[med-svn] [htsjdk] branch master updated (7170221 -> 640fd54)
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 change to branch master
in repository htsjdk.
from 7170221 Take over change from debian/jessie-backports branch to successfully obtain JAVA_HOME
new 759cd02 Imported Upstream version 2.3.0+dfsg.1
new 781d11d Merge tag 'upstream/2.3.0+dfsg.1'
new 4e7593d New upstream version
new cf41a49 Refresh patches
new 640fd54 Bump Standards-Version to 3.9.8
The 5 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 +-
debian/changelog | 6 +-
debian/control | 2 +-
debian/patches/10-build.xml | 15 +-
debian/patches/13-skip_network_tests | 72 +++-
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
101 files changed, 3167 insertions(+), 1201 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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