[med-svn] [picard-tools] 02/09: Merge tag 'upstream/1.106'

[Charles Plessy]

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

commit e3eeb8009a354426b5d4a6a7bb4012cacd5ded77
Merge: f458746 efaffda
Author: Charles Plessy <plessy at debian.org>
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(-)

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