[med-svn] [picard-tools] 06/09: Merge tag 'upstream/1.108'

[Charles Plessy]

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

commit 7abc4cec92598e69ad44f16f63daa8bb5d82d98a
Merge: 9cfa9d8 6ac75e2
Author: Charles Plessy <plessy at debian.org>
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 <plessy at debian.org> »

 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(-)

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