[med-svn] [picard-tools] 04/09: Merge tag 'upstream/1.107'

[Charles Plessy]

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

commit 9cfa9d8a64d1617107d454bc7544e0fae70dd7b5
Merge: e3eeb80 514b7eb
Author: Charles Plessy <plessy at debian.org>
Date:   Sat Mar 22 10:44:07 2014 +0900

    Merge tag 'upstream/1.107'
    
    Upstream version 1.107
    
    # gpg: Signature faite le sam. 22 mars 2014 10:44:07 JST avec la clef RSA d'identifiant 2295D502
    # gpg: Bonne signature de « Charles Plessy <plessy at debian.org> »

 build.xml                                          | 13 ++++++---
 .../picard/illumina/parser/readers/BclReader.java  |  3 +-
 src/java/net/sf/picard/sam/SamFormatConverter.java |  2 +-
 src/java/net/sf/picard/util/MathUtil.java          | 16 +++++++++--
 src/java/net/sf/picard/util/SamLocusIterator.java  |  4 +++
 src/java/net/sf/samtools/util/TestUtil.java        | 19 +++++++++----
 .../writer/VariantContextWriterFactory.java        | 29 +++++++++++++++----
 .../variant/vcf/AbstractVCFCodec.java              |  4 +--
 .../org/broadinstitute/variant/vcf/VCFCodec.java   |  4 +--
 .../variant/vcf/VCFCompoundHeaderLine.java         |  6 ++--
 .../variant/vcf/VCFHeaderLineTranslator.java       |  1 +
 .../variant/vcf/VCFHeaderVersion.java              | 24 +++++++++++++++-
 .../net/sf/picard/vcf/VcfFormatConverterTest.java  | 33 ++++++++++++++--------
 .../variantcontext/writer/VCFWriterUnitTest.java   |  2 +-
 14 files changed, 119 insertions(+), 41 deletions(-)

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