This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch master in repository picard-tools.
commit e87bdf5bcea5e18f01580429fc18a3d1856b338c Merge: 0ac9d98 ad4ec03 Author: Charles Plessy <[email protected]> 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 <[email protected]> » 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
