[med-svn] [htsjdk] branch upstream updated (a6a2d54 -> 759cd02)
Andreas Tille
tille at debian.org
Fri May 20 09:49:29 UTC 2016
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tille pushed a change to branch upstream
in repository htsjdk.
from a6a2d54 Imported Upstream version 2.1.1+dfsg.1
new 759cd02 Imported Upstream version 2.3.0+dfsg.1
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
been added to this reference.
Summary of changes:
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
.../htsjdk/{variant/ex2.vcf => tribble/test.vcf} | 15 +-
testdata/htsjdk/tribble/test.vcf.gz | Bin 0 -> 822 bytes
97 files changed, 3091 insertions(+), 1182 deletions(-)
create mode 100644 src/c/inteldeflater/README
create mode 100644 src/c/inteldeflater/igzip_lib.h
create mode 100644 src/c/inteldeflater/internal_state_size.h
create mode 100644 src/c/inteldeflater/types.h
rename src/java/htsjdk/samtools/{CRAMIndexer.java => CRAMBAIIndexer.java} (95%)
create mode 100644 src/java/htsjdk/samtools/cram/ref/CRAMReferenceSource.java
create mode 100755 src/java/htsjdk/samtools/example/PrintReadsExample.java
copy src/java/htsjdk/samtools/filter/{FilteringIterator.java => FilteringSamIterator.java} (89%)
create mode 100644 src/java/htsjdk/samtools/util/AsyncBufferedIterator.java
create mode 100755 src/java/htsjdk/variant/example/PrintVariantsExample.java
create mode 100644 src/java/htsjdk/variant/variantcontext/GenotypeJEXLContext.java
copy src/java/htsjdk/variant/variantcontext/filter/{FilteringIterator.java => FilteringVariantContextIterator.java} (93%)
rename src/tests/java/htsjdk/samtools/{CRAMFileIndexTest.java => CRAMFileBAIIndexTest.java} (96%)
rename src/tests/java/htsjdk/samtools/{CramFileWriterTest.java => CRAMFileWriterTest.java} (99%)
create mode 100644 src/tests/java/htsjdk/samtools/GenomicIndexUtilTest.java
create mode 100644 src/tests/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java
create mode 100644 src/tests/java/htsjdk/samtools/SamStreamsTest.java
create mode 100644 src/tests/java/htsjdk/samtools/util/AsyncBufferedIteratorTest.java
create mode 100644 src/tests/java/htsjdk/samtools/util/CloseableIteratorTest.java
create mode 100755 src/tests/java/htsjdk/samtools/util/IntelDeflaterTest.java
create mode 100644 src/tests/java/htsjdk/tribble/TribbleIndexFeatureReaderTest.java
create mode 100644 src/tests/java/htsjdk/variant/PrintVariantsExampleTest.java
rename src/tests/java/htsjdk/variant/variantcontext/filter/{FilteringIteratorTest.java => FilteringVariantContextIteratorTest.java} (88%)
create mode 100644 testdata/htsjdk/tribble/tabix/YRI.trio.2010_07.indel.sites.vcf.gz
create mode 100644 testdata/htsjdk/tribble/tabix/YRI.trio.2010_07.indel.sites.vcf.gz.tbi
copy testdata/htsjdk/{variant/ex2.vcf => tribble/test.vcf} (74%)
create mode 100644 testdata/htsjdk/tribble/test.vcf.gz
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