[med-svn] [picard-tools] 02/06: Merge tag 'upstream/1.110'
Charles Plessy
plessy at moszumanska.debian.org
Sun Apr 6 02:31:53 UTC 2014
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plessy pushed a commit to branch master
in repository picard-tools.
commit e87bdf5bcea5e18f01580429fc18a3d1856b338c
Merge: 0ac9d98 ad4ec03
Author: Charles Plessy <plessy at debian.org>
Date: Sun Apr 6 10:31:55 2014 +0900
Merge tag 'upstream/1.110'
Upstream version 1.110
# gpg: Signature faite le dim. 06 avril 2014 10:31:55 JST avec la clef RSA d'identifiant 2295D502
# gpg: Bonne signature de « Charles Plessy <plessy at debian.org> »
Picard-public.ipr | 20 +-
build.xml | 2 +-
.../net/sf/picard/analysis/InsertSizeMetrics.java | 2 +-
.../directed/InsertSizeMetricsCollector.java | 2 +-
src/java/net/sf/picard/fastq/BasicFastqWriter.java | 3 +-
src/java/net/sf/picard/fastq/FastqReader.java | 11 +-
.../net/sf/picard/filter/FilteringIterator.java | 2 +-
.../sf/picard/illumina/CheckIlluminaDirectory.java | 161 ++--
.../picard/illumina/ExtractIlluminaBarcodes.java | 11 +-
.../illumina/IlluminaBasecallsConverter.java | 14 +-
.../picard/illumina/IlluminaBasecallsToFastq.java | 5 +-
.../sf/picard/illumina/IlluminaBasecallsToSam.java | 8 +-
.../net/sf/picard/illumina/parser/BclParser.java | 14 +-
.../parser/IlluminaDataProviderFactory.java | 22 +-
.../picard/illumina/parser/IlluminaFileUtil.java | 683 ++++++++++----
.../illumina/parser/IlluminaMetricsCode.java | 42 +
.../picard/illumina/parser/MultiTileBclParser.java | 2 +-
.../illumina/parser/PerTilePerCycleParser.java | 4 +-
src/java/net/sf/picard/illumina/parser/Tile.java | 114 +++
.../net/sf/picard/illumina/parser/TileIndex.java | 3 +-
.../sf/picard/illumina/parser/TileMetricsUtil.java | 162 ++--
.../picard/illumina/parser/TilePhasingValue.java | 30 +
.../picard/illumina/parser/TileTemplateRead.java} | 38 +-
.../illumina/parser/fakers/BarcodeFileFaker.java | 25 +
.../illumina/parser/fakers/BciFileFaker.java | 52 ++
.../illumina/parser/fakers/BclFileFaker.java | 29 +
.../illumina/parser/fakers/CifFileFaker.java | 31 +
.../illumina/parser/fakers/ClocsFileFaker.java | 25 +
.../illumina/parser/fakers/CnfFileFaker.java | 31 +
.../picard/illumina/parser/fakers/FileFaker.java | 73 ++
.../illumina/parser/fakers/FilterFileFaker.java | 26 +
.../illumina/parser/fakers/LocsFileFaker.java | 28 +
.../parser/fakers/MultiTileBclFileFaker.java | 32 +
.../parser/fakers/MultiTileLocsFileFaker.java | 30 +
.../illumina/parser/fakers/PosFileFaker.java | 25 +
.../illumina/parser/fakers/QSeqFileFaker.java | 25 +
.../picard/illumina/parser/readers/BclReader.java | 67 +-
.../parser/readers/TileMetricsOutReader.java | 82 +-
src/java/net/sf/picard/io/IoUtil.java | 25 +-
.../net/sf/picard/sam/AbstractAlignmentMerger.java | 48 +-
src/java/net/sf/picard/sam/FastqToSam.java | 5 +-
src/java/net/sf/picard/sam/MergeBamAlignment.java | 9 +-
...RevertOriginalBaseQualitiesAndAddMateCigar.java | 2 +-
src/java/net/sf/picard/sam/SamAlignmentMerger.java | 16 +-
src/java/net/sf/picard/sam/SamFileValidator.java | 4 +-
src/java/net/sf/picard/sam/ValidateSamFile.java | 1 +
src/java/net/sf/picard/util/IntervalList.java | 4 +-
src/java/net/sf/picard/util/MathUtil.java | 13 +
src/java/net/sf/picard/util/OverlapDetector.java | 24 +-
.../sf/picard/util/QualityEncodingDetector.java | 110 ++-
src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java | 47 +-
src/java/net/sf/samtools/AbstractBAMFileIndex.java | 53 +-
src/java/net/sf/samtools/BAMFileReader.java | 11 +-
src/java/net/sf/samtools/BAMIndexContent.java | 156 +---
src/java/net/sf/samtools/BAMIndexer.java | 186 ++--
src/java/net/sf/samtools/Bin.java | 16 +-
src/java/net/sf/samtools/BinaryBAMIndexWriter.java | 20 +-
src/java/net/sf/samtools/BinningIndexBuilder.java | 187 ++++
...MIndexContent.java => BinningIndexContent.java} | 465 +++++-----
src/java/net/sf/samtools/CachingBAMFileIndex.java | 28 +-
src/java/net/sf/samtools/Chunk.java | 6 +-
src/java/net/sf/samtools/Defaults.java | 11 +
src/java/net/sf/samtools/GenomicIndexUtil.java | 100 +++
src/java/net/sf/samtools/LinearIndex.java | 30 +-
src/java/net/sf/samtools/SAMFileReader.java | 10 +-
src/java/net/sf/samtools/SAMFileWriterFactory.java | 6 +-
src/java/net/sf/samtools/SAMRecord.java | 13 +-
src/java/net/sf/samtools/SAMRecordSetBuilder.java | 185 +++-
src/java/net/sf/samtools/SAMUtils.java | 35 +-
.../sf/{picard/sam => samtools}/SamPairUtil.java | 43 +-
.../net/sf/samtools/TextualBAMIndexWriter.java | 12 +-
.../seekablestream/SeekableStreamFactory.java | 3 +-
src/java/net/sf/samtools/util/AsciiWriter.java | 4 +-
.../samtools/util/BlockCompressedInputStream.java | 9 +-
.../samtools/util/BlockCompressedOutputStream.java | 25 +-
.../net/sf/samtools/util/BufferedLineReader.java | 4 +-
src/java/net/sf/samtools/util/IOUtil.java | 81 +-
.../sf/samtools/util}/LocationAware.java | 6 +-
.../net/sf/samtools/util/SortingCollection.java | 6 +-
.../sf/samtools/util/SortingLongCollection.java | 4 +-
.../net/sf/samtools/util/TempStreamFactory.java | 16 +-
.../org/broad/tribble/AbstractFeatureReader.java | 3 +-
src/java/org/broad/tribble/AsciiFeatureCodec.java | 1 +
src/java/org/broad/tribble/BinaryFeatureCodec.java | 4 +-
src/java/org/broad/tribble/FeatureCodec.java | 2 +-
.../broad/tribble/TribbleIndexedFeatureReader.java | 75 +-
.../org/broad/tribble/index/AbstractIndex.java | 115 ++-
src/java/org/broad/tribble/index/Block.java | 14 +-
.../broad/tribble/index/DynamicIndexCreator.java | 83 +-
src/java/org/broad/tribble/index/Index.java | 36 +-
src/java/org/broad/tribble/index/IndexCreator.java | 25 -
src/java/org/broad/tribble/index/IndexFactory.java | 202 +++--
.../Positional.java => index/MutableIndex.java} | 38 +-
.../TribbleIndexCreator.java} | 39 +-
.../index/interval/IntervalIndexCreator.java | 46 +-
.../tribble/index/interval/IntervalTreeIndex.java | 66 +-
.../broad/tribble/index/linear/LinearIndex.java | 127 +--
.../tribble/index/linear/LinearIndexCreator.java | 25 +-
.../org/broad/tribble/index/tabix/TabixFormat.java | 109 +++
.../org/broad/tribble/index/tabix/TabixIndex.java | 364 ++++++++
.../tribble/index/tabix/TabixIndexCreator.java | 199 ++++
.../org/broad/tribble/readers/AsciiLineReader.java | 23 +-
.../tribble/readers/AsciiLineReaderIterator.java | 5 +-
.../tribble/readers/AsynchronousLineReader.java | 9 +-
src/java/org/broad/tribble/readers/Positional.java | 2 +
.../org/broad/tribble/readers/TabixReader.java | 3 +-
.../writer/IndexingVariantContextWriter.java | 60 +-
.../writer/VariantContextWriterFactory.java | 55 +-
.../picard/analysis/CollectRnaSeqMetricsTest.java | 1 +
.../illumina/CheckIlluminaDirectoryTest.java | 304 ++++---
.../illumina/parser/TileMetricsUtilTest.java | 999 ---------------------
.../illumina/parser/readers/BclReaderTest.java | 8 +-
src/tests/java/net/sf/picard/sam/CleanSamTest.java | 24 +-
.../java/net/sf/picard/sam/MarkDuplicatesTest.java | 171 ++++
.../net/sf/picard/sam/MergeBamAlignmentTest.java | 24 +-
...MergingSamRecordIteratorGroupCollisionTest.java | 10 +-
.../net/sf/picard/sam/ValidateSamFileTest.java | 10 +-
.../net/sf/picard/sam/testers/CleanSamTester.java | 52 ++
.../picard/sam/testers/MarkDuplicatesTester.java | 55 ++
.../net/sf/picard/sam/testers/SamFileTester.java | 213 +++++
.../picard/util/QualityEncodingDetectorTest.java | 40 +-
.../java/net/sf/samtools/BAMFileIndexTest.java | 35 +
.../java/net/sf/samtools/BAMFileWriterTest.java | 2 -
.../{picard/sam => samtools}/SamPairUtilTest.java | 3 +-
.../java/org/broad/tribble/FeatureReaderTest.java | 2 +-
.../tribble/index/linear/LinearIndexTest.java | 44 +-
.../broad/tribble/index/tabix/TabixIndexTest.java | 65 ++
.../writer/TabixOnTheFlyIndexCreationTest.java | 66 ++
.../variantcontext/writer/VCFWriterUnitTest.java | 118 +--
.../HiSeq2000TileMetricsOut.bin | Bin 115202 -> 0 bytes
.../HiSeq2500TileMetricsOut.bin | Bin 19202 -> 0 bytes
.../TileMetricsUtilTest/MiSeqTileMetricsOut.bin | Bin 2942 -> 0 bytes
testdata/tribble/tabix/bigger.vcf.gz.tbi | Bin 0 -> 595996 bytes
testdata/variant/ex2.bgzf.bcf | Bin 0 -> 1062 bytes
testdata/variant/ex2.bgzf.bcf.csi | Bin 0 -> 130 bytes
testdata/variant/ex2.uncompressed.bcf | Bin 0 -> 1892 bytes
136 files changed, 5044 insertions(+), 2907 deletions(-)
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