[med-svn] [htsjdk] 02/05: Merge tag 'upstream/2.3.0+dfsg.1'
Andreas Tille
tille at debian.org
Fri May 20 09:49:28 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository htsjdk.
commit 781d11d9eb1984706c9047fd4b25b10dd5513afa
Merge: 7170221 759cd02
Author: Andreas Tille <tille at debian.org>
Date: Fri May 20 11:30:07 2016 +0200
Merge tag 'upstream/2.3.0+dfsg.1'
Upstream version 2.3.0+dfsg.1
README.md | 8 +-
build.sbt | 9 +-
build.xml | 26 +-
src/c/inteldeflater/IntelDeflater.c | 389 ++++++++++++++-------
src/c/inteldeflater/README | 7 +
src/c/inteldeflater/igzip_lib.h | 50 +++
src/c/inteldeflater/internal_state_size.h | 32 ++
src/c/inteldeflater/types.h | 46 +++
src/java/htsjdk/samtools/BAMFileReader.java | 33 +-
src/java/htsjdk/samtools/BAMIndexMetaData.java | 2 +-
src/java/htsjdk/samtools/BAMIndexer.java | 28 +-
src/java/htsjdk/samtools/BinningIndexBuilder.java | 4 +-
.../{CRAMIndexer.java => CRAMBAIIndexer.java} | 12 +-
.../htsjdk/samtools/CRAMContainerStreamWriter.java | 11 +-
src/java/htsjdk/samtools/CRAMFileReader.java | 38 +-
src/java/htsjdk/samtools/CRAMFileWriter.java | 7 +-
src/java/htsjdk/samtools/CRAMIterator.java | 11 +-
src/java/htsjdk/samtools/Defaults.java | 83 ++++-
src/java/htsjdk/samtools/DuplicateSetIterator.java | 29 +-
src/java/htsjdk/samtools/GenomicIndexUtil.java | 8 +-
.../SAMBinaryTagAndUnsignedArrayValue.java | 7 +-
src/java/htsjdk/samtools/SAMBinaryTagAndValue.java | 90 ++++-
src/java/htsjdk/samtools/SAMFileReader.java | 83 +----
src/java/htsjdk/samtools/SAMFileWriterFactory.java | 5 +-
src/java/htsjdk/samtools/SAMRecord.java | 66 +---
src/java/htsjdk/samtools/SAMUtils.java | 4 +-
src/java/htsjdk/samtools/SamReaderFactory.java | 29 +-
src/java/htsjdk/samtools/SamStreams.java | 34 +-
src/java/htsjdk/samtools/cram/CRAIEntry.java | 83 +++--
src/java/htsjdk/samtools/cram/CRAIIndex.java | 11 +-
.../htsjdk/samtools/cram/build/CramNormalizer.java | 6 +-
.../samtools/cram/ref/CRAMReferenceSource.java | 22 ++
.../htsjdk/samtools/cram/ref/ReferenceSource.java | 19 +-
src/java/htsjdk/samtools/cram/structure/Slice.java | 10 -
.../htsjdk/samtools/example/PrintReadsExample.java | 104 ++++++
.../htsjdk/samtools/fastq/FastqWriterFactory.java | 2 +-
.../htsjdk/samtools/filter/FilteringIterator.java | 207 +++--------
...ringIterator.java => FilteringSamIterator.java} | 307 ++++++++--------
.../samtools/reference/ReferenceSequence.java | 12 +
.../htsjdk/samtools/util/AbstractAsyncWriter.java | 21 +-
.../samtools/util/AsyncBufferedIterator.java | 281 +++++++++++++++
.../samtools/util/BlockCompressedInputStream.java | 8 +
.../htsjdk/samtools/util/CloseableIterator.java | 24 +-
src/java/htsjdk/samtools/util/Log.java | 2 +-
.../htsjdk/samtools/util/SamLocusIterator.java | 4 +-
.../util/SamRecordIntervalIteratorFactory.java | 8 +-
src/java/htsjdk/samtools/util/SequenceUtil.java | 23 ++
src/java/htsjdk/samtools/util/Tuple.java | 3 +-
src/java/htsjdk/tribble/AbstractFeatureReader.java | 10 +
.../tribble/TribbleIndexedFeatureReader.java | 28 +-
src/java/htsjdk/tribble/index/IndexFactory.java | 45 +--
.../htsjdk/tribble/index/tabix/TabixIndex.java | 18 +-
.../htsjdk/tribble/readers/LineReaderUtil.java | 4 +-
.../variant/example/PrintVariantsExample.java | 105 ++++++
.../variantcontext/GenotypeJEXLContext.java | 58 +++
.../htsjdk/variant/variantcontext/JEXLMap.java | 75 +---
.../variant/variantcontext/VariantJEXLContext.java | 36 +-
.../variantcontext/filter/FilteringIterator.java | 94 +----
...r.java => FilteringVariantContextIterator.java} | 6 +-
.../writer/VariantContextWriterBuilder.java | 22 +-
.../writer/VariantContextWriterFactory.java | 2 +-
src/java/htsjdk/variant/vcf/AbstractVCFCodec.java | 7 +-
.../htsjdk/variant/vcf/VCFStandardHeaderLines.java | 2 +-
src/scripts/build_intel_deflater.sh | 29 +-
.../java/htsjdk/samtools/BAMIndexWriterTest.java | 9 +
.../java/htsjdk/samtools/CRAMBAIIndexerTest.java | 2 +-
.../java/htsjdk/samtools/CRAMComplianceTest.java | 67 ++--
...ileIndexTest.java => CRAMFileBAIIndexTest.java} | 14 +-
...FileWriterTest.java => CRAMFileWriterTest.java} | 4 +-
.../java/htsjdk/samtools/GenomicIndexUtilTest.java | 50 +++
.../samtools/SAMBinaryTagAndValueUnitTest.java | 183 ++++++++++
.../java/htsjdk/samtools/SAMFileReaderTest.java | 18 +-
.../htsjdk/samtools/SAMFileWriterFactoryTest.java | 22 ++
.../java/htsjdk/samtools/SAMIntegerTagTest.java | 2 +-
.../java/htsjdk/samtools/SAMRecordUnitTest.java | 169 ++++-----
src/tests/java/htsjdk/samtools/SamStreamsTest.java | 60 ++++
.../java/htsjdk/samtools/cram/CRAIEntryTest.java | 3 +-
.../java/htsjdk/samtools/cram/CRAIIndexTest.java | 110 +++++-
.../samtools/util/AsyncBufferedIteratorTest.java | 115 ++++++
.../util/BlockCompressedOutputStreamTest.java | 10 +
.../samtools/util/CloseableIteratorTest.java | 31 ++
.../htsjdk/samtools/util/IntelDeflaterTest.java | 130 +++++++
.../htsjdk/samtools/util/SequenceUtilTest.java | 20 ++
.../htsjdk/tribble/AbstractFeatureReaderTest.java | 61 ++++
.../tribble/TribbleIndexFeatureReaderTest.java | 86 +++++
.../htsjdk/tribble/index/tabix/TabixIndexTest.java | 79 ++++-
.../htsjdk/variant/PrintVariantsExampleTest.java | 65 ++++
.../variantcontext/VariantJEXLContextUnitTest.java | 46 ++-
...va => FilteringVariantContextIteratorTest.java} | 8 +-
.../filter/HeterozygosityFilterTest.java | 2 +-
.../filter/JavascriptVariantFilterTest.java | 2 +-
.../VariantContextWriterBuilderUnitTest.java | 17 +-
.../htsjdk/variant/vcf/AbstractVCFCodecTest.java | 24 +-
.../tabix/YRI.trio.2010_07.indel.sites.vcf.gz | Bin 0 -> 250626 bytes
.../tabix/YRI.trio.2010_07.indel.sites.vcf.gz.tbi | Bin 0 -> 32877 bytes
testdata/htsjdk/tribble/test.vcf | 24 ++
testdata/htsjdk/tribble/test.vcf.gz | Bin 0 -> 822 bytes
97 files changed, 3107 insertions(+), 1175 deletions(-)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/htsjdk.git
More information about the debian-med-commit
mailing list