-XAQ 505091110 9 2 3 16 0 2 TACTTAGC [[S__\F_ 1
-SL-XAQ 505091110 9 2 3 2013 0 2 GGTCCAGA Vaba[_^[ 0
-SL-XAQ 505091110 9 2 3 898 0 2 ACCAACTG ]W]`_\[_ 1
-SL-XAQ 505091110 9 2 3 1712 0 2 TACTTAGC aa]__^\] 1
-SL-XAQ 505091110 9 2 3 179 0 2 ...TA... BBBBBBBB 0
-SL-XAQ 505091110 9 2 3 151 0 2 GTATAACA _`WNZ`\\ 1
-SL-XAQ 505091110 9 2 3 983 0 2 GGTCCAGA `bbb_^`^ 1
-SL-XAQ 505091110 9 2 3 567 0 2 ATTATGTT _^_^`a_[ 1
-SL-XAQ 505091110 9 2 3 72 0 2 TCTGGCGA abab`]aa 1
-SL-XAQ 505091110 9 2 3 922 0 2 ATTATGTT a`[`ab^Z 1
-SL-XAQ 505091110 9 2 3 584 0 2 GCACATCT ]`^^[bbb 1
-SL-XAQ 505091110 9 2 3 274 0 2 TCTGGCGA __^^[^ab 1
-SL-XAQ 505091110 9 2 3 1602 0 2 TGCTCGAC ^U[`_a]W 1
-SL-XAQ 505091110 9 2 3 4 0 2 ........ BBBBBBBB 0
-SL-XAQ 505091110 9 2 3 663 0 2 ATTATGTT \[QR[b\W 0
-SL-XAQ 505091110 9 2 3 80 0 2 CACATCCT a_X`a`_W 1
-SL-XAQ 505091110 9 2 3 1179 0 2 GCACACGA HZZX__ZB 0
-SL-XAQ 505091110 9 2 3 589 0 2 TTCGCTGA ^aaXaa_X 1
-SL-XAQ 505091110 9 2 3 640 0 2 TCTGGCGA `\aaaZ[` 1
-SL-XAQ 505091110 9 2 3 2030 0 2 ...CA... GGG]G[_[ 0
-SL-XAQ 505091110 9 2 3 247 0 2 CG...... BBBBBBBB 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/L001/C1.1/s_1_1.cif b/testdata/net/sf/picard/illumina/IlluminaTests/L001/C1.1/s_1_1.cif
deleted file mode 100755
index 3c8d5f4..0000000
Binary files a/testdata/net/sf/picard/illumina/IlluminaTests/L001/C1.1/s_1_1.cif and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/L001/C1.1/s_1_1.cnf b/testdata/net/sf/picard/illumina/IlluminaTests/L001/C1.1/s_1_1.cnf
deleted file mode 100755
index 847c82b..0000000
Binary files a/testdata/net/sf/picard/illumina/IlluminaTests/L001/C1.1/s_1_1.cnf and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/L001/C1.1/s_1_2.cif b/testdata/net/sf/picard/illumina/IlluminaTests/L001/C1.1/s_1_2.cif
deleted file mode 100755
index 89e194d..0000000
Binary files a/testdata/net/sf/picard/illumina/IlluminaTests/L001/C1.1/s_1_2.cif and /dev/null differ
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/L001/C1.1/s_1_2.cnf b/testdata/net/sf/picard/illumina/IlluminaTests/L001/C1.1/s_1_2.cnf
deleted file mode 100755
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diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/rta/BasecallsDir/s_1_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/rta/BasecallsDir/s_1_1_0001_qseq.txt
deleted file mode 100644
index 7190a89..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/rta/BasecallsDir/s_1_1_0001_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBA 1 1 1 1793 1420 0 1 G....................C.....................T.....................T.......... \DDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1441 0 1 C....................C.....................G.....................G.......... GDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDJDDDDDDDDDDDDDDDDDDDDDTDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1483 0 1 G....................G.....................A.....................A.......... YDDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDDNDDDDDDDDDDDDDDDDDDDDDWDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1495 0 1 G....................C.....................G.....................C.......... VDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1527 0 1 G....................G.....................G.....................T.......... MDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1545 0 1 C....................A.....................A.....................C.......... HDDDDDDDDDDDDDDDDDDDDHDDDDDDDDDDDDDDDDDDDDDHDDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1583 0 1 G....................G.....................G.....................A.......... YDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1596 0 1 G....................C.....................C.....................T.......... TDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDTDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1658 0 1 C....................C.....................T.....................A.......... GDDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1718 0 1 G....................C.....................C.....................C.......... YDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDHDDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1745 0 1 C....................C.....................C.....................A.......... PDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDVDDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1777 0 1 G....................C.....................T.....................C.......... YDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDYDDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1813 0 1 G....................C.....................A.....................C.......... VDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1916 0 1 G....................T.....................T.....................C.......... [DDDDDDDDDDDDDDDDDDDDUDDDDDDDDDDDDDDDDDDDDD\DDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1959 0 1 G....................C.....................T.....................C.......... [DDDDDDDDDDDDDDDDDDDD[DDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDMDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 808 0 1 T....................C.....................C.....................T.......... YDDDDDDDDDDDDDDDDDDDD^DDDDDDDDDDDDDDDDDDDDD^DDDDDDDDDDDDDDDDDDDDD[DDDDDDDDDD 0
-SL-XBA 1 1 1 1793 602 0 1 T....................A.....................A.....................A.......... [DDDDDDDDDDDDDDDDDDDD]DDDDDDDDDDDDDDDDDDDDDVDDDDDDDDDDDDDDDDDDDDDQDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1602 0 1 C....................G.....................G.....................A.......... [DDDDDDDDDDDDDDDDDDDDGDDDDDDDDDDDDDDDDDDDDDKDDDDDDDDDDDDDDDDDDDDDGDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1681 0 1 C....................T.....................A.....................A.......... ^DDDDDDDDDDDDDDDDDDDDHDDDDDDDDDDDDDDDDDDDDDEDDDDDDDDDDDDDDDDDDDDDFDDDDDDDDDD 0
-SL-XBA 1 1 1 1793 1011 0 1 A....................C.....................G.....................G.......... GDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDDDDDDDDDDDDDPDDDDDDDDDDDDDDDDDDDDDZDDDDDDDDDD 0
diff --git a/testdata/net/sf/picard/illumina/IlluminaTests/rta/BasecallsDir/s_2_1_0001_qseq.txt b/testdata/net/sf/picard/illumina/IlluminaTests/rta/BasecallsDir/s_2_1_0001_qseq.txt
deleted file mode 100644
index 2e7626a..0000000
--- a/testdata/net/sf/picard/illumina/IlluminaTests/rta/BasecallsDir/s_2_1_0001_qseq.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-SL-XBB 2 2 1 0 357 0 1 GACTTTGGGAAGGGTCATTACTGCCCTTGTAGAAAGAACACCTCATGTTCCTTATCGAGAGCGGCCGCTGCTGATC W[`bbbb_baS\`_\bbabbaWR`bba``ab_bbbbbabbbaabb^^^\aa_ab`a_`[`VaST[^SWTXWNYEHM 1
-SL-XBB 2 2 1 0 300 0 1 CGGGTTGGGGCTCTGGAAGCGGATGTGTACGGGTGGAGTGTTAGTTACATTCTGGCCCGAGTGACTTTTGGTATCA [GI\LTNG[_KOIOWGGYOKOH^HYGTNRGU[HRGTPG[YHNGF[RV[PFNJFFFDKQMFKFQQMVLDMDDDGDDK 0
-SL-XBB 2 2 1 0 872 0 1 TTTTAAATTGAGACGCATGAAGGCTAAGCGGCCGCGGAAAGACACAGGGAGGTTTACTTATTTTATTAATCAGACT abbbb`aab`\W`aaaba^Z_WX]Z`_]a`[`^_[^`R[YXZZ]]^XXYXXWMXUTTZXSV\^[TTWUSQLMKHMD 1
-SL-XBB 2 2 1 0 458 0 1 CGCGTTGCGGCCGCTGAATCCAAATCCAATAGACTCACTTTTTATTTTTATTTTTAAAATTAAAGGTTGATCTCTC ZS`b^ab[Z^__L\a[`[``a^aZX_O\\TZJ]UXaZF[``_YP^a`[\Z]`a``NV[X_aYYSPRLXFOQX_UDI 1
-SL-XBB 2 2 1 0 1934 0 1 CGTCAGCGGGCGGAAGCGGGAGGGCGAACTGGAAAGCATGAACGGAGTGGCGGACTTACTGAGATAAGTGAGAGAG IIIIX_XHZG[IWG[`_R]GZ`JRJV^Z[GMP_TNN_[_HTX\QPFZ\PTGG]RUMGSRVFFGTZGPIDSTTFSKD 0
-SL-XBB 2 2 1 0 1688 0 1 AGAAGGAGGACGACCTCGAAGCCATGAACGCAGAGGAGGACTCACTGAGGAACGGGGGAGAGGAGGAGTACGAAGC I]_`_]TV[``]ZZa``b]TG_aaaa```XXZXG]aaaa^^a[^]`[Wa_^`[[[___XaTaXK]RRXFKPSUPNI 0
-SL-XBB 2 2 1 0 1366 0 1 AGTCATCTTCTTCTTTTTGGGGCCGCGTCTCTTGGGCTTTTGATCGTCATCCTCCTCTTCCTCTTCTTCCTCCTCT \bbbababbbbbbbbbb``abYb`ba\aa___aSWa`bbba\^b``^abba^_aba_abbabaa`]\^SWK_`RMD 1
-SL-XBB 2 2 1 0 287 0 1 AGGAGATTTATTACCTATTTAAAAAATGCATTTGTAATTGTAAAATGAAAAATCACTTGCAAACAGTCTGCGCGTC Z[a`aa^^`b`_aab_bbbabbbb_aaaabbbbbaab^ab^bbbbbbbaabbbbbaa^aa`aa_a^NSRSYSaYH^ 1
-SL-XBB 2 2 1 0 538 0 1 AATTGGGCAAGAAAATAAAGTCGTTGTGGGCGGCTGGGGAACCTGGCGTCAGTCCCCCGTGGCTGTTCGCCGGCAC TGZ]Z]XGI]\\aX^a`_a`]V]_a[[^^`PVZ^a_`_Z^```X\X_`ZYVUVVZa\XUQRTU]VIGMKJJDPKDI 0
-SL-XBB 2 2 1 0 1484 0 1 CAAAACAACTCAGTTTGTTCCAAAACAATGTGAGTTCCCAGATTTAGCCTTGTCTTAATATATTGACCTTAGTTCC a``aUI]^_Q_aaaabV\b`[`abb_Saa`ab]babb_Y`_aa]aa`^aabbXWa\`aaabaaa\ZYJQ\VY^SNJ 0
-SL-XBB 2 2 1 0 650 0 1 CATGCAACATCTCCACAGCCAGCCTCCTGATCCACTGACCCAGGGACCCCTAAAGCTGGAGGCCCCAGACTCTCTC a__a```a`aaaaa__aaaa``a`^`a`_```^^]\\^_VW]VXV\S\\\TXXTJMPUQQQSSRQRMJMPFRKDGD 1
-SL-XBB 2 2 1 0 932 0 1 TGAGGAGAAACATTCTTTTTGTAGGGGGTGCTAACTATGGCCTATGCAAAATTCTGAATTTTACCACCGTCTAAGC \GH]PSQ[I_\YHaabaaaWGZSSU`]NOXLMGS]aYFPRFV[\[FTP_Y^[NMZXNPLYYQNXSPSOKOMLTQNY 0
-SL-XBB 2 2 1 0 431 0 1 CCGATGAAAGCAACAAGGTAGGGTTAACTCATCTATGAATAAGCCTGACATGTGAGGAATCACAAGCAAATTGCAC ^NQLW\H\GLFFFZ\Q_\JGVY\Q_aK`^a_aa`XT]DF[[\QDIVZNTTZ]VXOYNSZXSPDLPFGPHNUMOJGS 0
-SL-XBB 2 2 1 0 978 0 1 AACCGGTGCATTATGCGGACCGGGAGGGCTTTCGAAACACCTGGGTGGTGCTGAACCCGGGAGTGGCGTCTCCCTC GGGI]_THV_GIW_]QTIGZZTGWZTOZ\`_NGGGGHZTZGGGMZ[HZRXU_IOKO_GQR\OVOYDLDPGTGJVFE 0
-SL-XBB 2 2 1 0 122 0 1 GCCCGCGCGTCCCTTGCCGCCGTGGGCAGGGACGGGGGGGAGGCAAGACCCCACCGATGCTCGTCATACGACCAGG L`aa\\J\\^X[_I]X_TI]TGFMZVIH`VIHXEG_aZTRXLH_PUFFFMMWNFPFFH^QNLPEUKKDGINKKVKF 0
-SL-XBB 2 2 1 0 1549 0 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA _Z_]JRR]ZVR[^^`X^aX^\\XPVGTPKTU]\TU\Y[S`\^V]NUFKMJJMUYQDQHFPKEMKMOKGIIFOJMOJ 1
-SL-XBB 2 2 1 0 1783 0 1 CACACCTCTCTCGTTTTGGGGCAAAACGGCTCAGCCATTGGAATATGGCACACTCGTCTGGCACAAGAAGGACATC a`_[W__\W[T_ZPZ_H_W_V`bJ`ba_aa[a_YROOW[]YGUI_T]RKGG^O]WGZSK[_ZGZZKNXRPRVZGUW 1
-SL-XBB 2 2 1 0 254 0 1 CCGCAAACAGCATACTTTGGTACTCTTGAAGTTTCAGGGCATACTTGTAATCTGCAACCACTGGATCTGTTCTTGT a`[_`Zaa]J_R_a\abbaaXbbaaa\VW_aQaT[Z[_GTa^_P^]aY^ababa``\aMaa]`[^XWWSOOX]MDD 1
-SL-XBB 2 2 1 0 1660 0 1 AACACTCATGGACATTATTCCTAATAATGGTTCTTATGGCAAAGTGAAAAAATAATCATCCAAGTACCTGTATCGC R^aa__bb```baaabbbb_bbaaabba`a^a^abb`^ababaaV`^`bbba^aba`aabaabb_`][V^V`aFF\ 1
-SL-XBB 2 2 1 0 1250 0 1 CACACACACACACACACACACACCACCTTTTGGCTTATCTGCACGCGGCCGCGTGCCCTACCCTACCCCATGGGAT a_aa^\Ra\`aaXa_aa_aaaaaaa[^X^``V[`_`a^aaO``^_SJUELTVMKVTPFOKJJMNKTRRJEEPFKTR 1
diff --git a/testdata/net/sf/picard/illumina/MakeSquashedMap/Homerus_Simpsonus_assembly18.fasta.0.2bpb b/testdata/net/sf/picard/illumina/MakeSquashedMap/Homerus_Simpsonus_assembly18.fasta.0.2bpb
deleted file mode 100644
index 1d197a1..0000000
--- a/testdata/net/sf/picard/illumina/MakeSquashedMap/Homerus_Simpsonus_assembly18.fasta.0.2bpb
+++ /dev/null
@@ -1 +0,0 @@
-
\ No newline at end of file
diff --git a/testdata/net/sf/picard/illumina/MakeSquashedMap/Homerus_Simpsonus_assembly18.fasta.1.2bpb b/testdata/net/sf/picard/illumina/MakeSquashedMap/Homerus_Simpsonus_assembly18.fasta.1.2bpb
deleted file mode 100644
index 9a62b29..0000000
--- a/testdata/net/sf/picard/illumina/MakeSquashedMap/Homerus_Simpsonus_assembly18.fasta.1.2bpb
+++ /dev/null
@@ -1 +0,0 @@
-
\ No newline at end of file
diff --git a/testdata/net/sf/picard/illumina/MakeSquashedMap/Map_to_genomic_coordinates.txt b/testdata/net/sf/picard/illumina/MakeSquashedMap/Map_to_genomic_coordinates.txt
deleted file mode 100644
index 240705f..0000000
--- a/testdata/net/sf/picard/illumina/MakeSquashedMap/Map_to_genomic_coordinates.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-0 0 0 47 chrBart
-1 0 48 35 chrLisa
-2 1 0 99 chrMaggie
diff --git a/testdata/net/sf/picard/illumina/MakeSquashedMap/test.dict b/testdata/net/sf/picard/illumina/MakeSquashedMap/test.dict
deleted file mode 100644
index 70cf53d..0000000
--- a/testdata/net/sf/picard/illumina/MakeSquashedMap/test.dict
+++ /dev/null
@@ -1,3 +0,0 @@
- at SQ SN:chrBart LN:47 UR:/seq/references/Homerus_Simpsonus_assembly18/v0/Homerus_Simpsonus_assembly18.fasta AS:HG18 SP:Homerus Simpsonus
- at SQ SN:chrLisa LN:35 UR:/seq/references/Homerus_Simpsonus_assembly18/v0/Homerus_Simpsonus_assembly18.fasta AS:HG18 SP:Homerus Simpsonus
- at SQ SN:chrMaggie LN:99 UR:/seq/references/Homerus_Simpsonus_assembly18/v0/Homerus_Simpsonus_assembly18.fasta AS:HG18 SP:Homerus Simpsonus
diff --git a/testdata/net/sf/picard/illumina/Map_to_genomic_coordinates.txt b/testdata/net/sf/picard/illumina/Map_to_genomic_coordinates.txt
deleted file mode 100755
index 5690578..0000000
--- a/testdata/net/sf/picard/illumina/Map_to_genomic_coordinates.txt
+++ /dev/null
@@ -1,45 +0,0 @@
-0 0 0 16571 chrM
-1 0 16572 247249719 chr1
-2 1 0 242951149 chr2
-3 2 0 199501827 chr3
-4 3 0 191273063 chr4
-5 4 0 180857866 chr5
-6 5 0 170899992 chr6
-7 6 0 158821424 chr7
-8 7 0 146274826 chr8
-9 8 0 140273252 chr9
-10 9 0 135374737 chr10
-11 10 0 134452384 chr11
-12 11 0 132349534 chr12
-13 12 0 114142980 chr13
-14 13 0 106368585 chr14
-15 14 0 100338915 chr15
-16 15 0 88827254 chr16
-17 15 88827255 78774742 chr17
-18 16 0 76117153 chr18
-19 16 76117154 63811651 chr19
-20 17 0 62435964 chr20
-21 17 62435965 46944323 chr21
-22 18 0 49691432 chr22
-23 18 49691433 154913754 chrX
-24 19 0 57772954 chrY
-25 19 57772955 1663265 chr1_random
-26 19 59436221 185571 chr2_random
-27 19 59621793 749256 chr3_random
-28 19 60371050 842648 chr4_random
-29 19 61213699 143687 chr5_random
-30 19 61357387 1875562 chr6_random
-31 19 63232950 549659 chr7_random
-32 19 63782610 943810 chr8_random
-33 19 64726421 1146434 chr9_random
-34 19 65872856 113275 chr10_random
-35 19 65986132 215294 chr11_random
-36 19 66201427 186858 chr13_random
-37 19 66388286 784346 chr15_random
-38 19 67172633 105485 chr16_random
-39 19 67278119 2617613 chr17_random
-40 19 69895733 4262 chr18_random
-41 19 69899996 301858 chr19_random
-42 19 70201855 1679693 chr21_random
-43 19 71881549 257318 chr22_random
-44 19 72138868 1719168 chrX_random
diff --git a/testdata/net/sf/picard/illumina/s_1_1_eland_extended.txt b/testdata/net/sf/picard/illumina/s_1_1_eland_extended.txt
deleted file mode 100755
index 4fbcfdf..0000000
--- a/testdata/net/sf/picard/illumina/s_1_1_eland_extended.txt
+++ /dev/null
@@ -1,9 +0,0 @@
->SL-XAV:1:1:0:1914#0/1 NTTTTTCTCCCNCNGTGCCTANTNTAGCCCCTNNNNNNNNNAANNNATNANNANNTTTACTTAAAAAACTGAAACTAGTAATGTGCANNANATCGNAAGAG QC -
->SL-XAV:1:1:0:1668#0/1 NATAGCATACTNTNCATTGGANTNCAGCACAANNNNNNNNNTGNNNCANTNNANNCCTTTGAGATCGGAAGAGCGGTTCAGCAGGAANNCNCAGACCGATC QC -
->SL-XAV:1:1:0:700#0/1 NGAAGCCCATTNTNGTGTTACNCNCCTGGAAGNNNNNNNNNACNNNGANACNTNNAACAATTCAGATCGGAAGAGCGGTTCAGCAGANNTNCCGAGACCGA QC -
->SL-XAV:1:1:0:68#0/1 NAATATTCATANGNTCAGCCTNTNCATTAATTNNNNNNNNNTTNNNATNATNANNTTTTTTATAACCATTTATAAATGAGAGAGATCNTANCACAATATCA QC -
->SL-XAV:1:1:0:1639#0/1 NCCCTCTCAGANTNTCTGCCANANCCTTAAGCNNNNNNNNNTANNNCTNAANCNNAAACTTTTGCCTCAGGCATCCGCAGAATGTTTNTCNGCCTATATCG QC -
->SL-XAV:1:1:0:1300#0/1 NAAACACAAGANANAGTCTTANCNGCTATTCCNNNNNNNNNCTNNNCTNAGNANNACATACAACAGTATCCACACAAGTGTACTCGTNCANACATGTGAAC QC -
->SL-XAV:1:1:0:764#0/1 NTGGAGTGTTGACGTACTCTANTATTGTATTGNNNNNNNNNTGNNCTTNAANGNNTGTTAATATTTGCATCTGTACGATCGTAAGAGNGCNTCAGCATGAA 1:0:0 Homo_sapiens_assembly18.fasta.1:94972462RG20T10CAGTCCATC2TC3T2A1CC20TTTAG2GCTT1A1TG1TG1TTGC1T
->SL-XAV:1:1:0:105#0/1 NCAGGTTCAACTGTGCAGCCCNTTTTGAGAGATNNNNNNNNTGNNCTGNAANANNGACACAGCTATTCCTAAGATGACAAGATCAGANAANAAGTCAAGCA 1:0:0 Homo_sapiens_assembly18.fasta.18:158213377FT20T11TCAGCAAC2AT3A2AGCA24CTGGTCCCCCTTC1TG1C1CAT
->SL-XAV:1:1:0:1721#0/1 NTCGGGAGGTTAGCTGCGGAANGAAATCGGGATNNNNNNNNGANNCGANAANCNNTTCAGCAGGAAATCCGAAACACAAACACAGATNCCNCCTTCTGTTG 1:0:0 Homo_sapiens_assembly18.fasta.15:18728003RG20A11GCCGCGGA1CACA2GTGATTTGGA1CTCCATTCCA1CTG2C1TGTGTGTACAAT1CAGGAAAAAAA
diff --git a/testdata/net/sf/picard/illumina/s_1_1_eland_query.txt b/testdata/net/sf/picard/illumina/s_1_1_eland_query.txt
deleted file mode 100755
index 8b13789..0000000
--- a/testdata/net/sf/picard/illumina/s_1_1_eland_query.txt
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/testdata/net/sf/picard/illumina/s_1_1_export.txt b/testdata/net/sf/picard/illumina/s_1_1_export.txt
deleted file mode 100755
index f1d7134..0000000
--- a/testdata/net/sf/picard/illumina/s_1_1_export.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-SL-XAV 1 1 1 0 1914 0 1 NTTTTTCTCCCNCNGTGCCTANTNTAGCCCCTNNNNNNNNNAANNNATNANNANNTTTACTTAAAAAACTGAAACTAGTAATGTGCANNANATCGNAAGAG DOYYYY[[ZXODNDMQSSVUODKDMSPSVXWNDDDDDDDDDOODDDOMDNDDLDDMSSVTUWVRURTOSMDMTTVNMIHUTMDNIMNDDMDMJIHDMMHMD QC N
-SL-XAV 1 1 1 0 1668 0 1 NATAGCATACTNTNCATTGGANTNCAGCACAANNNNNNNNNTGNNNCANTNNANNCCTTTGAGATCGGAAGAGCGGTTCAGCAGGAANNCNCAGACCGATC DPXWWXXWWXODODMWWURNNDMDMOLQWVTMDDDDDDDDDMHDDDMMDMDDMDDMTVWQLQJQUQHDLOLOTPOIMRRQLQMLKOIDDIDEMDLQLHOMK QC N
-SL-XAV 1 1 1 0 700 0 1 NGAAGCCCATTNTNGTGTTACNCNCCTGGAAGNNNNNNNNNACNNNGANACNTNNAACAATTCAGATCGGAAGAGCGGTTCAGCAGANNTNCCGAGACCGA DMWWWWWYWWNDODKORPWXMDNDMWNHHPQNDDDDDDDDDMNDDDDMDPMDHDDNRTXUQNUSRQLRDHKODNQJOKHKUPDLUKDDDEDNKMODMMMHO QC N
-SL-XAV 1 1 1 0 68 0 1 NAATATTCATANGNTCAGCCTNTNCATTAATTNNNNNNNNNTTNNNATNATNANNTTTTTTATAACCATTTATAAATGAGAGAGATCNTANCACAATATCA DO[[YYYYY[NDDDMVRFQXODMDOZYYYXODDDDDDDDDDMMDDDOHDOLDODDDMVSRVXXXXTQTRRSWTXVXQPMKMFOTOMIDMODHIHDDDDIHM QC N
-SL-XAV 1 1 1 0 1639 0 1 NCCCTCTCAGANTNTCTGCCANANCCTTAAGCNNNNNNNNNTANNNCTNAANCNNAAACTTTTGCCTCAGGCATCCGCAGAATGTTTNTCNGCCTATATCG DPYYYYYYUSNDNDOYRMQWODNDOWVWWPKNDDDDDDDDDMMDDDMMDKKDLDDKQUTRSPLHNTUWODLMTTTQLQTNRQQNSQNDHDDHMSQPDLDLN QC N
-SL-XAV 1 1 1 0 1300 0 1 NAAACACAAGANANAGTCTTANCNGCTATTCCNNNNNNNNNCTNNNCTNAGNANNACATACAACAGTATCCACACAAGTGTACTCGTNCANACATGTGAAC DITTRTHILKKDMDMILPHIKDEDHDPDDMKHDDDDDDDDDHODDDOEDDDDMDDIQFNSFFONIIDHDKFLDIKDKDDDMOMDHDDDIIDKMDDDEHDDH QC N
-SL-XAV 1 1 1 0 764 0 1 NTGGAGTGTTGACGTACTCTANTATTGTATTGNNNNNNNNNTGNNCTTNAANGNNTGTTAATATTTGCATCTGTACGATCGTAAGAGNGCNTCAGCATGAA DOZYYXUNUTQUTLTVVWYUPDKXXVTVVWPDDDDDDDDDDKIDDNOMDLPDKDDNDHQVTVRPSMDKSVWNKMNDHWUVODKNHMHDHDDNUNPMLDKND 1:0:0 Y
-SL-XAV 1 1 1 0 105 0 1 NCAGGTTCAACTGTGCAGCCCNTTTTGAGAGATNNNNNNNNTGNNCTGNAANANNGACACAGCTATTCCTAAGATGACAAGATCAGANAANAAGTCAAGCA DOUUUTTVWYYSPMINVTVVNDNVVSORLRQSMDDDDDDDDNMDDMMDDMODDDDEKYXYNLNGTTOOQOQOJRFPQJQNDMQLDNNDHKDIDDDDDDDTP 1:0:0 N
-SL-XAV 1 1 1 0 1721 0 1 NTCGGGAGGTTAGCTGCGGAANGAAATCGGGATNNNNNNNNGANNCGANAANCNNTTCAGCAGGAAATCCGAAACACAAACACAGATNCCNCCTTCTGTTG DNWUWURNNRWQNQNIOINUNDDOUSPOKNQRNDDDDDDDDIODDDHLDDMDKDDIMHMKMNMHMMDDLNKHDHDHLMDHLIDLHNIDEDDHHKQJMIMFH 1:0:0 N
diff --git a/testdata/net/sf/picard/illumina/s_1_2_eland_extended.txt b/testdata/net/sf/picard/illumina/s_1_2_eland_extended.txt
deleted file mode 100755
index fe43b80..0000000
--- a/testdata/net/sf/picard/illumina/s_1_2_eland_extended.txt
+++ /dev/null
@@ -1,9 +0,0 @@
->SL-XAV:1:1:0:1914#0/2 NTTGCACATTACTAGTTTCAGTTTTTTAAGTAAACGTATTCATCTCTTTTTATTAGCAGGGGCTATACTAGGCACTGTGGGCGACATAAAGAGCGCATACG 1:0:0 Homo_sapiens_assembly18.fasta.2:126477787RT55A24A2A1A3TTTATAGATTT
->SL-XAV:1:1:0:1668#0/2 NAAAGGTGTCCAGTGGATCAAAAATGGAGTTGTGCTGGAATCCAATGAAAAGTATGCTCTCAGATCGGAAGCGCGTCTGGTAGGACGCGCGTGTAGAGATG 1:0:0 Homo_sapiens_assembly18.fasta.1:179343459RC57A2TCTGTCA3GAACAA1TTACTCT1TGAG1AT2A1A1CT
->SL-XAV:1:1:0:700#0/2 NAATTGTTCTCAGTTTCTCGGTTTATGTGCTCTTCCAGGTGGGTAACACAATAATGGCCTTCCAGATCGTAAGAGCGACGTGTGTTGCACGAGTGTCGATC 1:0:0 Homo_sapiens_assembly18.fasta.13:53938010FG56G5TATCAA2T1TATATAT1T1T1AAT1TATT1T1ATTG1
->SL-XAV:1:1:0:68#0/2 NTCTCATTTATAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTTCATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCACGACGTTATCN 1:0:0 Homo_sapiens_assembly18.fasta.5:38987259FC67AC2A1G1A3T1GTAAGAGGAATG1AATGGA
->SL-XAV:1:1:0:1639#0/2 NGGCTGCAAAACATTCTGCGGATGCCTGAGGCAAAAGTTTATGGTTGAGAAATATAATAGACAGCTTCAGGCTTTGGCTGTGAACATGAGATGGTATCACG 1:0:0 Homo_sapiens_assembly18.fasta.3:93494052RA66A10A1AA2TC5G2A2TTTC
->SL-XAV:1:1:0:1300#0/2 NGATCATGGAAGACTCTCCCCATCCCCCGCTCCAGCGCTCAGTTATATGCCTAGCCTCGGACACGTCACCAACATCTCACGCACTCTGCACAGTCTCTCAC NM -
->SL-XAV:1:1:0:764#0/2 NACAGATGCAAATATTAACAGGCTTTAAAGGACAGATGGACTGCAATACAATAATAGAGTACGTCAACACTCCACAGATCGCTAGAGCATCACATCGGTGT 1:5:0 Homo_sapiens_assembly18.fasta.1:94972488FT74T1TAAT1A1C1C1CCACT4TGAA,Homo_sapiens_assembly18.fasta.8:42336261RT1T33G24ACCTC1ACACT1CACCG1AATC1ACA1CC3TATC1C1A,43145571FT1T33G25C12C1TAAT1A1C1C1CCACT4CGAA,44080574FT1T55T3C12C1TAAT1A1C1C1CCACT4CGAA,67494470RT1T33G25C12C1TAAT1A1C1C1CCACT4CGAA,68649702RT1T33G24ACCTC1ACACT1CACCG1AATC1ACA1CC3TATC1C1A
->SL-XAV:1:1:0:105#0/2 NGTCATCTTAGGAATAGCTGTGTCTGCTTTTCAGATCAGTTGCTCAATCTCTCACACATCGCTCCACATCTGAAACCGCAGATTGTAAGAGTCACGATGTG 1:0:0 Homo_sapiens_assembly18.fasta.18:158213355RT43G9A1A1GG3G4GT4C1T1AG1GC1T1G1CTTGGT1ACCT2
->SL-XAV:1:1:0:1721#0/2 NCGCGGCATCCCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCGAGAGCATACA 1:0:0 Homo_sapiens_assembly18.fasta.15:18728064FC40CG2T2T2TGT2TGTGGCAGA1AG1CAA1CTCCG1GT2AG4T3CTTGCTTT
diff --git a/testdata/net/sf/picard/illumina/s_1_2_eland_query.txt b/testdata/net/sf/picard/illumina/s_1_2_eland_query.txt
deleted file mode 100755
index 8b13789..0000000
--- a/testdata/net/sf/picard/illumina/s_1_2_eland_query.txt
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/testdata/net/sf/picard/illumina/s_1_2_export.txt b/testdata/net/sf/picard/illumina/s_1_2_export.txt
deleted file mode 100755
index 407cf8a..0000000
--- a/testdata/net/sf/picard/illumina/s_1_2_export.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-SL-XAV 1 1 1 0 1914 0 2 NTTGCACATTACTAGTTTCAGTTTTTTAAGTAAACGTATTCATCTCTTTTTATTAGCAGGGGCTATACTAGGCACTGTGGGCGACATAAAGAGCGCATACG DOYYXXXZXYYYWSSVXXWUUYYXXXVSTVVVTVVOQOVWRJRXWVWXXXXYYTKMNUKDKRZXXTVRRLDMXUUUNIDMDILMHNOPHKIOINIDDVKOG 1:0:0 N
-SL-XAV 1 1 1 0 1668 0 2 NAAAGGTGTCCAGTGGATCAAAAATGGAGTTGTGCTGGAATCCAATGAAAAGTATGCTCTCAGATCGGAAGCGCGTCTGGTAGGACGCGCGTGTAGAGATG DOWWSNUTSWWUUSSSSUWWWWQJROQRQSUSRNRWTNTNRTUSUWSLMQRJJLNUWMFPYUMRTURRLRNKNULFFQFDDDDPDDEPGNNNNOFNLFKNG 1:0:0 N
-SL-XAV 1 1 1 0 700 0 2 NAATTGTTCTCAGTTTCTCGGTTTATGTGCTCTTCCAGGTGGGTAACACAATAATGGCCTTCCAGATCGTAAGAGCGACGTGTGTTGCACGAGTGTCGATC DOYYWWVYYYYUNUSUYYWRWRWWWPPNUVXYWVUSODMNQJNLSNQWYRKTRUNSFFDDMVWNGNTTSNMNOQIHIEKLGTVGHDMUGUYGOUOPFNGKI 1:0:0 N
-SL-XAV 1 1 1 0 68 0 2 NTCTCATTTATAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTTCATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCACGACGTTATCN DP[[XXXZZZZ[[[WVTVXYTTUXVQVWXXVVSSSMEMOQRMDKVUQPNTSMSXMHNTROTTLQQLLFFJGMFLHHULPUWNGRDDOG[HMHHIDDDDDFO 1:0:0 N
-SL-XAV 1 1 1 0 1639 0 2 NGGCTGCAAAACATTCTGCGGATGCCTGAGGCAAAAGTTTATGGTTGAGAAATATAATAGACAGCTTCAGGCTTTGGCTGTGAACATGAGATGGTATCACG DIQWWWUTTVWUSUYYWWUTOUTNTVQONOJOKKSQQOOQUQLDMTLHNOMLVUQTNTPPVUWYZQROJMNPSOOJFKEHLFFGFPGQFPOJOMFDDMDMF 1:0:0 N
-SL-XAV 1 1 1 0 1300 0 2 NGATCATGGAAGACTCTCCCCATCCCCCGCTCCAGCGCTCAGTTATATGCCTAGCCTCGGACACGTCACCAACATCTCACGCACTCTGCACAGTCTCTCAC DDEJEERIDLNHNPFQUNILQLNTSQLIDLDNENINDLEDHLEHDMELNDDQJPQQIEDJKGNLDHGGKNLKKMEQGQEJHNDNDLUULDDNPUDHDIDFR NM N
-SL-XAV 1 1 1 0 764 0 2 NACAGATGCAAATATTAACAGGCTTTAAAGGACAGATGGACTGCAATACAATAATAGAGTACGTCAACACTCCACAGATCGCTAGAGCATCACATCGGTGT DNYTRTWYYXXXXYYXXXXWQTTYYVQVTKKNTTUVLFJRWVTRVWTVYTSLSMTPFRPOTXTSVRQOZVRNVQOJQQMSGUMZGGMZGZWGHGFEDDQDD 1:0:0 N
-SL-XAV 1 1 1 0 105 0 2 NGTCATCTTAGGAATAGCTGTGTCTGCTTTTCAGATCAGTTGCTCAATCTCTCACACATCGCTCCACATCTGAAACCGCAGATTGTAAGAGTCACGATGTG DMTWYYYWWURUWYUQTWUTRMRWTRTSPTWVMHILTKIHNNWLRHDNTQQFOIDMEIDDKWHEKDDFDHKSFHHMGKDLFMJJFJDDHDHGIDNLLRHHN 1:0:0 N
-SL-XAV 1 1 1 0 1721 0 2 NCGCGGCATCCCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCGAGAGCATACA DNPTSSTUUUUTPNTUUUUUTTRJQNPSNDNTTTTPQJRNHLENLDLEIJHHIEEPRJRHENNJJEENFHHNRJDITJJHDFQJDJNIDLDDIHDLMNPFP 1:0:0 N
diff --git a/testdata/net/sf/picard/illumina/s_2_eland_extended.txt b/testdata/net/sf/picard/illumina/s_2_eland_extended.txt
deleted file mode 100644
index d8864c7..0000000
--- a/testdata/net/sf/picard/illumina/s_2_eland_extended.txt
+++ /dev/null
@@ -1,3 +0,0 @@
->SL-XBG:1:29:818:454#0/2 CACACCCCCCAGCCGAAAATACCAAATGAATGGAGAGCTCCCGTGAGCGGGTAATAGGCTGATAGACCTGCGATAC 0:0:1 Homo_sapiens_assembly18.fasta.0:0R12A15C18T2T7G11T3CN
->SL-XBG:1:29:818:455#0/2 CACACCCCCCAGCCGAAAATACCAAATGAATGGAGAGCTCCCGTGAGCGGGTAATAGGCTGATAGACCTGCGATAC 0:0:1 Homo_sapiens_assembly18.fasta.0:16533R12A15C18T2T7G11T3CN
->SL-XAR:2:9:1184:1671#0/1 TAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTNGGGTTAGGGGTAGGGTTAGGGTTAGGGCTAGGGTTAGGGTTAGGGTTAGGGTTAGGG 1:255:139 Homo_sapiens_assembly18.fasta.16:-46R32A2G1TA2G1TA2G1TA3NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
diff --git a/testdata/net/sf/picard/illumina/s_2_export.txt b/testdata/net/sf/picard/illumina/s_2_export.txt
deleted file mode 100644
index 99d90be..0000000
--- a/testdata/net/sf/picard/illumina/s_2_export.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-SL-XBG 2 1 29 818 454 0 2 CACACCCCCCAGCCGAAAATACCAAATGAATGGAGAGCTCCCGTGAGCGGGTAATAGGCTGATAGACCTGCGATAC J`b]__WababVGTRWWa\K\_aaT__HYTX^`^R^^baa`WRJaH`T]]G]ZGH\aUFHa_aVa_NbU^IX_RKH 0:0:1 N
-SL-XBG 2 1 29 818 455 0 2 CACACCCCCCAGCCGAAAATACCAAATGAATGGAGAGCTCCCGTGAGCGGGTAATAGGCTGATAGACCTGCGATAC J`b]__WababVGTRWWa\K\_aaT__HYTX^`^R^^baa`WRJaH`T]]G]ZGH\aUFHa_aVa_NbU^IX_RKH 0:0:1 N
-SL-XAR 1 2 9 1184 1671 0 1 TAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTNGGGTTAGGGGTAGGGTTAGGGTTAGGGCTAGGGTTAGGGTTAGGGTTAGGGTTAGGG ]````TaabaTDZZ]__aabTaZDWVZaWD^Wa`^ZT^b]`G^DZZ_UbTba_FZSaaaGNNTaaM]^a_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1:255:139 N
diff --git a/testdata/net/sf/picard/illumina/s_4_1_eland_extended.txt b/testdata/net/sf/picard/illumina/s_4_1_eland_extended.txt
deleted file mode 100644
index 4fbcfdf..0000000
--- a/testdata/net/sf/picard/illumina/s_4_1_eland_extended.txt
+++ /dev/null
@@ -1,9 +0,0 @@
->SL-XAV:1:1:0:1914#0/1 NTTTTTCTCCCNCNGTGCCTANTNTAGCCCCTNNNNNNNNNAANNNATNANNANNTTTACTTAAAAAACTGAAACTAGTAATGTGCANNANATCGNAAGAG QC -
->SL-XAV:1:1:0:1668#0/1 NATAGCATACTNTNCATTGGANTNCAGCACAANNNNNNNNNTGNNNCANTNNANNCCTTTGAGATCGGAAGAGCGGTTCAGCAGGAANNCNCAGACCGATC QC -
->SL-XAV:1:1:0:700#0/1 NGAAGCCCATTNTNGTGTTACNCNCCTGGAAGNNNNNNNNNACNNNGANACNTNNAACAATTCAGATCGGAAGAGCGGTTCAGCAGANNTNCCGAGACCGA QC -
->SL-XAV:1:1:0:68#0/1 NAATATTCATANGNTCAGCCTNTNCATTAATTNNNNNNNNNTTNNNATNATNANNTTTTTTATAACCATTTATAAATGAGAGAGATCNTANCACAATATCA QC -
->SL-XAV:1:1:0:1639#0/1 NCCCTCTCAGANTNTCTGCCANANCCTTAAGCNNNNNNNNNTANNNCTNAANCNNAAACTTTTGCCTCAGGCATCCGCAGAATGTTTNTCNGCCTATATCG QC -
->SL-XAV:1:1:0:1300#0/1 NAAACACAAGANANAGTCTTANCNGCTATTCCNNNNNNNNNCTNNNCTNAGNANNACATACAACAGTATCCACACAAGTGTACTCGTNCANACATGTGAAC QC -
->SL-XAV:1:1:0:764#0/1 NTGGAGTGTTGACGTACTCTANTATTGTATTGNNNNNNNNNTGNNCTTNAANGNNTGTTAATATTTGCATCTGTACGATCGTAAGAGNGCNTCAGCATGAA 1:0:0 Homo_sapiens_assembly18.fasta.1:94972462RG20T10CAGTCCATC2TC3T2A1CC20TTTAG2GCTT1A1TG1TG1TTGC1T
->SL-XAV:1:1:0:105#0/1 NCAGGTTCAACTGTGCAGCCCNTTTTGAGAGATNNNNNNNNTGNNCTGNAANANNGACACAGCTATTCCTAAGATGACAAGATCAGANAANAAGTCAAGCA 1:0:0 Homo_sapiens_assembly18.fasta.18:158213377FT20T11TCAGCAAC2AT3A2AGCA24CTGGTCCCCCTTC1TG1C1CAT
->SL-XAV:1:1:0:1721#0/1 NTCGGGAGGTTAGCTGCGGAANGAAATCGGGATNNNNNNNNGANNCGANAANCNNTTCAGCAGGAAATCCGAAACACAAACACAGATNCCNCCTTCTGTTG 1:0:0 Homo_sapiens_assembly18.fasta.15:18728003RG20A11GCCGCGGA1CACA2GTGATTTGGA1CTCCATTCCA1CTG2C1TGTGTGTACAAT1CAGGAAAAAAA
diff --git a/testdata/net/sf/picard/illumina/s_4_1_eland_query.txt b/testdata/net/sf/picard/illumina/s_4_1_eland_query.txt
deleted file mode 100644
index 8b13789..0000000
--- a/testdata/net/sf/picard/illumina/s_4_1_eland_query.txt
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/testdata/net/sf/picard/illumina/s_4_1_export.txt b/testdata/net/sf/picard/illumina/s_4_1_export.txt
deleted file mode 100644
index f1d7134..0000000
--- a/testdata/net/sf/picard/illumina/s_4_1_export.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-SL-XAV 1 1 1 0 1914 0 1 NTTTTTCTCCCNCNGTGCCTANTNTAGCCCCTNNNNNNNNNAANNNATNANNANNTTTACTTAAAAAACTGAAACTAGTAATGTGCANNANATCGNAAGAG DOYYYY[[ZXODNDMQSSVUODKDMSPSVXWNDDDDDDDDDOODDDOMDNDDLDDMSSVTUWVRURTOSMDMTTVNMIHUTMDNIMNDDMDMJIHDMMHMD QC N
-SL-XAV 1 1 1 0 1668 0 1 NATAGCATACTNTNCATTGGANTNCAGCACAANNNNNNNNNTGNNNCANTNNANNCCTTTGAGATCGGAAGAGCGGTTCAGCAGGAANNCNCAGACCGATC DPXWWXXWWXODODMWWURNNDMDMOLQWVTMDDDDDDDDDMHDDDMMDMDDMDDMTVWQLQJQUQHDLOLOTPOIMRRQLQMLKOIDDIDEMDLQLHOMK QC N
-SL-XAV 1 1 1 0 700 0 1 NGAAGCCCATTNTNGTGTTACNCNCCTGGAAGNNNNNNNNNACNNNGANACNTNNAACAATTCAGATCGGAAGAGCGGTTCAGCAGANNTNCCGAGACCGA DMWWWWWYWWNDODKORPWXMDNDMWNHHPQNDDDDDDDDDMNDDDDMDPMDHDDNRTXUQNUSRQLRDHKODNQJOKHKUPDLUKDDDEDNKMODMMMHO QC N
-SL-XAV 1 1 1 0 68 0 1 NAATATTCATANGNTCAGCCTNTNCATTAATTNNNNNNNNNTTNNNATNATNANNTTTTTTATAACCATTTATAAATGAGAGAGATCNTANCACAATATCA DO[[YYYYY[NDDDMVRFQXODMDOZYYYXODDDDDDDDDDMMDDDOHDOLDODDDMVSRVXXXXTQTRRSWTXVXQPMKMFOTOMIDMODHIHDDDDIHM QC N
-SL-XAV 1 1 1 0 1639 0 1 NCCCTCTCAGANTNTCTGCCANANCCTTAAGCNNNNNNNNNTANNNCTNAANCNNAAACTTTTGCCTCAGGCATCCGCAGAATGTTTNTCNGCCTATATCG DPYYYYYYUSNDNDOYRMQWODNDOWVWWPKNDDDDDDDDDMMDDDMMDKKDLDDKQUTRSPLHNTUWODLMTTTQLQTNRQQNSQNDHDDHMSQPDLDLN QC N
-SL-XAV 1 1 1 0 1300 0 1 NAAACACAAGANANAGTCTTANCNGCTATTCCNNNNNNNNNCTNNNCTNAGNANNACATACAACAGTATCCACACAAGTGTACTCGTNCANACATGTGAAC DITTRTHILKKDMDMILPHIKDEDHDPDDMKHDDDDDDDDDHODDDOEDDDDMDDIQFNSFFONIIDHDKFLDIKDKDDDMOMDHDDDIIDKMDDDEHDDH QC N
-SL-XAV 1 1 1 0 764 0 1 NTGGAGTGTTGACGTACTCTANTATTGTATTGNNNNNNNNNTGNNCTTNAANGNNTGTTAATATTTGCATCTGTACGATCGTAAGAGNGCNTCAGCATGAA DOZYYXUNUTQUTLTVVWYUPDKXXVTVVWPDDDDDDDDDDKIDDNOMDLPDKDDNDHQVTVRPSMDKSVWNKMNDHWUVODKNHMHDHDDNUNPMLDKND 1:0:0 Y
-SL-XAV 1 1 1 0 105 0 1 NCAGGTTCAACTGTGCAGCCCNTTTTGAGAGATNNNNNNNNTGNNCTGNAANANNGACACAGCTATTCCTAAGATGACAAGATCAGANAANAAGTCAAGCA DOUUUTTVWYYSPMINVTVVNDNVVSORLRQSMDDDDDDDDNMDDMMDDMODDDDEKYXYNLNGTTOOQOQOJRFPQJQNDMQLDNNDHKDIDDDDDDDTP 1:0:0 N
-SL-XAV 1 1 1 0 1721 0 1 NTCGGGAGGTTAGCTGCGGAANGAAATCGGGATNNNNNNNNGANNCGANAANCNNTTCAGCAGGAAATCCGAAACACAAACACAGATNCCNCCTTCTGTTG DNWUWURNNRWQNQNIOINUNDDOUSPOKNQRNDDDDDDDDIODDDHLDDMDKDDIMHMKMNMHMMDDLNKHDHDHLMDHLIDLHNIDEDDHHKQJMIMFH 1:0:0 N
diff --git a/testdata/net/sf/picard/illumina/s_4_2_eland_extended.txt b/testdata/net/sf/picard/illumina/s_4_2_eland_extended.txt
deleted file mode 100644
index 6cf7fb4..0000000
--- a/testdata/net/sf/picard/illumina/s_4_2_eland_extended.txt
+++ /dev/null
@@ -1,9 +0,0 @@
->SL-XAV:1:1:0:1914#0/2 NTTGCACATTACTAGTTTCAGTTTTTTAAGTAAACGTATTCATCTCTTTTTATTAGCAGGGGCTATACTAGGCACTGTGGGCGACATAAAGAGCGCATACG 1:0:0 Homo_sapiens_assembly18.fasta.2:126477787RT55A24A2A1A3TTTATAGATTT
->SL-XAV:1:1:0:1668#0/2 NAAAGGTGTCCAGTGGATCAAAAATGGAGTTGTGCTGGAATCCAATGAAAAGTATGCTCTCAGATCGGAAGCGCGTCTGGTAGGACGCGCGTGTAGAGATG 1:0:0 Homo_sapiens_assembly18.fasta.1:179343459RC57A2TCTGTCA3GAACAA1TTACTCT1TGAG1AT2A1A1CT
->SL-XAV:1:1:0:700#0/2 NAATTGTTCTCAGTTTCTCGGTTTATGTGCTCTTCCAGGTGGGTAACACAATAATGGCCTTCCAGATCGTAAGAGCGACGTGTGTTGCACGAGTGTCGATC 1:0:0 Homo_sapiens_assembly18.fasta.13:53938010FG56G5TATCAA2T1TATATAT1T1T1AAT1TATT1T1ATTG1
->SL-XAV:1:1:0:68#0/2 NTCTCATTTATAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTTCATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCACGACGTTATCT 1:0:0 Homo_sapiens_assembly18.fasta.5:38987259FC67AC2A1G1A3T1GTAAGAGGAATG1AATGGA
->SL-XAV:1:1:0:1639#0/2 NGGCTGCAAAACATTCTGCGGATGCCTGAGGCAAAAGTTTATGGTTGAGAAATATAATAGACAGCTTCAGGCTTTGGCTGTGAACATGAGATGGTATCACG 1:0:0 Homo_sapiens_assembly18.fasta.3:93494052RA66A10A1AA2TC5G2A2TTTC
->SL-XAV:1:1:0:1300#0/2 NGATCATGGAAGACTCTCCCCATCCCCCGCTCCAGCGCTCAGTTATATGCCTAGCCTCGGACACGTCACCAACATCTCACGCACTCTGCACAGTCTCTCAC NM -
->SL-XAV:1:1:0:764#0/2 NACAGATGCAAATATTAACAGGCTTTAAAGGACAGATGGACTGCAATACAATAATAGAGTACGTCAACACTCCACAGATCGCTAGAGCATCACATCGGTGT 1:5:0 Homo_sapiens_assembly18.fasta.1:94972488FT74T1TAAT1A1C1C1CCACT4TGAA,Homo_sapiens_assembly18.fasta.8:42336261RT1T33G24ACCTC1ACACT1CACCG1AATC1ACA1CC3TATC1C1A,43145571FT1T33G25C12C1TAAT1A1C1C1CCACT4CGAA,44080574FT1T55T3C12C1TAAT1A1C1C1CCACT4CGAA,67494470RT1T33G25C12C1TAAT1A1C1C1CCACT4CGAA,68649702RT1T33G24ACCTC1ACACT1CACCG1AATC1ACA1CC3TATC1C1A
->SL-XAV:1:1:0:105#0/2 NGTCATCTTAGGAATAGCTGTGTCTGCTTTTCAGATCAGTTGCTCAATCTCTCACACATCGCTCCACATCTGAAACCGCAGATTGTAAGAGTCACGATGTG 1:0:0 Homo_sapiens_assembly18.fasta.18:158213355RT43G9A1A1GG3G4GT4C1T1AG1GC1T1G1CTTGGT1ACCT2
->SL-XAV:1:1:0:1721#0/2 NCGCGGCATCCCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCGAGAGCATACA 1:0:0 Homo_sapiens_assembly18.fasta.15:18728064FC40CG2T2T2TGT2TGTGGCAGA1AG1CAA1CTCCG1GT2AG4T3CTTGCTTT
diff --git a/testdata/net/sf/picard/illumina/s_4_2_eland_query.txt b/testdata/net/sf/picard/illumina/s_4_2_eland_query.txt
deleted file mode 100644
index 8b13789..0000000
--- a/testdata/net/sf/picard/illumina/s_4_2_eland_query.txt
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/testdata/net/sf/picard/illumina/s_4_2_export.txt b/testdata/net/sf/picard/illumina/s_4_2_export.txt
deleted file mode 100644
index 68a88e2..0000000
--- a/testdata/net/sf/picard/illumina/s_4_2_export.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-SL-XAV 1 1 1 0 1914 0 2 NTTGCACATTACTAGTTTCAGTTTTTTAAGTAAACGTATTCATCTCTTTTTATTAGCAGGGGCTATACTAGGCACTGTGGGCGACATAAAGAGCGCATACG DOYYXXXZXYYYWSSVXXWUUYYXXXVSTVVVTVVOQOVWRJRXWVWXXXXYYTKMNUKDKRZXXTVRRLDMXUUUNIDMDILMHNOPHKIOINIDDVKOG 1:0:0 N
-SL-XAV 1 1 1 0 1668 0 2 NAAAGGTGTCCAGTGGATCAAAAATGGAGTTGTGCTGGAATCCAATGAAAAGTATGCTCTCAGATCGGAAGCGCGTCTGGTAGGACGCGCGTGTAGAGATG DOWWSNUTSWWUUSSSSUWWWWQJROQRQSUSRNRWTNTNRTUSUWSLMQRJJLNUWMFPYUMRTURRLRNKNULFFQFDDDDPDDEPGNNNNOFNLFKNG 1:0:0 N
-SL-XAV 1 1 1 0 700 0 2 NAATTGTTCTCAGTTTCTCGGTTTATGTGCTCTTCCAGGTGGGTAACACAATAATGGCCTTCCAGATCGTAAGAGCGACGTGTGTTGCACGAGTGTCGATC DOYYWWVYYYYUNUSUYYWRWRWWWPPNUVXYWVUSODMNQJNLSNQWYRKTRUNSFFDDMVWNGNTTSNMNOQIHIEKLGTVGHDMUGUYGOUOPFNGKI 1:0:0 N
-SL-XAV 1 1 1 0 68 0 2 NTCTCATTTATAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTTCATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCACGACGTTATCT DP[[XXXZZZZ[[[WVTVXYTTUXVQVWXXVVSSSMEMOQRMDKVUQPNTSMSXMHNTROTTLQQLLFFJGMFLHHULPUWNGRDDOG[HMHHIDDDDDFO 1:0:0 N
-SL-XAV 1 1 1 0 1639 0 2 NGGCTGCAAAACATTCTGCGGATGCCTGAGGCAAAAGTTTATGGTTGAGAAATATAATAGACAGCTTCAGGCTTTGGCTGTGAACATGAGATGGTATCACG DIQWWWUTTVWUSUYYWWUTOUTNTVQONOJOKKSQQOOQUQLDMTLHNOMLVUQTNTPPVUWYZQROJMNPSOOJFKEHLFFGFPGQFPOJOMFDDMDMF 1:0:0 N
-SL-XAV 1 1 1 0 1300 0 2 NGATCATGGAAGACTCTCCCCATCCCCCGCTCCAGCGCTCAGTTATATGCCTAGCCTCGGACACGTCACCAACATCTCACGCACTCTGCACAGTCTCTCAC DDEJEERIDLNHNPFQUNILQLNTSQLIDLDNENINDLEDHLEHDMELNDDQJPQQIEDJKGNLDHGGKNLKKMEQGQEJHNDNDLUULDDNPUDHDIDFR NM N
-SL-XAV 1 1 1 0 764 0 2 NACAGATGCAAATATTAACAGGCTTTAAAGGACAGATGGACTGCAATACAATAATAGAGTACGTCAACACTCCACAGATCGCTAGAGCATCACATCGGTGT DNYTRTWYYXXXXYYXXXXWQTTYYVQVTKKNTTUVLFJRWVTRVWTVYTSLSMTPFRPOTXTSVRQOZVRNVQOJQQMSGUMZGGMZGZWGHGFEDDQDD 1:0:0 N
-SL-XAV 1 1 1 0 105 0 2 NGTCATCTTAGGAATAGCTGTGTCTGCTTTTCAGATCAGTTGCTCAATCTCTCACACATCGCTCCACATCTGAAACCGCAGATTGTAAGAGTCACGATGTG DMTWYYYWWURUWYUQTWUTRMRWTRTSPTWVMHILTKIHNNWLRHDNTQQFOIDMEIDDKWHEKDDFDHKSFHHMGKDLFMJJFJDDHDHGIDNLLRHHN 1:0:0 N
-SL-XAV 1 1 1 0 1721 0 2 NCGCGGCATCCCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCGAGAGCATACA DNPTSSTUUUUTPNTUUUUUTTRJQNPSNDNTTTTPQJRNHLENLDLEIJHHIEEPRJRHENNJJEENFHHNRJDITJJHDFQJDJNIDLDDIHDLMNPFP 1:0:0 N
diff --git a/testdata/net/sf/picard/illumina/s_5_eland_extended.txt b/testdata/net/sf/picard/illumina/s_5_eland_extended.txt
deleted file mode 100644
index d8864c7..0000000
--- a/testdata/net/sf/picard/illumina/s_5_eland_extended.txt
+++ /dev/null
@@ -1,3 +0,0 @@
->SL-XBG:1:29:818:454#0/2 CACACCCCCCAGCCGAAAATACCAAATGAATGGAGAGCTCCCGTGAGCGGGTAATAGGCTGATAGACCTGCGATAC 0:0:1 Homo_sapiens_assembly18.fasta.0:0R12A15C18T2T7G11T3CN
->SL-XBG:1:29:818:455#0/2 CACACCCCCCAGCCGAAAATACCAAATGAATGGAGAGCTCCCGTGAGCGGGTAATAGGCTGATAGACCTGCGATAC 0:0:1 Homo_sapiens_assembly18.fasta.0:16533R12A15C18T2T7G11T3CN
->SL-XAR:2:9:1184:1671#0/1 TAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTNGGGTTAGGGGTAGGGTTAGGGTTAGGGCTAGGGTTAGGGTTAGGGTTAGGGTTAGGG 1:255:139 Homo_sapiens_assembly18.fasta.16:-46R32A2G1TA2G1TA2G1TA3NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
diff --git a/testdata/net/sf/picard/illumina/s_5_export.txt b/testdata/net/sf/picard/illumina/s_5_export.txt
deleted file mode 100644
index 99d90be..0000000
--- a/testdata/net/sf/picard/illumina/s_5_export.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-SL-XBG 2 1 29 818 454 0 2 CACACCCCCCAGCCGAAAATACCAAATGAATGGAGAGCTCCCGTGAGCGGGTAATAGGCTGATAGACCTGCGATAC J`b]__WababVGTRWWa\K\_aaT__HYTX^`^R^^baa`WRJaH`T]]G]ZGH\aUFHa_aVa_NbU^IX_RKH 0:0:1 N
-SL-XBG 2 1 29 818 455 0 2 CACACCCCCCAGCCGAAAATACCAAATGAATGGAGAGCTCCCGTGAGCGGGTAATAGGCTGATAGACCTGCGATAC J`b]__WababVGTRWWa\K\_aaT__HYTX^`^R^^baa`WRJaH`T]]G]ZGH\aUFHa_aVa_NbU^IX_RKH 0:0:1 N
-SL-XAR 1 2 9 1184 1671 0 1 TAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTNGGGTTAGGGGTAGGGTTAGGGTTAGGGCTAGGGTTAGGGTTAGGGTTAGGGTTAGGG ]````TaabaTDZZ]__aabTaZDWVZaWD^Wa`^ZT^b]`G^DZZ_UbTba_FZSaaaGNNTaaM]^a_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 1:255:139 N
diff --git a/testdata/net/sf/picard/intervallist/IntervalListchr123_empty.interval_list b/testdata/net/sf/picard/intervallist/IntervalListchr123_empty.interval_list
new file mode 100644
index 0000000..f8fd99b
--- /dev/null
+++ b/testdata/net/sf/picard/intervallist/IntervalListchr123_empty.interval_list
@@ -0,0 +1,4 @@
+ at SQ SN:1 LN:249250621
+ at SQ SN:2 LN:243199373
+ at SQ SN:3 LN:198022430
+1 1 1 + test
\ No newline at end of file
diff --git a/testdata/net/sf/picard/sam/CompareSAMs/bigger_seq_dict.sam b/testdata/net/sf/picard/sam/CompareSAMs/bigger_seq_dict.sam
index 869fd8a..af3854f 100755
--- a/testdata/net/sf/picard/sam/CompareSAMs/bigger_seq_dict.sam
+++ b/testdata/net/sf/picard/sam/CompareSAMs/bigger_seq_dict.sam
@@ -1,7 +1,7 @@
@HD VN:1.0 SO:coordinate
@SQ SN:chr20 AS:HG18 LN:62435964
@SQ SN:chr21 AS:HG18 LN:62435964
- at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891
- at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891
+ at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 PL:ILLUMINA
+ at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 PL:ILLUMINA
read_28833_29006_6945 99 chr20 28833 20 10M1D25M = 28993 195 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< MF:i:130 Nm:i:1 H0:i:0 H1:i:0 RG:Z:L1
read_28701_28881_323b 147 chr21 28834 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
diff --git a/testdata/net/sf/picard/sam/CompareSAMs/chr21.sam b/testdata/net/sf/picard/sam/CompareSAMs/chr21.sam
index 0925385..42fab28 100755
--- a/testdata/net/sf/picard/sam/CompareSAMs/chr21.sam
+++ b/testdata/net/sf/picard/sam/CompareSAMs/chr21.sam
@@ -1,6 +1,6 @@
@HD VN:1.0 SO:coordinate
@SQ SN:chr21 AS:HG18 LN:62435964
- at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891
- at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891
+ at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 PL:ILLUMINA
+ at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 PL:ILLUMINA
read_28833_29006_6945 99 chr21 28833 20 10M1D25M = 28993 195 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< MF:i:130 Nm:i:1 H0:i:0 H1:i:0 RG:Z:L1
read_28701_28881_323b 147 chr21 28834 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
diff --git a/testdata/net/sf/picard/sam/CompareSAMs/diff_coords.sam b/testdata/net/sf/picard/sam/CompareSAMs/diff_coords.sam
index 386ae2d..575c205 100755
--- a/testdata/net/sf/picard/sam/CompareSAMs/diff_coords.sam
+++ b/testdata/net/sf/picard/sam/CompareSAMs/diff_coords.sam
@@ -1,7 +1,7 @@
@HD VN:1.0 SO:coordinate
@SQ SN:chr20 AS:HG18 LN:62435964
- at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891
- at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891
+ at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 PL:ILLUMINA
+ at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 PL:ILLUMINA
read_28833_29006_6945 99 chr20 1 20 10M1D25M = 28993 195 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< MF:i:130 Nm:i:1 H0:i:0 H1:i:0 RG:Z:L1
read_28701_28881_323b 147 chr20 2 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
read_3 147 chr20 28850 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
diff --git a/testdata/net/sf/picard/sam/CompareSAMs/example2.sam b/testdata/net/sf/picard/sam/CompareSAMs/example2.sam
index 23f703d..8158b90 100755
--- a/testdata/net/sf/picard/sam/CompareSAMs/example2.sam
+++ b/testdata/net/sf/picard/sam/CompareSAMs/example2.sam
@@ -1,6 +1,6 @@
@HD VN:1.1
@SQ SN:chr20 AS:HG17 LN:62435963
- at RG ID:L1 PU:SC_1_10x LB:SC_1x SM:NA12891x
- at RG ID:L2 PU:SC_2_12x LB:SC_2x SM:NA12891x
+ at RG ID:L1 PU:SC_1_10x LB:SC_1x SM:NA12891x PL:ILLUMINA
+ at RG ID:L2 PU:SC_2_12x LB:SC_2x SM:NA12891x PL:ILLUMINA
read_28833_29006_6945 99 chr20 28833 10 10M1D25M = 28993 195 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< MF:i:130 Nm:i:1 H0:i:0 H1:i:0 RG:Z:L1
read_28701_28881_323b 147 chr20 28834 10 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
diff --git a/testdata/net/sf/picard/sam/CompareSAMs/genomic_sorted.sam b/testdata/net/sf/picard/sam/CompareSAMs/genomic_sorted.sam
index b53d161..9fc40d7 100755
--- a/testdata/net/sf/picard/sam/CompareSAMs/genomic_sorted.sam
+++ b/testdata/net/sf/picard/sam/CompareSAMs/genomic_sorted.sam
@@ -1,6 +1,6 @@
@HD VN:1.0 SO:coordinate
@SQ SN:chr20 AS:HG18 LN:62435964
- at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891
- at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891
+ at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 PL:ILLUMINA
+ at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 PL:ILLUMINA
read_28833_29006_6945 99 chr20 28833 20 10M1D25M = 28993 195 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< MF:i:130 Nm:i:1 H0:i:0 H1:i:0 RG:Z:L1
read_28701_28881_323b 147 chr20 28834 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
diff --git a/testdata/net/sf/picard/sam/CompareSAMs/genomic_sorted_5.sam b/testdata/net/sf/picard/sam/CompareSAMs/genomic_sorted_5.sam
index e5fd5ae..112efd4 100755
--- a/testdata/net/sf/picard/sam/CompareSAMs/genomic_sorted_5.sam
+++ b/testdata/net/sf/picard/sam/CompareSAMs/genomic_sorted_5.sam
@@ -1,7 +1,7 @@
@HD VN:1.0 SO:coordinate
@SQ SN:chr20 AS:HG18 LN:62435964
- at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891
- at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891
+ at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 PL:ILLUMINA
+ at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 PL:ILLUMINA
read_28833_29006_6945 99 chr20 28833 20 10M1D25M = 28993 195 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< MF:i:130 Nm:i:1 H0:i:0 H1:i:0 RG:Z:L1
read_28701_28881_323b 147 chr20 28834 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
read_3 147 chr20 30000 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
diff --git a/testdata/net/sf/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam b/testdata/net/sf/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam
index 0d2ebe5..323968e 100755
--- a/testdata/net/sf/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam
+++ b/testdata/net/sf/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam
@@ -1,7 +1,7 @@
@HD VN:1.0 SO:coordinate
@SQ SN:chr20 AS:HG18 LN:62435964
- at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891
- at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891
+ at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 PL:ILLUMINA
+ at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 PL:ILLUMINA
read_28833_29006_6945 99 chr20 28833 20 10M1D25M = 28993 195 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< MF:i:130 Nm:i:1 H0:i:0 H1:i:0 RG:Z:L1
read_28701_28881_323b 147 chr20 28834 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
read_3 147 chr20 30001 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
diff --git a/testdata/net/sf/picard/sam/CompareSAMs/group_same_coord.sam b/testdata/net/sf/picard/sam/CompareSAMs/group_same_coord.sam
index 661a855..3102821 100755
--- a/testdata/net/sf/picard/sam/CompareSAMs/group_same_coord.sam
+++ b/testdata/net/sf/picard/sam/CompareSAMs/group_same_coord.sam
@@ -1,7 +1,7 @@
@HD VN:1.0 SO:coordinate
@SQ SN:chr20 AS:HG18 LN:62435964
- at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891
- at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891
+ at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 PL:ILLUMINA
+ at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 PL:ILLUMINA
read_28833_29006_6945 99 chr20 28833 20 10M1D25M = 28993 195 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< MF:i:130 Nm:i:1 H0:i:0 H1:i:0 RG:Z:L1
read_28701_28881_323b 147 chr20 28833 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
read_3 147 chr20 28833 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
diff --git a/testdata/net/sf/picard/sam/CompareSAMs/group_same_coord_diff_order.sam b/testdata/net/sf/picard/sam/CompareSAMs/group_same_coord_diff_order.sam
index 951b8e6..f3631be 100755
--- a/testdata/net/sf/picard/sam/CompareSAMs/group_same_coord_diff_order.sam
+++ b/testdata/net/sf/picard/sam/CompareSAMs/group_same_coord_diff_order.sam
@@ -1,7 +1,7 @@
@HD VN:1.0 SO:coordinate
@SQ SN:chr20 AS:HG18 LN:62435964
- at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891
- at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891
+ at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 PL:ILLUMINA
+ at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 PL:ILLUMINA
read_5 147 chr20 28833 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
read_4x 147 chr20 28833 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
read_28701_28881_323b 147 chr20 28833 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
diff --git a/testdata/net/sf/picard/sam/CompareSAMs/has_non_primary.sam b/testdata/net/sf/picard/sam/CompareSAMs/has_non_primary.sam
index 70d712f..55f3877 100755
--- a/testdata/net/sf/picard/sam/CompareSAMs/has_non_primary.sam
+++ b/testdata/net/sf/picard/sam/CompareSAMs/has_non_primary.sam
@@ -1,7 +1,7 @@
@HD VN:1.0 SO:coordinate
@SQ SN:chr20 AS:HG18 LN:62435964
- at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891
- at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891
+ at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 PL:ILLUMINA
+ at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 PL:ILLUMINA
read_28833_29006_6945 355 chr20 28833 20 10M1D25M = 28993 195 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< MF:i:130 Nm:i:1 H0:i:0 H1:i:0 RG:Z:L1
read_28833_29006_6945 99 chr20 28833 20 10M1D25M = 28993 195 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< MF:i:130 Nm:i:1 H0:i:0 H1:i:0 RG:Z:L1
read_28833_29006_6945 355 chr20 28833 20 10M1D25M = 28993 195 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< MF:i:130 Nm:i:1 H0:i:0 H1:i:0 RG:Z:L1
diff --git a/testdata/net/sf/picard/sam/CompareSAMs/unmapped_first.sam b/testdata/net/sf/picard/sam/CompareSAMs/unmapped_first.sam
index 686633a..c95f3a9 100755
--- a/testdata/net/sf/picard/sam/CompareSAMs/unmapped_first.sam
+++ b/testdata/net/sf/picard/sam/CompareSAMs/unmapped_first.sam
@@ -1,6 +1,6 @@
@HD VN:1.0 SO:coordinate
@SQ SN:chr20 AS:HG18 LN:62435964
- at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891
- at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891
+ at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 PL:ILLUMINA
+ at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 PL:ILLUMINA
read_28833_29006_6945 101 chr20 28833 0 * = 28993 195 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< MF:i:130 Nm:i:1 H0:i:0 H1:i:0 RG:Z:L1
read_28701_28881_323b 147 chr20 28834 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
diff --git a/testdata/net/sf/picard/sam/CompareSAMs/unmapped_second.sam b/testdata/net/sf/picard/sam/CompareSAMs/unmapped_second.sam
index b376fe2..72e4da4 100755
--- a/testdata/net/sf/picard/sam/CompareSAMs/unmapped_second.sam
+++ b/testdata/net/sf/picard/sam/CompareSAMs/unmapped_second.sam
@@ -1,6 +1,6 @@
@HD VN:1.0 SO:coordinate
@SQ SN:chr20 AS:HG18 LN:62435964
- at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891
- at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891
+ at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 PL:ILLUMINA
+ at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 PL:ILLUMINA
read_28833_29006_6945 99 chr20 28833 20 10M1D25M = 28993 195 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< MF:i:130 Nm:i:1 H0:i:0 H1:i:0 RG:Z:L1
read_28701_28881_323b 1101 chr20 28834 0 * * 0 0 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
diff --git a/testdata/net/sf/picard/sam/CompareSAMs/unsorted.sam b/testdata/net/sf/picard/sam/CompareSAMs/unsorted.sam
index efb93a3..5703850 100755
--- a/testdata/net/sf/picard/sam/CompareSAMs/unsorted.sam
+++ b/testdata/net/sf/picard/sam/CompareSAMs/unsorted.sam
@@ -1,6 +1,6 @@
@HD VN:1.0
@SQ SN:chr20 AS:HG18 LN:62435964
- at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891
- at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891
+ at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 PL:ILLUMINA
+ at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 PL:ILLUMINA
read_28833_29006_6945 99 chr20 28833 20 10M1D25M = 28993 195 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< MF:i:130 Nm:i:1 H0:i:0 H1:i:0 RG:Z:L1
read_28701_28881_323b 147 chr20 28834 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
diff --git a/testdata/net/sf/picard/sam/MarkDuplicates/merge1.sam b/testdata/net/sf/picard/sam/MarkDuplicates/merge1.sam
index 7e1c583..a71674d 100644
--- a/testdata/net/sf/picard/sam/MarkDuplicates/merge1.sam
+++ b/testdata/net/sf/picard/sam/MarkDuplicates/merge1.sam
@@ -7,7 +7,7 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
- at RG ID:1AAXX.1 SM:Hi,Mom! LB:mylib
+ at RG ID:1AAXX.1 SM:Hi,Mom! LB:mylib PL:ILLUMINA
@PG ID:MarkDuplicates PN:MarkDuplicates VN:1 CL:MarkDuplicates merge1.sam PP:bwa
@PG ID:bwa PN:bwa VN:1 CL:bwa aln
1AAXX.1.1 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1AAXX.1 PG:Z:MarkDuplicates
diff --git a/testdata/net/sf/picard/sam/MarkDuplicates/merge2.sam b/testdata/net/sf/picard/sam/MarkDuplicates/merge2.sam
index 10f4ed3..b501566 100644
--- a/testdata/net/sf/picard/sam/MarkDuplicates/merge2.sam
+++ b/testdata/net/sf/picard/sam/MarkDuplicates/merge2.sam
@@ -7,7 +7,7 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
- at RG ID:1AAXX.2 SM:Hi,Mom! LB:mylib
+ at RG ID:1AAXX.2 SM:Hi,Mom! LB:mylib PL:ILLUMINA
@PG ID:bwa PN:bwa VN:2 CL:bwa aln
1AAXX.2.1 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1AAXX.2 PG:Z:bwa
1AAXX.2.1 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:1AAXX.2 PG:Z:bwa
diff --git a/testdata/net/sf/picard/sam/MarkDuplicates/merge3.sam b/testdata/net/sf/picard/sam/MarkDuplicates/merge3.sam
index 05cdbe1..0b9ef37 100644
--- a/testdata/net/sf/picard/sam/MarkDuplicates/merge3.sam
+++ b/testdata/net/sf/picard/sam/MarkDuplicates/merge3.sam
@@ -7,7 +7,7 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
- at RG ID:1AAXX.3 SM:Hi,Mom! LB:mylib
+ at RG ID:1AAXX.3 SM:Hi,Mom! LB:mylib PL:ILLUMINA
@PG ID:bwa PN:bwa VN:3 CL:bwa aln
1AAXX.3.1 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1AAXX.3
1AAXX.3.1 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:1AAXX.3
diff --git a/testdata/net/sf/picard/sam/MergeBamAlignment/aligned.badorder.sam b/testdata/net/sf/picard/sam/MergeBamAlignment/aligned.badorder.sam
index f89d6d5..c86e002 100755
--- a/testdata/net/sf/picard/sam/MergeBamAlignment/aligned.badorder.sam
+++ b/testdata/net/sf/picard/sam/MergeBamAlignment/aligned.badorder.sam
@@ -7,7 +7,7 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
@PG ID:1 PN:Hey! VN:2.0
test 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
test 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
diff --git a/testdata/net/sf/picard/sam/MergeBamAlignment/aligned.supplement.sam b/testdata/net/sf/picard/sam/MergeBamAlignment/aligned.supplement.sam
index 3b9dd0e..092d15d 100644
--- a/testdata/net/sf/picard/sam/MergeBamAlignment/aligned.supplement.sam
+++ b/testdata/net/sf/picard/sam/MergeBamAlignment/aligned.supplement.sam
@@ -7,7 +7,7 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
@PG ID:1 PN:Hey! VN:2.0
both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
diff --git a/testdata/net/sf/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam b/testdata/net/sf/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam
index 4b5bc48..0767c2f 100755
--- a/testdata/net/sf/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam
+++ b/testdata/net/sf/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam
@@ -7,7 +7,7 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
@PG ID:1 PN:Hey! VN:2.0
test:1 0 chr1 10 37 35M1S * 0 0 TCTCTCCTTGCCCTTCATGATCTTGGCACTTTCGGA DDDEBDCCCCDBBD at DBCBCCCC:ACAA?CBCCCAB XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36
test:2 0 chr7 50 37 36M * 0 0 GGTAACTGCTGACGGGAAGCTTGCTTTAAACCAGAT FDBEEDCDEDDDDDCCCCDCCCCDCDCDBCEBCB at C XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36
diff --git a/testdata/net/sf/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam b/testdata/net/sf/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam
index 3e91454..f700bf3 100755
--- a/testdata/net/sf/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam
+++ b/testdata/net/sf/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam
@@ -7,7 +7,7 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
@PG ID:1 PN:Hey! VN:2.0
test:1 16 chr1 50 37 1S35M * 0 0 CACTGCACTCCAGCATATGTGACAACAGTGAAACTC F?EDEFCEECEC:-EEEGDGGFGGFGGGGGGGFGGG XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36
test:2 16 chr7 201 37 36M * 0 0 TCCTGAGAACTTGCTATGTGTTAGGTCCTAGGCTGG GDDDGFEECEEFF<FEGGGFGGGGFGGGGGGGGGGG XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:13A22
diff --git a/testdata/net/sf/picard/sam/MergeBamAlignment/cliptest.unmapped.sam b/testdata/net/sf/picard/sam/MergeBamAlignment/cliptest.unmapped.sam
index 5e572fb..d18395d 100644
--- a/testdata/net/sf/picard/sam/MergeBamAlignment/cliptest.unmapped.sam
+++ b/testdata/net/sf/picard/sam/MergeBamAlignment/cliptest.unmapped.sam
@@ -1,5 +1,5 @@
@HD VN:1.0 SO:queryname
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
FF:80:175 77 * 0 0 * * 0 0 GTACCCGGGGATCCCACTCTCTCCTTGCCCTTCATGATCTTGGCACTTTCGGAGTAATGGTCATAACATCAGTAAA ECEEEEEDDCCCDDDCDDDDEBDCCCCDBBD at DBCBCCCC:ACAA?CBCCCABCBBBBBBB?BBB?<?A?<7<<=9 RG:Z:0
FF:80:175 141 * 0 0 * * 0 0 TCGACTCTAGAGGATCCCACGAGTTTCACTGTTGTCACATATGCTGGAGTGCAGTGGTGCAATCTTGGCTTACTGC GGGGGGGGGGFGGGGGGGGGGGGFGGGGGGGFGGFGGDGEEE-:CECEECFEDE?FBCFD=@CBBADCF=CC:CCD RG:Z:0
FR_clip:100:155 77 * 0 0 * * 0 0 GTACCCGGGGATCCCACTCTCTCCTTGCCCTTCATGATCTTGGCACTTTCGGAGTAATGGTCATAACATCAGTAAA ECEEEEEDDCCCDDDCDDDDEBDCCCCDBBD at DBCBCCCC:ACAA?CBCCCABCBBBBBBB?BBB?<?A?<7<<=9 RG:Z:0
diff --git a/testdata/net/sf/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam b/testdata/net/sf/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam
index e28074f..75a1590 100755
--- a/testdata/net/sf/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam
+++ b/testdata/net/sf/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam
@@ -7,7 +7,7 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
@PG ID:1 PN:Hey! VN:2.0
test:1 0 chr1 10 37 35M1S * 0 0 TCTCTCCTTGCCCTTCATGATCTTGGCACTTTCGGA DDDEBDCCCCDBBD at DBCBCCCC:ACAA?CBCCCAB XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36
test:6 16 chr1 15 37 36M * 0 0 CCTCATGCTCTGCTCCCCAGAGTGGAAACAAGGTGG BCCCDDDCDCDDDCBDCDDEDEDEDEECFEGEEEEF XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36
diff --git a/testdata/net/sf/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam b/testdata/net/sf/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam
index 54c5f4b..c5c6012 100755
--- a/testdata/net/sf/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam
+++ b/testdata/net/sf/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam
@@ -7,7 +7,7 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
@PG ID:1 PN:Hey! VN:2.0
test:2 16 chr7 201 37 36M * 0 0 TCCTGAGAACTTGCTATGTGTTAGGTCCTAGGCTGG GDDDGFEECEEFF<FEGGGFGGGGFGGGGGGGGGGG XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:13A22
test:3 4 * 0 0 * * 0 0 GCTCACACCACTGCATTCCCGCATGGGCGCCAGACT ?:D=5*05A@*>AA5???################## XC:i:35
diff --git a/testdata/net/sf/picard/sam/MergeBamAlignment/multihit.aligned.sam b/testdata/net/sf/picard/sam/MergeBamAlignment/multihit.aligned.sam
index 07bc1bb..9f30d36 100644
--- a/testdata/net/sf/picard/sam/MergeBamAlignment/multihit.aligned.sam
+++ b/testdata/net/sf/picard/sam/MergeBamAlignment/multihit.aligned.sam
@@ -7,7 +7,7 @@
@SQ SN:chr6 LN:101 UR:file:testdata/net/sf/picard/sam/merger.fasta M5:7be2f5e7ee39e60a6c3b5b6a41178c6d
@SQ SN:chr7 LN:404 UR:file:testdata/net/sf/picard/sam/merger.fasta M5:da488fc432cdaf2c20c96da473a7b630
@SQ SN:chr8 LN:202 UR:file:testdata/net/sf/picard/sam/merger.fasta M5:d339678efce576d5546e88b49a487b63
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
@CO frag_hit: Single alignment
@CO frag_multihit: chr2 is primary alignment
@CO pair_both_multihit: chr8 is primary alignment
diff --git a/testdata/net/sf/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam b/testdata/net/sf/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam
index 63e2c4f..64c04e2 100644
--- a/testdata/net/sf/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam
+++ b/testdata/net/sf/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam
@@ -1,3 +1,3 @@
@HD VN:1.0 SO:queryname
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
fragment_read 4 * 0 0 * * 0 0 CAACAG )'.*.+ RG:Z:0
diff --git a/testdata/net/sf/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam b/testdata/net/sf/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam
index b131c48..aa39faf 100644
--- a/testdata/net/sf/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam
+++ b/testdata/net/sf/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam
@@ -1,4 +1,4 @@
@HD VN:1.0 SO:queryname
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
pair_read 77 * 0 0 * * 0 0 CAACAG )'.*.+ RG:Z:0
pair_read 141 * 0 0 * * 0 0 NCGCGG &/1544 RG:Z:0
diff --git a/testdata/net/sf/picard/sam/MergeBamAlignment/multihit.unmapped.sam b/testdata/net/sf/picard/sam/MergeBamAlignment/multihit.unmapped.sam
index c65cf25..722dfac 100644
--- a/testdata/net/sf/picard/sam/MergeBamAlignment/multihit.unmapped.sam
+++ b/testdata/net/sf/picard/sam/MergeBamAlignment/multihit.unmapped.sam
@@ -1,5 +1,5 @@
@HD VN:1.0 SO:queryname
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
frag_hit 4 * 0 0 * * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
frag_multihit 4 * 0 0 * * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
frag_no_hit 4 * 0 0 * * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
diff --git a/testdata/net/sf/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam b/testdata/net/sf/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam
index 93b8fd8..4d9f3b6 100755
--- a/testdata/net/sf/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam
+++ b/testdata/net/sf/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam
@@ -7,7 +7,7 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
@PG ID:1 PN:Hey! VN:2.0
test:5 16 chr7 300 37 1S35M * 0 0 CCTGGGCACAGATGAGGAATTCTGGCTTCTCCTCCT +9???=?<08:,1===2=3=5:??=5??5B=B:@@D XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36
test:4 4 * 0 0 * * 0 0 AGAGACTACGAAAAGGGGGGTGGAACAGTACTCTAA #################################### XC:i:35
diff --git a/testdata/net/sf/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam b/testdata/net/sf/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam
index 3bfa8f2..030c693 100755
--- a/testdata/net/sf/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam
+++ b/testdata/net/sf/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam
@@ -7,7 +7,7 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
@PG ID:1 PN:Hey! VN:2.0
test:1 16 chr1 50 37 1S35M * 0 0 CACTGCACTCCAGCATATGTGACAACAGTGAAACTC F?EDEFCEECEC:-EEEGDGGFGGFGGGGGGGFGGG XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36
test:6 0 chr1 62 37 36M * 0 0 CAATGGGAGCCATTTCCTCATCTGTAAAAACAATAA GGGGFGGGDGGEDGGGGGGDFFCFDFFEFFGD at GAC XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36
diff --git a/testdata/net/sf/picard/sam/MergeBamAlignment/unmapped.badorder.sam b/testdata/net/sf/picard/sam/MergeBamAlignment/unmapped.badorder.sam
index c51db94..7aecda1 100755
--- a/testdata/net/sf/picard/sam/MergeBamAlignment/unmapped.badorder.sam
+++ b/testdata/net/sf/picard/sam/MergeBamAlignment/unmapped.badorder.sam
@@ -1,4 +1,4 @@
@HD VN:1.0 SO:queryname
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
test 141 * 0 0 * * 0 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
test 77 * 0 0 * * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
diff --git a/testdata/net/sf/picard/sam/MergeBamAlignment/unmapped.sam b/testdata/net/sf/picard/sam/MergeBamAlignment/unmapped.sam
index d7881ad..c602014 100755
--- a/testdata/net/sf/picard/sam/MergeBamAlignment/unmapped.sam
+++ b/testdata/net/sf/picard/sam/MergeBamAlignment/unmapped.sam
@@ -1,5 +1,5 @@
@HD VN:1.0 SO:queryname
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
test:1 77 * 0 0 * * 0 0 GTACCCGGGGATCCCACTCTCTCCTTGCCCTTCATGATCTTGGCACTTTCGGAGTAATGGTCATAACATCAGTAAA ECEEEEEDDCCCDDDCDDDDEBDCCCCDBBD at DBCBCCCC:ACAA?CBCCCABCBBBBBBB?BBB?<?A?<7<<=9 RG:Z:0
test:1 141 * 0 0 * * 0 0 TCGACTCTAGAGGATCCCACGAGTTTCACTGTTGTCACATATGCTGGAGTGCAGTGGTGCAATCTTGGCTTACTGC GGGGGGGGGGFGGGGGGGGGGGGFGGGGGGGFGGFGGDGEEE-:CECEECFEDE?FBCFD=@CBBADCF=CC:CCD RG:Z:0
test:2 77 * 0 0 * * 0 0 GTACCCGGGGATCCCACGGTAACTGCTGACGGGAAGCTTGCTTTAAACCAGATTAGCCAGATCTCCATGAAGTCGC FDFFFFEDDDDCDFDDDFDBEEDCDEDDDDDCCCCDCCCCDCDCDBCEBCB at CAC=CCBCC?CAA at A@?@:?77<A RG:Z:0
diff --git a/testdata/net/sf/picard/sam/MergeSamFiles/case1/chr11sub_file1.sam b/testdata/net/sf/picard/sam/MergeSamFiles/case1/chr11sub_file1.sam
index fb010c5..f8b478d 100644
--- a/testdata/net/sf/picard/sam/MergeSamFiles/case1/chr11sub_file1.sam
+++ b/testdata/net/sf/picard/sam/MergeSamFiles/case1/chr11sub_file1.sam
@@ -1,5 +1,5 @@
@HD VN:1.0 GO:none SO:coordinate
@SQ SN:chrM LN:16571 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:d2ed829b8a1628d16cbeee88e88e39eb SP:Homo sapiens
- at RG ID:1 SM:sample1
+ at RG ID:1 SM:sample1 PL:ILLUMINA
@PG ID:1 PN:something
6194MAAXX100108:2:55:3087:12679:BI 99 chrM 50418 0 101M = 50678 360 TCAAACATAGTCAAAGAGAGGGAGATTTCTGGATAATCACTTAAGCCCATGGTTAAACATAAATGCAAATATGTTAATGTTTACTGAATAACTTATCTGTG 9<9 at A?A@?A=@BCCA at B@BAA at B@ABBACAA at A@C at ABACB@CBAA at BABA>BACCABAACDABABCCAA at B?BACAB>CCAABBACAAD?CB>?>?<9< RG:Z:1 E2:Z:CAGGGAGGGCGAGGGTGAGATTGTGGGGAGATGGGTGAGACGTTAAGACATTGATCCACATTTATACCCATAAGATTATGAATAATTTATTAGATATCTGT OQ:Z:CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCC at CCDCCDDCDACCC@@C [...]
diff --git a/testdata/net/sf/picard/sam/MergeSamFiles/case1/chr11sub_file2.sam b/testdata/net/sf/picard/sam/MergeSamFiles/case1/chr11sub_file2.sam
index 23715a2..3b9b566 100644
--- a/testdata/net/sf/picard/sam/MergeSamFiles/case1/chr11sub_file2.sam
+++ b/testdata/net/sf/picard/sam/MergeSamFiles/case1/chr11sub_file2.sam
@@ -1,6 +1,6 @@
@HD VN:1.0 GO:none SO:coordinate
@SQ SN:chrM LN:16571 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:d2ed829b8a1628d16cbeee88e88e39eb SP:Homo sapiens
- at RG ID:1 SM:sample1
+ at RG ID:1 SM:sample1 PL:ILLUMINA
@PG ID:1 PN:A
@PG ID:1.1 PN:B
@PG ID:2 PN:C PP:1
diff --git a/testdata/net/sf/picard/sam/MergeSamFiles/case1/expected_output.sam b/testdata/net/sf/picard/sam/MergeSamFiles/case1/expected_output.sam
index bf3b62d..e604911 100644
--- a/testdata/net/sf/picard/sam/MergeSamFiles/case1/expected_output.sam
+++ b/testdata/net/sf/picard/sam/MergeSamFiles/case1/expected_output.sam
@@ -1,6 +1,6 @@
@HD VN:1.4 GO:none SO:coordinate
@SQ SN:chrM LN:16571 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:d2ed829b8a1628d16cbeee88e88e39eb SP:Homo sapiens
- at RG ID:1 SM:sample1
+ at RG ID:1 PL:ILLUMINA SM:sample1
@PG ID:1 PN:something
@PG ID:1.1 PN:A
@PG ID:1.1.2 PN:B
diff --git a/testdata/net/sf/picard/sam/MergeSamFiles/case2/chr11sub_file1.sam b/testdata/net/sf/picard/sam/MergeSamFiles/case2/chr11sub_file1.sam
index 2578e13..a2575f0 100644
--- a/testdata/net/sf/picard/sam/MergeSamFiles/case2/chr11sub_file1.sam
+++ b/testdata/net/sf/picard/sam/MergeSamFiles/case2/chr11sub_file1.sam
@@ -1,6 +1,6 @@
@HD VN:1.0 GO:none SO:coordinate
@SQ SN:chrM LN:16571 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:d2ed829b8a1628d16cbeee88e88e39eb SP:Homo sapiens
- at RG ID:1 SM:sample1
+ at RG ID:1 SM:sample1 PL:ILLUMINA
@PG ID:1 PN:A
@PG ID:2 PN:B PP:1
@PG ID:3 PN:C PP:1
diff --git a/testdata/net/sf/picard/sam/MergeSamFiles/case2/chr11sub_file2.sam b/testdata/net/sf/picard/sam/MergeSamFiles/case2/chr11sub_file2.sam
index e6c574c..5e6e7ea 100644
--- a/testdata/net/sf/picard/sam/MergeSamFiles/case2/chr11sub_file2.sam
+++ b/testdata/net/sf/picard/sam/MergeSamFiles/case2/chr11sub_file2.sam
@@ -1,6 +1,6 @@
@HD VN:1.0 GO:none SO:coordinate
@SQ SN:chrM LN:16571 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:d2ed829b8a1628d16cbeee88e88e39eb SP:Homo sapiens
- at RG ID:1 SM:sample1
+ at RG ID:1 SM:sample1 PL:ILLUMINA
@PG ID:1 PN:A
@PG ID:2 PN:B PP:1
6194MAAXX100108:2:55:3087:12679:BI 99 chrM 50418 0 101M = 50678 360 TCAAACATAGTCAAAGAGAGGGAGATTTCTGGATAATCACTTAAGCCCATGGTTAAACATAAATGCAAATATGTTAATGTTTACTGAATAACTTATCTGTG 9<9 at A?A@?A=@BCCA at B@BAA at B@ABBACAA at A@C at ABACB@CBAA at BABA>BACCABAACDABABCCAA at B?BACAB>CCAABBACAAD?CB>?>?<9< RG:Z:1 E2:Z:CAGGGAGGGCGAGGGTGAGATTGTGGGGAGATGGGTGAGACGTTAAGACATTGATCCACATTTATACCCATAAGATTATGAATAATTTATTAGATATCTGT OQ:Z:CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCC at CCDCCDDCDACCC@@C [...]
diff --git a/testdata/net/sf/picard/sam/MergeSamFiles/case2/chr11sub_file3.sam b/testdata/net/sf/picard/sam/MergeSamFiles/case2/chr11sub_file3.sam
index f43de61..6bda955 100644
--- a/testdata/net/sf/picard/sam/MergeSamFiles/case2/chr11sub_file3.sam
+++ b/testdata/net/sf/picard/sam/MergeSamFiles/case2/chr11sub_file3.sam
@@ -1,6 +1,6 @@
@HD VN:1.0 GO:none SO:coordinate
@SQ SN:chrM LN:16571 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:d2ed829b8a1628d16cbeee88e88e39eb SP:Homo sapiens
- at RG ID:1 SM:sample2
+ at RG ID:1 SM:sample2 PL:ILLUMINA
@PG ID:1 PN:X
@PG ID:2 PN:B PP:1
@PG ID:3 PN:Y PP:2
diff --git a/testdata/net/sf/picard/sam/MergeSamFiles/case2/chr11sub_file4.sam b/testdata/net/sf/picard/sam/MergeSamFiles/case2/chr11sub_file4.sam
index c659234..d0c43d7 100644
--- a/testdata/net/sf/picard/sam/MergeSamFiles/case2/chr11sub_file4.sam
+++ b/testdata/net/sf/picard/sam/MergeSamFiles/case2/chr11sub_file4.sam
@@ -1,5 +1,5 @@
@HD VN:1.0 GO:none SO:coordinate
@SQ SN:chrM LN:16571 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:d2ed829b8a1628d16cbeee88e88e39eb SP:Homo sapiens
- at RG ID:1.1 SM:sample3
+ at RG ID:1.1 SM:sample3 PL:ILLUMINA
@PG ID:2 PN:B
6194MAAXX100108:2:55:3087:12679:BI 99 chrM 50418 0 101M = 50678 360 TCAAACATAGTCAAAGAGAGGGAGATTTCTGGATAATCACTTAAGCCCATGGTTAAACATAAATGCAAATATGTTAATGTTTACTGAATAACTTATCTGTG 9<9 at A?A@?A=@BCCA at B@BAA at B@ABBACAA at A@C at ABACB@CBAA at BABA>BACCABAACDABABCCAA at B?BACAB>CCAABBACAAD?CB>?>?<9< RG:Z:1.1 E2:Z:CAGGGAGGGCGAGGGTGAGATTGTGGGGAGATGGGTGAGACGTTAAGACATTGATCCACATTTATACCCATAAGATTATGAATAATTTATTAGATATCTGT OQ:Z:CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCC at CCDCCDDCDACCC@ [...]
diff --git a/testdata/net/sf/picard/sam/MergeSamFiles/case2/expected_output.sam b/testdata/net/sf/picard/sam/MergeSamFiles/case2/expected_output.sam
index 0df01ae..89ba32d 100644
--- a/testdata/net/sf/picard/sam/MergeSamFiles/case2/expected_output.sam
+++ b/testdata/net/sf/picard/sam/MergeSamFiles/case2/expected_output.sam
@@ -1,8 +1,8 @@
@HD VN:1.4 GO:none SO:coordinate
@SQ SN:chrM LN:16571 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:d2ed829b8a1628d16cbeee88e88e39eb SP:Homo sapiens
- at RG ID:1 SM:sample1
- at RG ID:1.1 SM:sample2
- at RG ID:1.1.2 SM:sample3
+ at RG ID:1 PL:ILLUMINA SM:sample1
+ at RG ID:1.1 PL:ILLUMINA SM:sample2
+ at RG ID:1.1.2 PL:ILLUMINA SM:sample3
@PG ID:1 PN:A
@PG ID:1.1 PN:X
@PG ID:2 PN:B
diff --git a/testdata/net/sf/picard/sam/MergeSamFiles/unsorted_input/1.sam b/testdata/net/sf/picard/sam/MergeSamFiles/unsorted_input/1.sam
index 15e6ca5..f4f16f8 100644
--- a/testdata/net/sf/picard/sam/MergeSamFiles/unsorted_input/1.sam
+++ b/testdata/net/sf/picard/sam/MergeSamFiles/unsorted_input/1.sam
@@ -1,6 +1,6 @@
@HD VN:1.0 GO:none SO:unsorted
@SQ SN:chrM LN:16571 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:d2ed829b8a1628d16cbeee88e88e39eb SP:Homo sapiens
- at RG ID:1 SM:sample1
+ at RG ID:1 SM:sample1 PL:ILLUMINA
@PG ID:1 PN:A
@PG ID:1.1 PN:B
@PG ID:2 PN:C PP:1
diff --git a/testdata/net/sf/picard/sam/MergeSamFiles/unsorted_input/2.sam b/testdata/net/sf/picard/sam/MergeSamFiles/unsorted_input/2.sam
index 1e0137a..70991a7 100644
--- a/testdata/net/sf/picard/sam/MergeSamFiles/unsorted_input/2.sam
+++ b/testdata/net/sf/picard/sam/MergeSamFiles/unsorted_input/2.sam
@@ -1,6 +1,6 @@
@HD VN:1.0 GO:none SO:unsorted
@SQ SN:chrM LN:16571 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:d2ed829b8a1628d16cbeee88e88e39eb SP:Homo sapiens
- at RG ID:1 SM:sample1
+ at RG ID:1 SM:sample1 PL:ILLUMINA
@PG ID:1 PN:A
@PG ID:1.1 PN:B
@PG ID:2 PN:C PP:1
diff --git a/testdata/net/sf/picard/sam/ValidateSamFileTest/duplicate_rg.sam b/testdata/net/sf/picard/sam/ValidateSamFileTest/duplicate_rg.sam
new file mode 100644
index 0000000..2558e9a
--- /dev/null
+++ b/testdata/net/sf/picard/sam/ValidateSamFileTest/duplicate_rg.sam
@@ -0,0 +1,11 @@
+ at HD VN:1.4 SO:coordinate
+ at SQ SN:chr1 LN:101 UR:merger.fasta M5:bd01f7e11515bb6beda8f7257902aa67
+ at SQ SN:chr2 LN:101 UR:merger.fasta M5:31c33e2155b3de5e2554b693c475b310
+ at SQ SN:chr3 LN:101 UR:merger.fasta M5:631593c6dd2048ae88dcce2bd505d295
+ at SQ SN:chr4 LN:101 UR:merger.fasta M5:c60cb92f1ee5b78053c92bdbfa19abf1
+ at SQ SN:chr5 LN:101 UR:merger.fasta M5:07ebc213c7611db0eacbb1590c3e9bda
+ at SQ SN:chr6 LN:101 UR:merger.fasta M5:7be2f5e7ee39e60a6c3b5b6a41178c6d
+ at SQ SN:chr7 LN:404 UR:merger.fasta M5:da488fc432cdaf2c20c96da473a7b630
+ at SQ SN:chr8 LN:202 UR:merger.fasta M5:d339678efce576d5546e88b49a487b63
+ at RG ID:H7U2W.1 PU:H7U2WADXX140408.1.AAGTAGAG LB:Solexa-1 PI:0 DT:2014-04-08T00:00:00-0400 SM:K-562 CN:BI
+ at RG ID:H7U2W.1 PU:H7U2WADXX140408.1.AAGTAGAG LB:Solexa-2 PI:0 DT:2014-04-08T00:00:00-0400 SM:K-562 CN:BI
\ No newline at end of file
diff --git a/testdata/net/sf/picard/sam/ValidateSamFileTest/missing_platform_unit.sam b/testdata/net/sf/picard/sam/ValidateSamFileTest/missing_platform_unit.sam
new file mode 100644
index 0000000..5f644d2
--- /dev/null
+++ b/testdata/net/sf/picard/sam/ValidateSamFileTest/missing_platform_unit.sam
@@ -0,0 +1,10 @@
+ at HD VN:1.4 SO:coordinate
+ at SQ SN:chr1 LN:101 UR:merger.fasta M5:bd01f7e11515bb6beda8f7257902aa67
+ at SQ SN:chr2 LN:101 UR:merger.fasta M5:31c33e2155b3de5e2554b693c475b310
+ at SQ SN:chr3 LN:101 UR:merger.fasta M5:631593c6dd2048ae88dcce2bd505d295
+ at SQ SN:chr4 LN:101 UR:merger.fasta M5:c60cb92f1ee5b78053c92bdbfa19abf1
+ at SQ SN:chr5 LN:101 UR:merger.fasta M5:07ebc213c7611db0eacbb1590c3e9bda
+ at SQ SN:chr6 LN:101 UR:merger.fasta M5:7be2f5e7ee39e60a6c3b5b6a41178c6d
+ at SQ SN:chr7 LN:404 UR:merger.fasta M5:da488fc432cdaf2c20c96da473a7b630
+ at SQ SN:chr8 LN:202 UR:merger.fasta M5:d339678efce576d5546e88b49a487b63
+ at RG ID:H7U2W.1 PU:H7U2WADXX140408.1.AAGTAGAG LB:Solexa-219641 PI:0 DT:2014-04-08T00:00:00-0400 SM:K-562 CN:BI
\ No newline at end of file
diff --git a/testdata/net/sf/picard/sam/ValidateSamFileTest/valid.sam b/testdata/net/sf/picard/sam/ValidateSamFileTest/valid.sam
new file mode 100644
index 0000000..3ac3ca8
--- /dev/null
+++ b/testdata/net/sf/picard/sam/ValidateSamFileTest/valid.sam
@@ -0,0 +1,21 @@
+ at HD VN:1.0 SO:coordinate
+ at SQ SN:chr1 LN:101
+ at SQ SN:chr2 LN:101
+ at SQ SN:chr3 LN:101
+ at SQ SN:chr4 LN:101
+ at SQ SN:chr5 LN:101
+ at SQ SN:chr6 LN:101
+ at SQ SN:chr7 LN:404
+ at SQ SN:chr8 LN:202
+ at RG ID:0 SM:Hi,Mom! LB:my-library PL:ILLUMINA
+ at RG ID:1 SM:Hi,Mom! LB:my-library PL:ILLUMINA
+ at RG ID:2 SM:Hi,Mom! LB:my-library PL:ILLUMINA
+ at PG ID:1 PN:Hey! VN:2.0
+both_reads_align_clip_marked 1107 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 PG:Z:1 NM:i:0 MQ:i:255 XT:Z:foo OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
+both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1 PG:Z:1 NM:i:3 MQ:i:255 XT:Z:foo OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
+read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:2 PG:Z:1 NM:i:8 MQ:i:255 XT:Z:foo2 OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
+both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1 PG:Z:1 NM:i:1 MQ:i:255 XT:Z:foo2 OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
+both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1 PG:Z:1 NM:i:1 MQ:i:255 XT:Z:foo2 OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
+both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 PG:Z:1 NM:i:5 MQ:i:255 OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
+read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:2 PG:Z:1 NM:i:6 MQ:i:255 OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
+both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:1 PG:Z:1
diff --git a/testdata/net/sf/picard/sam/aligned.sam b/testdata/net/sf/picard/sam/aligned.sam
index 32cdc53..d1b2165 100644
--- a/testdata/net/sf/picard/sam/aligned.sam
+++ b/testdata/net/sf/picard/sam/aligned.sam
@@ -7,7 +7,7 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
@PG ID:1 PN:Hey! VN:2.0
both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
diff --git a/testdata/net/sf/picard/sam/aligned_queryname_sorted.bam b/testdata/net/sf/picard/sam/aligned_queryname_sorted.bam
new file mode 100644
index 0000000..bd6f04f
Binary files /dev/null and b/testdata/net/sf/picard/sam/aligned_queryname_sorted.bam differ
diff --git a/testdata/net/sf/picard/sam/aligned_queryname_sorted.sam b/testdata/net/sf/picard/sam/aligned_queryname_sorted.sam
index 3979088..eed2b77 100755
--- a/testdata/net/sf/picard/sam/aligned_queryname_sorted.sam
+++ b/testdata/net/sf/picard/sam/aligned_queryname_sorted.sam
@@ -7,7 +7,7 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
@PG ID:1 PN:Hey! VN:2.0
both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/net/sf/picard/sam/bam2fastq/nonpaired/.gitignore
similarity index 100%
copy from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
copy to testdata/net/sf/picard/sam/bam2fastq/nonpaired/.gitignore
diff --git a/testdata/net/sf/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam b/testdata/net/sf/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam
index 6403ecc..82b961d 100755
--- a/testdata/net/sf/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam
+++ b/testdata/net/sf/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam
@@ -1,6 +1,6 @@
@HD VN:1.0 SO:unsorted
- at RG ID:rg1 SM:s1 PU:rg1
- at RG ID:rg2 SM:s2 PU:rg2
+ at RG ID:rg1 SM:s1 PU:rg1 PL:ILLUMINA
+ at RG ID:rg2 SM:s2 PU:rg2 PL:ILLUMINA
foo:record:1 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
foo:record:1 141 * 0 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
foo:record:2 141 * 0 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
diff --git a/testdata/net/sf/picard/sam/bam2fastq/paired/bad/unpaired-mate.sam b/testdata/net/sf/picard/sam/bam2fastq/paired/bad/unpaired-mate.sam
index 013579e..a599762 100644
--- a/testdata/net/sf/picard/sam/bam2fastq/paired/bad/unpaired-mate.sam
+++ b/testdata/net/sf/picard/sam/bam2fastq/paired/bad/unpaired-mate.sam
@@ -1,5 +1,5 @@
@HD VN:1.0 SO:unsorted
- at RG ID:rg1 SM:s1
+ at RG ID:rg1 SM:s1 PL:ILLUMINA
bar:record:1 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
bar:record:1 141 * 0 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
bar:record:2 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
diff --git a/testdata/net/sf/picard/sam/bam2fastq/paired/ok/clipping_test.sam b/testdata/net/sf/picard/sam/bam2fastq/paired/ok/clipping_test.sam
index 48b1173..f9b4a62 100644
--- a/testdata/net/sf/picard/sam/bam2fastq/paired/ok/clipping_test.sam
+++ b/testdata/net/sf/picard/sam/bam2fastq/paired/ok/clipping_test.sam
@@ -1,6 +1,6 @@
@HD VN:1.0 SO:queryname
@SQ SN:chr1 LN:247249719
- at RG ID:rg1 SM:s1
+ at RG ID:rg1 SM:s1 PL:ILLUMINA
bar:record:1 77 * 0 0 * * 0 0 AAAAAAAAAA 1111111111 RG:Z:rg1 XT:i:8
bar:record:1 141 * 0 0 * * 0 0 CCCCCCCCCC 2222222222 RG:Z:rg1 XT:i:9
bar:record:2 97 chr1 150 0 10M chr1 250 100 AAAAAAAAAA 1111111111 RG:Z:rg1 XT:i:7
diff --git a/testdata/net/sf/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam b/testdata/net/sf/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam
index d827649..7f5915b 100644
--- a/testdata/net/sf/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam
+++ b/testdata/net/sf/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam
@@ -1,5 +1,5 @@
@HD VN:1.0 SO:unsorted
- at RG ID:rg1 SM:s1
+ at RG ID:rg1 SM:s1 PL:ILLUMINA
bar:record:1 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
bar:record:2 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
bar:record:2 141 * 0 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
diff --git a/testdata/net/sf/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam b/testdata/net/sf/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam
index c977922..e745104 100755
--- a/testdata/net/sf/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam
+++ b/testdata/net/sf/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam
@@ -1,6 +1,6 @@
@HD VN:1.0 SO:queryname
- at RG ID:rg1 SM:s1 PU:rg1
- at RG ID:rg2 SM:s2 PU:rg2
+ at RG ID:rg1 SM:s1 PU:rg1 PL:ILLUMINA
+ at RG ID:rg2 SM:s2 PU:rg2 PL:ILLUMINA
foo:record:1 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
foo:record:1 141 * 0 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
foo:record:2 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
diff --git a/testdata/net/sf/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam b/testdata/net/sf/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam
index 592bf18..2eb4ba0 100644
--- a/testdata/net/sf/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam
+++ b/testdata/net/sf/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam
@@ -1,5 +1,5 @@
@HD VN:1.0 SO:queryname
- at RG ID:rg1 SM:s1
+ at RG ID:rg1 SM:s1 PL:ILLUMINA
bar:record:1 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
bar:record:1 141 * 0 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
bar:record:2 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
diff --git a/testdata/net/sf/picard/sam/bam2fastq/paired/ok/sorted-pair.sam b/testdata/net/sf/picard/sam/bam2fastq/paired/ok/sorted-pair.sam
index 08e8faa..048045e 100644
--- a/testdata/net/sf/picard/sam/bam2fastq/paired/ok/sorted-pair.sam
+++ b/testdata/net/sf/picard/sam/bam2fastq/paired/ok/sorted-pair.sam
@@ -1,5 +1,5 @@
@HD VN:1.0 SO:queryname
- at RG ID:rg1 SM:s1
+ at RG ID:rg1 SM:s1 PL:ILLUMINA
bar:record:1 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
bar:record:1 141 * 0 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
bar:record:2 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
diff --git a/testdata/net/sf/picard/sam/onehalfaligned.sam b/testdata/net/sf/picard/sam/onehalfaligned.sam
index bef88ec..b987982 100755
--- a/testdata/net/sf/picard/sam/onehalfaligned.sam
+++ b/testdata/net/sf/picard/sam/onehalfaligned.sam
@@ -7,7 +7,7 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
@PG ID:1 PN:Hey! VN:2.0
both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
diff --git a/testdata/net/sf/picard/sam/otherhalfaligned.sam b/testdata/net/sf/picard/sam/otherhalfaligned.sam
index 7123d18..c9a3fef 100755
--- a/testdata/net/sf/picard/sam/otherhalfaligned.sam
+++ b/testdata/net/sf/picard/sam/otherhalfaligned.sam
@@ -7,7 +7,7 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
@PG ID:1 PN:Hey! VN:2.0
both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
diff --git a/testdata/net/sf/picard/sam/readWithBadRname.sam b/testdata/net/sf/picard/sam/readWithBadRname.sam
index 043d359..71bafb9 100644
--- a/testdata/net/sf/picard/sam/readWithBadRname.sam
+++ b/testdata/net/sf/picard/sam/readWithBadRname.sam
@@ -1,6 +1,6 @@
@HD VN:1.0 SO:coordinate
@SQ SN:chr21 afterspace AS:HG18 LN:62435964
- at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891
- at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891
+ at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 PL:ILLUMINA
+ at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 PL:ILLUMINA
read_28833_29006_6945 99 = 28833 20 10M1D25M = 28993 195 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< MF:i:130 Nm:i:1 H0:i:0 H1:i:0 RG:Z:L1
read_28701_28881_323b 147 chr21 afterspace 28834 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
diff --git a/testdata/net/sf/picard/sam/revert_sam_basic.sam b/testdata/net/sf/picard/sam/revert_sam_basic.sam
index f970643..3ac3ca8 100755
--- a/testdata/net/sf/picard/sam/revert_sam_basic.sam
+++ b/testdata/net/sf/picard/sam/revert_sam_basic.sam
@@ -7,9 +7,9 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
- at RG ID:0 SM:Hi,Mom! LB:my-library
- at RG ID:1 SM:Hi,Mom! LB:my-library
- at RG ID:2 SM:Hi,Mom! LB:my-library
+ at RG ID:0 SM:Hi,Mom! LB:my-library PL:ILLUMINA
+ at RG ID:1 SM:Hi,Mom! LB:my-library PL:ILLUMINA
+ at RG ID:2 SM:Hi,Mom! LB:my-library PL:ILLUMINA
@PG ID:1 PN:Hey! VN:2.0
both_reads_align_clip_marked 1107 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 PG:Z:1 NM:i:0 MQ:i:255 XT:Z:foo OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1 PG:Z:1 NM:i:3 MQ:i:255 XT:Z:foo OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
diff --git a/testdata/net/sf/picard/sam/revert_sam_negative.sam b/testdata/net/sf/picard/sam/revert_sam_negative.sam
index 2b3ec13..f1aa7ba 100755
--- a/testdata/net/sf/picard/sam/revert_sam_negative.sam
+++ b/testdata/net/sf/picard/sam/revert_sam_negative.sam
@@ -7,9 +7,9 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
- at RG ID:0 SM:Hi,Mom! LB:my-library
- at RG ID:1 SM:Hi,Dad! LB:my-library
- at RG ID:2 SM:Hi,Mom! LB:my-other-library
+ at RG ID:0 SM:Hi,Mom! LB:my-library PL:ILLUMINA
+ at RG ID:1 SM:Hi,Dad! LB:my-library PL:ILLUMINA
+ at RG ID:2 SM:Hi,Mom! LB:my-other-library PL:ILLUMINA
@PG ID:1 PN:Hey! VN:2.0
both_reads_align_clip_marked 1107 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 PG:Z:1 NM:i:0 MQ:i:255 XT:Z:foo OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1 PG:Z:1 NM:i:3 MQ:i:255 XT:Z:foo OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
diff --git a/testdata/net/sf/picard/sam/samHeaderProvider.sam b/testdata/net/sf/picard/sam/samHeaderProvider.sam
new file mode 100755
index 0000000..45b55e4
--- /dev/null
+++ b/testdata/net/sf/picard/sam/samHeaderProvider.sam
@@ -0,0 +1,15 @@
+ at HD VN:1.4 SO:queryname
+ at SQ SN:chr1 LN:101
+ at SQ SN:chr2 LN:101
+ at SQ SN:chr3 LN:101
+ at SQ SN:chr4 LN:101
+ at SQ SN:chr5 LN:101
+ at SQ SN:chr6 LN:101
+ at SQ SN:chr7 LN:404
+ at SQ SN:chr8 LN:202
+ at RG ID:0 SM:derpderp
+ at PG ID:1 PN:blahblah VN:2.0
+both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
+both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
+read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
+read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
diff --git a/testdata/net/sf/picard/sam/sequenceWithSpace.sam b/testdata/net/sf/picard/sam/sequenceWithSpace.sam
index 8e5d2e8..766bc67 100755
--- a/testdata/net/sf/picard/sam/sequenceWithSpace.sam
+++ b/testdata/net/sf/picard/sam/sequenceWithSpace.sam
@@ -1,6 +1,6 @@
@HD VN:1.0 SO:coordinate
@SQ SN:chr21 afterspace AS:HG18 LN:62435964
- at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891
- at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891
+ at RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 PL:ILLUMINA
+ at RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 PL:ILLUMINA
read_28833_29006_6945 99 chr21 afterspace 28833 20 10M1D25M = 28993 195 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< MF:i:130 Nm:i:1 H0:i:0 H1:i:0 RG:Z:L1
read_28701_28881_323b 147 chr21 afterspace 28834 30 35M = 28701 -168 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 Nm:i:0 H0:i:1 H1:i:0 RG:Z:L2
diff --git a/testdata/net/sf/picard/sam/summary_alignment_bisulfite_test.sam b/testdata/net/sf/picard/sam/summary_alignment_bisulfite_test.sam
index eb6d075..a1e05aa 100644
--- a/testdata/net/sf/picard/sam/summary_alignment_bisulfite_test.sam
+++ b/testdata/net/sf/picard/sam/summary_alignment_bisulfite_test.sam
@@ -7,6 +7,6 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:202
@SQ SN:chr8 LN:202
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
SL-XAV:1:1:0:1721#0/1 83 chr7 1 255 101M = 102 40 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
SL-XAV:1:1:0:1721#0/2 163 chr7 102 255 101M = 1 -40 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
diff --git a/testdata/net/sf/picard/sam/summary_alignment_stats_test.sam b/testdata/net/sf/picard/sam/summary_alignment_stats_test.sam
index a824605..3fcb6da 100644
--- a/testdata/net/sf/picard/sam/summary_alignment_stats_test.sam
+++ b/testdata/net/sf/picard/sam/summary_alignment_stats_test.sam
@@ -7,7 +7,7 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:202
@SQ SN:chr8 LN:202
- at RG ID:0 SM:Hi,Momma! LB:whatever PU:me
+ at RG ID:0 SM:Hi,Momma! LB:whatever PU:me PL:ILLUMINA
SL-XAV:1:1:0:764#0/1 89 chr1 1 255 101M * 0 0 TTCATGCTGANGCNCTCTTACGATCGTACAGATGCAAATATTAACANNCNTTNAAGNNCANNNNNNNNNCAATACAATANTAGAGTACGTNAACACTCCAN &/,&-.1/6/&&)&).)/,&0768)&/.,/874,&.4137572)&/&&,&1-&.0/&&*,&&&&&&&&&&18775799,&16:8775-56256/69::;0& RG:Z:0 XN:i:1
SL-XAV:1:1:0:1668#0/2 153 chr2 1 255 101M * 0 0 CATCTCTACANGCGCGTCCTACCAGACGCGCTTCCGATCTGAGAGCATACTTTTCATTGGATTCCAGCACAACTCCATTTTTGATCCACTNGACACCTTTN (/,'-/'0////(1'&&1&&&&'2''-6/,/3-33653.6:1'.86/-++32.-4864653/5/583/346423203+28888644446688456/4880& RG:Z:0 XN:i:1
SL-XAV:1:1:0:1914#0/2 153 chr3 1 255 101M * 0 0 CGTATGCGCTNTTTATGTCGCCCACAGTGCCTAGTATAGCCCCTGCTAATAAAAAGAGATGAATACGTTTACTTAAAAAACTGAAACTAGNAATGTGCAAN (0,7&&*/*0*,)10/).-*&.&*/6669.&-337599;3,&,6/.,5::999987893+387020775777547999::668997448:::9;999::0& RG:Z:0
diff --git a/testdata/net/sf/picard/sam/summary_alignment_stats_test_multiple.sam b/testdata/net/sf/picard/sam/summary_alignment_stats_test_multiple.sam
index 55c14a2..eae5452 100755
--- a/testdata/net/sf/picard/sam/summary_alignment_stats_test_multiple.sam
+++ b/testdata/net/sf/picard/sam/summary_alignment_stats_test_multiple.sam
@@ -7,10 +7,10 @@
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:202
@SQ SN:chr8 LN:202
- at RG ID:0 SM:Ma LB:whatever PU:me
- at RG ID:1 SM:Pa LB:lib1 PU:myself
- at RG ID:2 SM:Pa LB:lib2 PU:i
- at RG ID:3 SM:Pa LB:lib2 PU:i2
+ at RG ID:0 SM:Ma LB:whatever PU:me PL:ILLUMINA
+ at RG ID:1 SM:Pa LB:lib1 PU:myself PL:ILLUMINA
+ at RG ID:2 SM:Pa LB:lib2 PU:i PL:ILLUMINA
+ at RG ID:3 SM:Pa LB:lib2 PU:i2 PL:ILLUMINA
SL-XAV:1:1:0:764#0/1 89 chr1 1 255 101M * 0 0 TTCATGCTGANGCNCTCTTACGATCGTACAGATGCAAATATTAACANNCNTTNAAGNNCANNNNNNNNNCAATACAATANTAGAGTACGTNAACACTCCAN &/,&-.1/6/&&)&).)/,&0768)&/.,/874,&.4137572)&/&&,&1-&.0/&&*,&&&&&&&&&&18775799,&16:8775-56256/69::;0& RG:Z:0 XN:i:1
SL-XAV:1:1:0:1668#0/2 153 chr2 1 255 101M * 0 0 CATCTCTACANGCGCGTCCTACCAGACGCGCTTCCGATCTGAGAGCATACTTTTCATTGGATTCCAGCACAACTCCATTTTTGATCCACTNGACACCTTTN (/,'-/'0////(1'&&1&&&&'2''-6/,/3-33653.6:1'.86/-++32.-4864653/5/583/346423203+28888644446688456/4880& RG:Z:1 XN:i:1
SL-XAV:1:1:0:1914#0/2 153 chr3 1 255 101M * 0 0 CGTATGCGCTNTTTATGTCGCCCACAGTGCCTAGTATAGCCCCTGCTAATAAAAAGAGATGAATACGTTTACTTAAAAAACTGAAACTAGNAATGTGCAAN (0,7&&*/*0*,)10/).-*&.&*/6669.&-337599;3,&,6/.,5::999987893+387020775777547999::668997448:::9;999::0& RG:Z:3
diff --git a/testdata/net/sf/picard/sam/unmapped.sam b/testdata/net/sf/picard/sam/unmapped.sam
index b59d6bf..b47ad2b 100644
--- a/testdata/net/sf/picard/sam/unmapped.sam
+++ b/testdata/net/sf/picard/sam/unmapped.sam
@@ -1,5 +1,5 @@
@HD VN:1.0 SO:queryname
- at RG ID:0 SM:Hi,Mom!
+ at RG ID:0 SM:Hi,Mom! PL:ILLUMINA
both_reads_align_clip_adapter 77 * 0 0 * * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
both_reads_align_clip_adapter 141 * 0 0 * * 0 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
both_reads_align_clip_marked 77 * 0 0 * * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 XT:i:97
diff --git a/testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam b/testdata/tribble/tmp/.gitignore
similarity index 100%
rename from testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam
rename to testdata/tribble/tmp/.gitignore
--
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