[med-svn] [htsjdk] 02/05: Merge tag 'upstream/2.8.1+dfsg'
Andreas Tille
tille at debian.org
Sun Dec 11 07:57:13 UTC 2016
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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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