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commit 89db57e0b7c25fadb0d8cb50ce0bb3a8134ad0a3 Merge: 7abc4ce a6e579a Author: Charles Plessy <[email protected]> Date: Sat Mar 22 10:49:44 2014 +0900 Merge tag 'upstream/1.109' Upstream version 1.109 # gpg: Signature faite le sam. 22 mars 2014 10:49:43 JST avec la clef RSA d'identifiant 2295D502 # gpg: Bonne signature de « Charles Plessy <[email protected]> » build.xml | 3 +- .../net/sf/picard/sam/AbstractAlignmentMerger.java | 59 ++++- src/java/net/sf/picard/sam/CleanSam.java | 19 +- src/java/net/sf/picard/sam/ReorderSam.java | 9 +- ...RevertOriginalBaseQualitiesAndAddMateCigar.java | 234 ++++++++++++++++++ src/java/net/sf/picard/sam/RevertSam.java | 16 +- src/java/net/sf/picard/sam/SamFileValidator.java | 43 +++- src/java/net/sf/picard/sam/SamPairUtil.java | 83 ++++--- src/java/net/sf/picard/sam/SortSam.java | 2 + src/java/net/sf/picard/util/ProgressLogger.java | 10 +- src/java/net/sf/samtools/AsyncSAMFileWriter.java | 13 +- src/java/net/sf/samtools/SAMFileWriter.java | 11 +- src/java/net/sf/samtools/SAMFileWriterFactory.java | 42 ++-- src/java/net/sf/samtools/SAMFileWriterImpl.java | 14 +- .../net/sf/samtools/SAMHeaderRecordComparator.java | 66 +++++ src/java/net/sf/samtools/SAMRecord.java | 267 +++++++++++++++++---- src/java/net/sf/samtools/SAMRecordSetBuilder.java | 14 +- src/java/net/sf/samtools/SAMRecordUtil.java | 1 - src/java/net/sf/samtools/SAMTag.java | 2 +- src/java/net/sf/samtools/SAMTagUtil.java | 66 ++--- src/java/net/sf/samtools/SAMUtils.java | 65 +++++ src/java/net/sf/samtools/SAMValidationError.java | 42 ++-- .../net/sf/samtools/util/AbstractAsyncWriter.java | 3 + .../ProgressLoggerInterface.java} | 31 ++- .../net/sf/picard/sam/ValidateSamFileTest.java | 68 ++++-- .../java/net/sf/samtools/BAMFileIndexTest.java | 3 + .../sf/samtools/SamHeaderRecordComparatorTest.java | 72 ++++++ .../intervallist/IntervalListFromVCFTest.vcf | 53 ++++ .../IntervalListFromVCFTestComp.interval_list | 7 + ...ntervalListFromVCFTestCompInverse.interval_list | 10 + ...lListFromVCFTestCompInverseManual.interval_list | 10 + .../intervallist/IntervalListFromVCFTestManual.vcf | 57 +++++ ...IntervalListFromVCFTestManualComp.interval_list | 12 + .../inappropriate_mate_cigar_string.sam | 13 + .../invalid_mate_cigar_string.sam | 19 ++ .../net/sf/picard/sam/mate_cigar_and_no_oqs.sam | 4 + testdata/net/sf/picard/sam/mate_cigar_and_oqs.sam | 4 + .../net/sf/picard/sam/no_mate_cigar_and_no_oqs.sam | 4 + .../net/sf/picard/sam/no_mate_cigar_and_oqs.sam | 4 + testdata/net/sf/picard/sam/no_mates_and_no_oqs.sam | 6 + .../no_mates_and_no_oqs_in_first_four_records.sam | 7 + testdata/net/sf/picard/sam/no_mates_and_oqs.sam | 6 + 42 files changed, 1233 insertions(+), 241 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
