This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch master in repository picard-tools.
commit e3eeb8009a354426b5d4a6a7bb4012cacd5ded77 Merge: f458746 efaffda Author: Charles Plessy <[email protected]> Date: Sat Mar 22 10:41:31 2014 +0900 Merge tag 'upstream/1.106' Upstream version 1.106 Conflicts: build.xml build.xml | 2 +- src/java/net/sf/picard/pedigree/PedFile.java | 76 +++- src/java/net/sf/picard/pedigree/PedTrio.java | 45 --- .../reference/ReferenceSequenceFileFactory.java | 2 + .../net/sf/picard/sam/AbstractAlignmentMerger.java | 71 ++-- src/java/net/sf/picard/sam/CleanSam.java | 6 +- src/java/net/sf/picard/sam/HitsForInsert.java | 5 + src/java/net/sf/picard/sam/MarkDuplicates.java | 4 +- .../sf/picard/sam/MultiHitAlignedReadIterator.java | 54 ++- src/java/net/sf/picard/sam/SamAlignmentMerger.java | 5 +- src/java/net/sf/picard/sam/SamPairUtil.java | 15 + src/java/net/sf/picard/util/ProgressLogger.java | 17 +- src/java/net/sf/picard/util/SamLocusIterator.java | 5 +- .../sf/picard/util/SamRecordIntervalIterator.java | 188 --------- .../util/SamRecordIntervalIteratorFactory.java | 13 +- src/java/net/sf/samtools/AbstractBAMFileIndex.java | 114 +++--- src/java/net/sf/samtools/BAMFileReader.java | 419 ++++++++++++++------- src/java/net/sf/samtools/CachingBAMFileIndex.java | 34 +- src/java/net/sf/samtools/Chunk.java | 50 ++- .../net/sf/samtools/DiskBasedBAMFileIndex.java | 14 +- src/java/net/sf/samtools/SAMFileHeader.java | 5 +- src/java/net/sf/samtools/SAMFileReader.java | 224 ++++++++++- src/java/net/sf/samtools/SAMFileSpan.java | 48 +-- src/java/net/sf/samtools/SAMTextReader.java | 5 + .../variant/variantcontext/Allele.java | 17 +- .../variant/variantcontext/VariantContext.java | 25 +- .../variantcontext/VariantContextBuilder.java | 17 +- .../variantcontext/writer/BCF2FieldEncoder.java | 16 +- .../variant/vcf/AbstractVCFCodec.java | 26 +- src/tests/java/net/sf/picard/sam/CleanSamTest.java | 78 ++++ .../net/sf/picard/sam/MergeBamAlignmentTest.java | 21 +- .../java/net/sf/picard/vcf/MergeVcfsTest.java | 12 +- .../java/net/sf/samtools/BAMFileIndexTest.java | 96 ++++- .../variantcontext/writer/VCFWriterUnitTest.java | 13 +- .../sf/picard/sam/CleanSam/fits_with_deletion.sam | 3 + .../sam/CleanSam/long_trailing_insertion.sam | 3 + .../picard/sam/CleanSam/overhang_with_deletion.sam | 3 + .../net/sf/picard/sam/CleanSam/simple_fits.sam | 3 + .../net/sf/picard/sam/CleanSam/simple_overhang.sam | 3 + .../sf/picard/sam/CleanSam/trailing_insertion.sam | 3 + 40 files changed, 1113 insertions(+), 647 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
