[med-svn] [picard-tools] 04/05: Merge tag 'upstream/1.100'
Charles Plessy
plessy at alioth.debian.org
Sun Oct 20 01:39:07 UTC 2013
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch master
in repository picard-tools.
commit 2a7549d51bef01ed11a916fb789fe2878d4e20e9
Merge: 4d81451 d02872e
Author: Charles Plessy <plessy at debian.org>
Date: Sat Oct 19 12:28:34 2013 +0900
Merge tag 'upstream/1.100'
Upstream version 1.100
# gpg: Signature faite le sam. 19 oct. 2013 12:28:33 JST avec la clef RSA d'identifiant 2295D502
# gpg: Bonne signature de « Charles Plessy <plessy at debian.org> »
Picard-public.iml | 8 +-
Picard-public.ipr | 17 +
build.xml | 21 +-
.../analysis/AlignmentSummaryMetricsCollector.java | 4 +-
.../analysis/CollectAlignmentSummaryMetrics.java | 2 +-
.../picard/analysis/CollectInsertSizeMetrics.java | 2 +-
.../sf/picard/analysis/CollectMultipleMetrics.java | 2 +-
.../sf/picard/analysis/CollectRnaSeqMetrics.java | 1 +
.../net/sf/picard/analysis/MeanQualityByCycle.java | 2 +-
.../picard/analysis/QualityScoreDistribution.java | 2 +-
.../analysis/directed/CollectTargetedMetrics.java | 3 +-
.../directed/InsertSizeMetricsCollector.java | 2 +-
.../analysis/directed/RnaSeqMetricsCollector.java | 2 +-
.../analysis/directed/TargetMetricsCollector.java | 2 +-
.../net/sf/picard/cmdline/CommandLineParser.java | 2 +-
src/java/net/sf/picard/filter/ReadNameFilter.java | 35 +-
.../filter/SecondaryOrSupplementaryFilter.java | 32 ++
.../picard/illumina/ExtractIlluminaBarcodes.java | 16 +-
.../illumina/IlluminaBasecallsConverter.java | 14 +-
.../picard/illumina/IlluminaBasecallsToFastq.java | 13 +-
.../sf/picard/illumina/IlluminaBasecallsToSam.java | 14 +-
.../sf/picard/illumina/MarkIlluminaAdapters.java | 235 ++++++++++
.../sf/picard/illumina/parser/BarcodeParser.java | 2 +-
.../net/sf/picard/illumina/parser/BclParser.java | 16 +-
.../net/sf/picard/illumina/parser/CifParser.java | 2 +-
.../net/sf/picard/illumina/parser/CnfParser.java | 2 +-
.../sf/picard/illumina/parser/FilterParser.java | 2 +-
.../parser/IlluminaDataProviderFactory.java | 12 +-
.../picard/illumina/parser/IlluminaFileUtil.java | 4 +-
.../illumina/parser/IlluminaIntensityParser.java | 2 +-
.../illumina/parser/PerTilePerCycleParser.java | 6 +-
.../net/sf/picard/illumina/parser/PosParser.java | 2 +-
.../net/sf/picard/illumina/parser/QseqParser.java | 1 +
.../sf/picard/illumina/parser/TileMetricsUtil.java | 2 +-
.../readers/BclQualityEvaluationStrategy.java | 95 ++++
.../picard/illumina/parser/readers/BclReader.java | 11 +-
src/java/net/sf/picard/io/IoUtil.java | 114 ++++-
.../picard/reference/IndexedFastaSequenceFile.java | 12 +-
.../net/sf/picard/sam/AbstractAlignmentMerger.java | 51 +-
.../sam/AbstractDuplicateFindingAlgorithm.java | 5 +-
.../net/sf/picard/sam/AddOrReplaceReadGroups.java | 5 +-
src/java/net/sf/picard/sam/CompareSAMs.java | 18 +-
src/java/net/sf/picard/sam/DownsampleSam.java | 2 +-
src/java/net/sf/picard/sam/FastqToSam.java | 4 +-
src/java/net/sf/picard/sam/FixMateInformation.java | 4 +-
src/java/net/sf/picard/sam/HitsForInsert.java | 25 +-
src/java/net/sf/picard/sam/MarkDuplicates.java | 4 +-
src/java/net/sf/picard/sam/MergeBamAlignment.java | 6 +-
src/java/net/sf/picard/sam/MergeSamFiles.java | 2 +-
...stDistantPrimaryAlignmentSelectionStrategy.java | 2 +-
.../sf/picard/sam/MultiHitAlignedReadIterator.java | 25 +-
src/java/net/sf/picard/sam/RevertSam.java | 3 +-
src/java/net/sf/picard/sam/SamAlignmentMerger.java | 3 +-
src/java/net/sf/picard/sam/SamFileValidator.java | 2 +-
src/java/net/sf/picard/sam/SamToFastq.java | 2 +-
.../net/sf/picard/util/AbstractInputParser.java | 1 +
src/java/net/sf/picard/util/CsvInputParser.java | 36 ++
.../util/DelimitedTextFileWithHeaderIterator.java | 111 +++++
src/java/net/sf/picard/util/IntervalTreeMap.java | 3 +-
src/java/net/sf/picard/util/IterableAdapter.java | 29 ++
.../net/sf/picard/util/IterableOnceIterator.java | 42 ++
src/java/net/sf/picard/util/MathUtil.java | 11 +-
src/java/net/sf/picard/util/ProcessExecutor.java | 60 +++
src/java/net/sf/picard/util/RExecutor.java | 1 +
src/java/net/sf/picard/util/SamLocusIterator.java | 2 +-
src/java/net/sf/picard/util/TabbedInputParser.java | 3 +-
.../util/TabbedTextFileWithHeaderParser.java | 1 -
src/java/net/sf/picard/vcf/BcfIterator.java | 84 ----
src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java | 90 ++++
src/java/net/sf/picard/vcf/MergeVcfs.java | 55 ++-
src/java/net/sf/picard/vcf/SplitVcfs.java | 59 ++-
.../net/sf/picard/vcf/VariantContextIterator.java | 34 --
.../picard/vcf/VariantContextIteratorFactory.java | 49 --
.../net/sf/picard/vcf/VariantContextUtils.java | 64 ---
src/java/net/sf/picard/vcf/VcfFormatConverter.java | 54 ++-
src/java/net/sf/picard/vcf/VcfIterator.java | 92 ----
src/java/net/sf/samtools/SAMFileReader.java | 17 +-
src/java/net/sf/samtools/SAMRecord.java | 56 ++-
.../sf/samtools/SAMRecordQueryNameComparator.java | 3 +
src/java/net/sf/samtools/SAMSequenceRecord.java | 2 +-
src/java/net/sf/samtools/SAMValidationError.java | 3 +
.../SecondaryOrSupplementarySkippingIterator.java | 41 ++
.../seekablestream/SeekableStreamFactory.java | 9 +
.../util/AbstractIterator.java | 16 +-
src/java/net/sf/samtools/util/BinaryCodec.java | 3 +-
.../net/sf/samtools/util/BufferedLineReader.java | 2 +
.../{picard => samtools}/util/CollectionUtil.java | 14 +-
src/java/net/sf/samtools/util/Tuple.java | 16 +
.../org/broad/tribble/AbstractFeatureCodec.java | 16 +-
.../org/broad/tribble/AbstractFeatureReader.java | 29 +-
src/java/org/broad/tribble/AsciiFeatureCodec.java | 108 ++---
src/java/org/broad/tribble/BinaryFeatureCodec.java | 42 ++
.../broad/tribble/CloseableTribbleIterator.java | 8 +-
src/java/org/broad/tribble/FeatureCodec.java | 93 ++--
src/java/org/broad/tribble/TabixFeatureReader.java | 38 +-
.../broad/tribble/TribbleIndexedFeatureReader.java | 190 +++++---
src/java/org/broad/tribble/bed/BEDCodec.java | 15 +-
.../org/broad/tribble/dbsnp/OldDbSNPCodec.java | 8 +-
.../broad/tribble/example/ExampleBinaryCodec.java | 27 +-
.../org/broad/tribble/gelitext/GeliTextCodec.java | 68 +--
src/java/org/broad/tribble/index/IndexFactory.java | 93 ++--
.../org/broad/tribble/readers/AsciiLineReader.java | 25 +-
.../tribble/readers/AsciiLineReaderIterator.java | 99 ++++
.../tribble/readers/AsynchronousLineReader.java | 97 ++++
.../org/broad/tribble/readers/LineIterator.java | 12 +
.../broad/tribble/readers/LineIteratorImpl.java | 33 ++
.../org/broad/tribble/readers/LineReaderUtil.java | 61 +++
.../org/broad/tribble/readers/LocationAware.java | 24 +
.../tribble/readers/LongLineBufferedReader.java | 490 ++++++++++++++++++++
src/java/org/broad/tribble/readers/Positional.java | 20 +-
.../tribble/readers/PositionalBufferedStream.java | 13 +-
.../tribble/readers/TabixIteratorLineReader.java | 8 +-
src/java/org/broad/tribble/util/IOUtil.java | 66 ---
.../org/broadinstitute/variant/bcf2/BCF2Codec.java | 14 +-
.../org/broadinstitute/variant/bcf2/BCF2Utils.java | 2 +-
.../variant/variantcontext/VariantContext.java | 16 +-
.../variantcontext}/VariantContextComparator.java | 3 +-
.../writer/IndexingVariantContextWriter.java | 8 +-
.../variant/variantcontext/writer/VCFWriter.java | 16 +-
.../writer/VariantContextWriterFactory.java | 6 +-
.../variant/vcf/AbstractVCFCodec.java | 9 +-
.../org/broadinstitute/variant/vcf/VCF3Codec.java | 62 ++-
.../org/broadinstitute/variant/vcf/VCFCodec.java | 70 ++-
.../broadinstitute/variant/vcf/VCFConstants.java | 1 +
.../variant/vcf/VCFContigHeaderLine.java | 38 +-
.../broadinstitute/variant/vcf/VCFFileReader.java | 69 +++
.../variant/vcf/VCFFilterHeaderLine.java | 5 +
.../variant/vcf/VCFFormatHeaderLine.java | 5 +
.../org/broadinstitute/variant/vcf/VCFHeader.java | 63 ++-
.../broadinstitute/variant/vcf/VCFHeaderLine.java | 10 +-
.../variant/vcf/VCFInfoHeaderLine.java | 5 +
.../variant/vcf/VCFSimpleHeaderLine.java | 12 +-
src/scripts/explain_sam_flags.py | 3 +-
.../net/sf/picard/analysis/insertSizeHistogram.R | 108 ++---
.../net/sf/picard/analysis/rnaSeqCoverage.R | 18 +-
src/scripts/release_picard.sh | 6 +
.../picard/analysis/MultiLevelCollectorTest.java | 2 +-
.../sf/picard/cmdline/CommandLineParserTest.java | 2 +-
.../illumina/CheckIlluminaDirectoryTest.java | 2 +-
.../illumina/ExtractIlluminaBarcodesTest.java | 4 +-
.../net/sf/picard/illumina/ReadStructureTest.java | 5 +-
.../sf/picard/illumina/parser/BclParserTest.java | 5 +-
.../net/sf/picard/illumina/parser/BinTdUtil.java | 2 +-
.../illumina/parser/CycleIlluminaFileMapTest.java | 2 +-
.../parser/IlluminaDataProviderFactoryTest.java | 4 +-
.../illumina/parser/IlluminaDataProviderTest.java | 13 +-
.../illumina/parser/IlluminaFileUtilTest.java | 2 +-
.../picard/illumina/parser/PerTileParserTest.java | 2 +-
.../illumina/parser/PerTilePerCycleParserTest.java | 3 +-
.../sf/picard/illumina/parser/PosParserTest.java | 2 +-
.../sf/picard/illumina/parser/QseqParserTest.java | 2 +-
.../illumina/parser/readers/BclReaderTest.java | 159 +++++--
src/tests/java/net/sf/picard/io/IoUtilTest.java | 15 +
.../net/sf/picard/sam/MergeBamAlignmentTest.java | 83 +++-
.../DelimitedTextFileWithHeaderIteratorTest.java | 95 ++++
.../net/sf/picard/util/IntervalTreeMapTest.java} | 42 +-
.../net/sf/picard/util/SamLocusIteratorTest.java | 2 -
.../java/net/sf/picard/vcf/MergeVcfsTest.java | 88 ++--
.../java/net/sf/picard/vcf/SplitVcfsTest.java | 35 +-
.../picard/vcf/VariantContextComparatorTest.java | 1 +
.../sf/picard/vcf/VariantContextIteratorTest.java | 24 -
.../net/sf/picard/vcf/VcfFormatConverterTest.java | 62 +--
.../seekablestream/SeekableStreamFactoryTest.java | 15 +
.../broad/tribble/AbstractFeatureReaderTest.java | 39 +-
.../java/org/broad/tribble/BinaryFeaturesTest.java | 9 +-
.../java/org/broad/tribble/FeatureReaderTest.java | 51 +-
.../org/broad/tribble/index/IndexFactoryTest.java | 3 +-
.../tribble/index/interval/IntervalTreeTest.java | 2 +-
.../readers/AsynchronousLineReaderTest.java | 31 ++
.../broad/tribble/readers/LineReaderUtilTest.java | 27 ++
.../readers/LongLineBufferedReaderTest.java | 33 ++
.../java/org/broad/tribble/readers/ReaderTest.java | 7 +-
.../variant/bcf2/BCF2UtilsUnitTest.java | 30 ++
.../variantcontext/VariantContextTestProvider.java | 108 +++--
.../variantcontext/VariantContextUnitTest.java | 36 +-
.../variantcontext/writer/VCFWriterUnitTest.java | 51 +-
.../writer/VariantContextWritersUnitTest.java | 27 +-
.../variant/vcf/IndexFactoryUnitTest.java | 6 +-
.../variant/vcf/VCFHeaderUnitTest.java | 6 +-
testdata/net/sf/picard/io/slurptest.txt | 3 +
.../sam/MergeBamAlignment/aligned.supplement.sam | 21 +
.../picard/vcf/CEUTrio-indels-bad-samples.vcf.idx | Bin 0 -> 15212 bytes
.../vcf/CEUTrio-indels-dissimilar-contigs.vcf.idx | Bin 0 -> 13460 bytes
testdata/net/sf/picard/vcf/CEUTrio-indels.vcf.idx | Bin 0 -> 15200 bytes
.../picard/vcf/CEUTrio-merged-indels-snps.vcf.idx | Bin 0 -> 26611 bytes
.../sf/picard/vcf/CEUTrio-random-scatter-0.vcf.idx | Bin 0 -> 17156 bytes
.../sf/picard/vcf/CEUTrio-random-scatter-1.vcf.idx | Bin 0 -> 18707 bytes
.../sf/picard/vcf/CEUTrio-random-scatter-2.vcf.idx | Bin 0 -> 18693 bytes
.../sf/picard/vcf/CEUTrio-random-scatter-3.vcf.idx | Bin 0 -> 14381 bytes
.../sf/picard/vcf/CEUTrio-random-scatter-4.vcf.idx | Bin 0 -> 14620 bytes
.../sf/picard/vcf/CEUTrio-random-scatter-5.vcf.idx | Bin 0 -> 15823 bytes
testdata/net/sf/picard/vcf/CEUTrio-snps.vcf.idx | Bin 0 -> 26434 bytes
testdata/net/sf/picard/vcf/vcfFormatTest.bcf | Bin 28266 -> 86444 bytes
testdata/net/sf/picard/vcf/vcfFormatTest.bcf.idx | Bin 0 -> 26598 bytes
testdata/net/sf/picard/vcf/vcfFormatTest.vcf | 264 +++++++++++
testdata/net/sf/picard/vcf/vcfFormatTest.vcf.idx | Bin 0 -> 26586 bytes
testdata/tribble/large.txt | 165 +++++++
197 files changed, 4266 insertions(+), 1500 deletions(-)
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