[med-svn] [picard-tools] 08/09: Merge tag 'upstream/1.109'

[Charles Plessy]

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plessy pushed a commit to branch master
in repository picard-tools.

commit 89db57e0b7c25fadb0d8cb50ce0bb3a8134ad0a3
Merge: 7abc4ce a6e579a
Author: Charles Plessy <plessy at debian.org>
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 <plessy at debian.org> »

 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(-)

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