[med-svn] [htsjdk] 02/05: Merge tag 'upstream/2.8.1+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository htsjdk.

commit b30682748030bed1278f62282a4ac6a39851e46c
Merge: 022e46c ed6db4b
Author: Andreas Tille <tille at debian.org>
Date:   Sun Dec 11 08:48:53 2016 +0100

    Merge tag 'upstream/2.8.1+dfsg'
    
    Upstream version 2.8.1+dfsg

 .../samtools/SAMSequenceDictionaryCodec.java       | 114 ++++
 .../java/htsjdk/samtools/SAMTextHeaderCodec.java   |  38 +-
 .../java/htsjdk/samtools/SamFileValidator.java     |  39 +-
 .../java/htsjdk/samtools/SamInputResource.java     |  26 +-
 src/main/java/htsjdk/samtools/SamPairUtil.java     |  49 +-
 src/main/java/htsjdk/samtools/SamReader.java       |  24 +
 .../java/htsjdk/samtools/SamReaderFactory.java     |  44 +-
 .../seekablestream/ByteArraySeekableStream.java    |  24 +
 .../htsjdk/samtools/util/AbstractLocusInfo.java    | 146 +++++
 ...cusIterator.java => AbstractLocusIterator.java} | 407 +++++---------
 .../samtools/util/AbstractRecordAndOffset.java     | 130 +++++
 .../samtools/util/BlockCompressedInputStream.java  |  61 +-
 .../java/htsjdk/samtools/util/CollectionUtil.java  |  10 +-
 .../samtools/util/CustomGzipOutputStream.java      |  24 +
 .../htsjdk/samtools/util/EdgeReadIterator.java     | 228 ++++++++
 .../samtools/util/EdgingRecordAndOffset.java       | 219 ++++++++
 src/main/java/htsjdk/samtools/util/IOUtil.java     |  21 +-
 .../java/htsjdk/samtools/util/IntervalList.java    |  49 +-
 src/main/java/htsjdk/samtools/util/Log.java        |   2 +-
 .../htsjdk/samtools/util/SamLocusIterator.java     | 613 ++++-----------------
 src/main/java/htsjdk/tribble/Feature.java          |   4 +-
 src/main/java/htsjdk/tribble/SimpleFeature.java    |   5 -
 .../java/htsjdk/tribble/bed/SimpleBEDFeature.java  |   8 -
 .../java/htsjdk/tribble/example/CountRecords.java  |   4 -
 .../htsjdk/tribble/example/ExampleBinaryCodec.java |   2 +-
 .../htsjdk/tribble/gelitext/GeliTextFeature.java   |   6 -
 .../java/htsjdk/tribble/index/IndexFactory.java    |  12 +-
 .../index/interval/IntervalIndexCreator.java       |   4 +-
 .../tribble/index/linear/LinearIndexCreator.java   |   4 +-
 .../tribble/index/tabix/TabixIndexCreator.java     |   2 +-
 .../htsjdk/variant/variantcontext/CommonInfo.java  |  54 +-
 .../htsjdk/variant/variantcontext/JEXLMap.java     | 115 ++--
 .../variantcontext/JexlMissingValueTreatment.java  |  39 ++
 .../variantcontext/StructuralVariantType.java}     |  32 +-
 .../variant/variantcontext/VariantContext.java     | 117 ++--
 .../variantcontext/VariantContextComparator.java   |   2 +-
 .../variantcontext/VariantContextUtils.java        |  35 +-
 .../variant/variantcontext/VariantJEXLContext.java |   2 +-
 .../variantcontext/writer/BCF2FieldWriter.java     |   2 +-
 .../variant/variantcontext/writer/BCF2Writer.java  |   6 +-
 .../writer/SortingVariantContextWriterBase.java    |  10 +-
 src/main/java/htsjdk/variant/vcf/VCFConstants.java |   5 +-
 src/main/java/htsjdk/variant/vcf/VCFEncoder.java   |   4 +-
 .../java/htsjdk/variant/vcf/VCFFileReader.java     |   2 +-
 .../htsjdk/variant/vcf/VCFFilterHeaderLine.java    |  18 +-
 .../samtools/SAMSequenceDictionaryCodecTest.java   | 122 ++++
 .../java/htsjdk/samtools/SamReaderFactoryTest.java |  38 +-
 .../java/htsjdk/samtools/ValidateSamFileTest.java  | 108 +++-
 .../java/htsjdk/samtools/sra/AbstractSRATest.java  |   4 +-
 .../samtools/util/AbstractLocusInfoTest.java       |  79 +++
 .../util/AbstractLocusIteratorTestTemplate.java    |  68 +++
 .../samtools/util/AbstractRecordAndOffsetTest.java |  63 +++
 .../util/BlockCompressedOutputStreamTest.java      |  57 +-
 .../htsjdk/samtools/util/EdgeReadIteratorTest.java | 402 ++++++++++++++
 .../samtools/util/EdgingRecordAndOffsetTest.java   |  94 ++++
 .../htsjdk/samtools/util/SamLocusIteratorTest.java |  35 +-
 src/test/java/htsjdk/tribble/bed/BEDCodecTest.java |  18 +-
 .../java/htsjdk/tribble/gelitext/GeliTextTest.java |   2 +-
 .../variantcontext/VariantContextTestProvider.java |   2 +-
 .../variantcontext/VariantContextUnitTest.java     | 195 ++++++-
 .../variantcontext/VariantJEXLContextUnitTest.java |  52 +-
 .../java/htsjdk/variant/vcf/VCFHeaderUnitTest.java |   4 +-
 .../htsjdk/tribble/vcfexample.vcf.truncated.gz     | Bin 0 -> 470 bytes
 .../htsjdk/tribble/vcfexample.vcf.truncated.hdr.gz | Bin 0 -> 460 bytes
 .../htsjdk/variant/structuralvariants.vcf          |  22 +
 65 files changed, 3012 insertions(+), 1115 deletions(-)

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