[med-svn] [htsjdk] 02/03: Merge tag 'upstream/2.6.1+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository htsjdk.

commit d86706f716d5073a27c2b8b73ea699c2a82b302a
Merge: 262dc02 00ff79c
Author: Andreas Tille <tille at debian.org>
Date:   Sat Sep 10 08:03:09 2016 +0200

    Merge tag 'upstream/2.6.1+dfsg'
    
    Upstream version 2.6.1+dfsg

 README.md                                          |   2 +
 build.gradle                                       |   1 +
 src/main/java/htsjdk/samtools/CRAMIterator.java    |  12 +-
 .../htsjdk/samtools/DuplicateScoringStrategy.java  |  10 +-
 src/main/java/htsjdk/samtools/SAMRecordUtil.java   | 104 ++++++++++++-----
 src/main/java/htsjdk/samtools/SAMUtils.java        | 124 ++++++++++++++++++++
 src/main/java/htsjdk/samtools/SRAFileReader.java   |   3 +-
 src/main/java/htsjdk/samtools/SamPairUtil.java     |   5 +-
 .../java/htsjdk/samtools/cram/build/Utils.java     |   4 +-
 .../cram/encoding/reader/DataReaderFactory.java    |   4 +-
 .../samtools/cram/ref/CRAMReferenceSource.java     |   4 +-
 .../htsjdk/samtools/cram/ref/ReferenceSource.java  |  22 ++--
 .../samtools/cram/structure/CompressionHeader.java |   4 +-
 .../htsjdk/samtools/filter/IntervalFilter.java     |   5 +-
 .../samtools/filter/IntervalKeepPairFilter.java    | 108 +++++++++++++++++
 .../java/htsjdk/samtools/sra/SRAAccession.java     |   4 +-
 .../htsjdk/samtools/util/AbstractAsyncWriter.java  |   7 +-
 .../java/htsjdk/samtools/util/BlockGunzipper.java  |  29 ++++-
 src/main/java/htsjdk/samtools/util/Lazy.java       |   1 +
 .../htsjdk/samtools/util/SamLocusIterator.java     |   2 +
 src/main/java/htsjdk/samtools/util/TestUtil.java   |   5 +
 .../java/htsjdk/tribble/BinaryFeatureCodec.java    |   9 ++
 src/main/java/htsjdk/tribble/FeatureCodec.java     |  14 +++
 .../tribble/TribbleIndexedFeatureReader.java       |  10 +-
 src/main/java/htsjdk/tribble/bed/BEDCodec.java     |   5 +
 .../java/htsjdk/tribble/index/IndexFactory.java    |  31 ++++-
 .../variant/variantcontext/FastGenotype.java       |   5 +-
 .../htsjdk/variant/variantcontext/Genotype.java    |   6 +-
 .../variant/variantcontext/GenotypeBuilder.java    |  35 +++++-
 .../java/htsjdk/variant/vcf/AbstractVCFCodec.java  |   6 +
 .../htsjdk/variant/vcf/VCFStandardHeaderLines.java | 129 +++++++++------------
 .../java/htsjdk/samtools/BAMRemoteFileTest.java    |   3 +-
 .../java/htsjdk/samtools/CRAMCRAIIndexerTest.java  |   5 +
 .../java/htsjdk/samtools/SAMRecordUtilTest.java    |  29 +++++
 src/test/java/htsjdk/samtools/SAMUtilsTest.java    |  77 +++++++++++-
 .../java/htsjdk/samtools/SamReaderFactoryTest.java |  13 +--
 .../htsjdk/samtools/cram/structure/SliceTests.java |  34 ++++++
 .../filter/IntervalKeepPairFilterTest.java         | 123 ++++++++++++++++++++
 .../seekablestream/SeekableStreamFactoryTest.java  |   9 +-
 .../java/htsjdk/samtools/sra/AbstractSRATest.java  |  34 +++++-
 .../java/htsjdk/samtools/sra/SRAAccessionTest.java |   3 +-
 .../java/htsjdk/samtools/sra/SRAIndexTest.java     |   2 +-
 .../htsjdk/samtools/sra/SRALazyRecordTest.java     |   2 +-
 src/test/java/htsjdk/samtools/sra/SRATest.java     |  78 +++++++------
 .../java/htsjdk/samtools/util/AsyncWriterTest.java |  77 ++++++++++++
 .../htsjdk/samtools/util/SamLocusIteratorTest.java |  24 +++-
 .../htsjdk/tribble/AbstractFeatureReaderTest.java  |   3 +-
 .../java/htsjdk/tribble/BinaryFeaturesTest.java    |   5 +
 .../tribble/TribbleIndexFeatureReaderTest.java     |   4 +-
 src/test/java/htsjdk/tribble/bed/BEDCodecTest.java |   5 +
 .../htsjdk/tribble/readers/TabixReaderTest.java    |   3 +-
 .../variantcontext/GenotypeBuilderTest.java        |  75 ++++++++++++
 .../variant/variantcontext/GenotypeUnitTest.java   |   4 +
 .../htsjdk/variant/vcf/AbstractVCFCodecTest.java   |   7 ++
 .../vcf/VCFStandardHeaderLinesUnitTest.java        |  56 ++++++++-
 .../htsjdk/samtools/cram/auxf.alteredForMD5test.fa |   2 +
 .../samtools/cram/auxf.alteredForMD5test.fa.fai    |   1 +
 src/test/resources/htsjdk/samtools/cram/auxf.fasta |   2 -
 src/test/resources/htsjdk/samtools/cram/test.fasta |   2 -
 .../resources/htsjdk/samtools/cram/test2.fasta     |   2 -
 .../resources/htsjdk/tribble/test with spaces.vcf  |  24 ++++
 src/test/resources/htsjdk/tribble/test.vcf.bgz     | Bin 0 -> 849 bytes
 src/test/resources/htsjdk/variant/ex2.bgzf.bcf     | Bin 1062 -> 0 bytes
 .../resources/htsjdk/variant/ex2.uncompressed.bcf  | Bin 1892 -> 0 bytes
 64 files changed, 1197 insertions(+), 221 deletions(-)

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