This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch master in repository picard-tools.
commit 7abc4cec92598e69ad44f16f63daa8bb5d82d98a Merge: 9cfa9d8 6ac75e2 Author: Charles Plessy <[email protected]> Date: Sat Mar 22 10:47:24 2014 +0900 Merge tag 'upstream/1.108' Upstream version 1.108 # gpg: Signature faite le sam. 22 mars 2014 10:47:24 JST avec la clef RSA d'identifiant 2295D502 # gpg: Bonne signature de « Charles Plessy <[email protected]> » Picard-public.ipr | 2 + build.xml | 3 +- src/java/net/sf/picard/fastq/BasicFastqWriter.java | 4 +- .../sf/picard/illumina/MarkIlluminaAdapters.java | 204 +++++++------- .../net/sf/picard/illumina/parser/BclParser.java | 16 +- .../parser/ClusterIntensityFileReader.java | 2 +- .../illumina/parser/CycleIlluminaFileMap.java | 59 ++-- .../parser/IlluminaDataProviderFactory.java | 69 +++-- .../picard/illumina/parser/IlluminaFileUtil.java | 212 ++++++++++++++- .../illumina/parser/IlluminaIntensityParser.java | 2 +- .../parser/MultiTileBclCycleFilesIterator.java} | 45 +-- .../picard/illumina/parser/MultiTileBclParser.java | 111 ++++++++ .../illumina/parser/MultiTileFilterParser.java} | 59 ++-- .../illumina/parser/MultiTileLocsParser.java | 77 ++++++ .../sf/picard/illumina/parser/MultiTileParser.java | 128 +++++++++ .../sf/picard/illumina/parser/PerTileParser.java | 6 +- .../illumina/parser/PerTilePerCycleParser.java | 5 +- .../net/sf/picard/illumina/parser/TileIndex.java | 153 +++++++++++ .../AbstractIlluminaPositionFileReader.java | 32 ++- .../illumina/parser/readers/BclIndexReader.java | 75 +++++ .../picard/illumina/parser/readers/BclReader.java | 30 +- .../illumina/parser/readers/FilterFileReader.java | 4 + .../illumina/parser/readers/LocsFileReader.java | 16 +- .../parser/readers/MMapBackedIteratorFactory.java | 20 ++ src/java/net/sf/picard/io/IoUtil.java | 23 +- src/java/net/sf/picard/sam/MergeBamAlignment.java | 10 +- src/java/net/sf/picard/sam/RevertSam.java | 218 ++++++++++++--- src/java/net/sf/picard/sam/SamAlignmentMerger.java | 50 ++-- src/java/net/sf/picard/sam/SamToFastq.java | 301 +++++++++++++-------- src/java/net/sf/picard/util/IntervalListTools.java | 2 +- .../sf/picard/util/ListMap.java} | 51 ++-- src/java/net/sf/picard/util/SamLocusIterator.java | 2 + src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java | 28 +- src/java/net/sf/picard/vcf/VcfFormatConverter.java | 8 +- .../samtools/util/BlockCompressedInputStream.java | 15 +- src/java/net/sf/samtools/util/Lazy.java | 4 + src/java/org/broad/tribble/util/TabixUtils.java | 50 ++++ .../org/broadinstitute/variant/bcf2/BCF2Utils.java | 5 + .../variant/variantcontext/VariantContext.java | 30 +- .../writer/AsyncVariantContextWriter.java | 49 ++++ .../variant/variantcontext/writer/Options.java | 3 +- .../writer/VariantContextWriterFactory.java | 164 ++++++++--- .../variant/vcf/AbstractVCFCodec.java | 5 +- .../broadinstitute/variant/vcf/VCFFileReader.java | 2 +- .../illumina/parser/IlluminaFileUtilTest.java | 36 ++- .../illumina/parser/PerTilePerCycleParserTest.java | 2 +- .../AbstractIlluminaPositionFileReaderTest.java | 4 +- .../reference/ReferenceSequenceFileWalkerTest.java | 60 ++++ .../net/sf/picard/sam/MergeBamAlignmentTest.java | 2 +- .../variantcontext/VariantContextUnitTest.java | 41 ++- 50 files changed, 1931 insertions(+), 568 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
