[med-svn] [htsjdk] branch upstream updated (023be94 -> 00ff79c)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository htsjdk.

      from  023be94   Imported Upstream version 2.5.0+dfsg.2
       new  00ff79c   New upstream version 2.6.1+dfsg

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
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Summary of changes:
 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 -
 .../tribble/{test.vcf => test with spaces.vcf}     |   0
 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, 1173 insertions(+), 221 deletions(-)
 create mode 100644 src/main/java/htsjdk/samtools/filter/IntervalKeepPairFilter.java
 create mode 100644 src/test/java/htsjdk/samtools/SAMRecordUtilTest.java
 create mode 100644 src/test/java/htsjdk/samtools/filter/IntervalKeepPairFilterTest.java
 create mode 100644 src/test/java/htsjdk/samtools/util/AsyncWriterTest.java
 create mode 100644 src/test/java/htsjdk/variant/variantcontext/GenotypeBuilderTest.java
 create mode 100644 src/test/resources/htsjdk/samtools/cram/auxf.alteredForMD5test.fa
 create mode 100644 src/test/resources/htsjdk/samtools/cram/auxf.alteredForMD5test.fa.fai
 delete mode 100644 src/test/resources/htsjdk/samtools/cram/auxf.fasta
 delete mode 100644 src/test/resources/htsjdk/samtools/cram/test.fasta
 delete mode 100644 src/test/resources/htsjdk/samtools/cram/test2.fasta
 copy src/test/resources/htsjdk/tribble/{test.vcf => test with spaces.vcf} (100%)
 create mode 100644 src/test/resources/htsjdk/tribble/test.vcf.bgz
 delete mode 100755 src/test/resources/htsjdk/variant/ex2.bgzf.bcf
 delete mode 100755 src/test/resources/htsjdk/variant/ex2.uncompressed.bcf

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