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commit a877967c881b26846a011b01f5deb1a5170b2e52 Merge: b3ba8c0 1c8643b Author: Vincent Danjean <[email protected]> Date: Fri Nov 11 20:46:00 2016 +0100 Merge tag 'upstream/2.7.0+dfsg' into sid Upstream version 2.7.0+dfsg .../java/htsjdk/samtools/AbstractBAMFileIndex.java | 3 +- .../htsjdk/samtools/AbstractSAMHeaderRecord.java | 3 +- src/main/java/htsjdk/samtools/BAMIndexer.java | 6 +- src/main/java/htsjdk/samtools/CRAMFileReader.java | 66 +- .../htsjdk/samtools/DefaultSAMRecordFactory.java | 2 +- .../htsjdk/samtools/MergingSamRecordIterator.java | 3 +- src/main/java/htsjdk/samtools/SAMFileHeader.java | 6 + src/main/java/htsjdk/samtools/SAMFileReader.java | 751 --------------------- .../htsjdk/samtools/SAMFileTruncatedReader.java | 69 -- src/main/java/htsjdk/samtools/SAMRecord.java | 154 ++++- .../java/htsjdk/samtools/SAMRecordSetBuilder.java | 2 +- src/main/java/htsjdk/samtools/SAMRecordUtil.java | 100 +-- .../htsjdk/samtools/SAMSequenceDictionary.java | 109 ++- .../java/htsjdk/samtools/SAMSequenceRecord.java | 3 +- src/main/java/htsjdk/samtools/SAMUtils.java | 63 +- .../java/htsjdk/samtools/SamFileHeaderMerger.java | 30 +- .../java/htsjdk/samtools/SamFileValidator.java | 7 +- src/main/java/htsjdk/samtools/SamReader.java | 26 +- src/main/java/htsjdk/samtools/TextTagCodec.java | 5 +- .../java/htsjdk/samtools/sra/SRAAccession.java | 3 +- .../java/htsjdk/samtools/util/IntervalList.java | 11 +- .../samtools/util/PositionalOutputStream.java | 65 ++ .../samtools/util/QualityEncodingDetector.java | 10 +- .../util/SamRecordIntervalIteratorFactory.java | 2 +- .../java/htsjdk/samtools/util/SequenceUtil.java | 174 ++--- src/main/java/htsjdk/samtools/util/StringUtil.java | 55 ++ src/main/java/htsjdk/samtools/util/TestUtil.java | 3 +- src/main/java/htsjdk/tribble/bed/BEDCodec.java | 12 +- .../java/htsjdk/tribble/index/AbstractIndex.java | 13 +- src/main/java/htsjdk/tribble/index/Index.java | 8 + .../java/htsjdk/tribble/index/IndexCreator.java | 7 + .../java/htsjdk/tribble/index/IndexFactory.java | 16 +- .../htsjdk/tribble/index/TribbleIndexCreator.java | 16 + .../htsjdk/tribble/index/tabix/TabixIndex.java | 9 +- .../variantcontext/GenotypeJEXLContext.java | 25 +- .../htsjdk/variant/variantcontext/JEXLMap.java | 174 ++--- .../variantcontext/VariantContextUtils.java | 54 +- .../variant/variantcontext/VariantJEXLContext.java | 16 +- .../writer/IndexingVariantContextWriter.java | 54 +- .../java/htsjdk/samtools/BAMFileWriterTest.java | 2 +- .../java/htsjdk/samtools/CRAMFileReaderTest.java | 96 ++- .../java/htsjdk/samtools/SAMIntegerTagTest.java | 46 ++ .../java/htsjdk/samtools/SAMRecordUnitTest.java | 78 +++ .../java/htsjdk/samtools/SAMRecordUtilTest.java | 29 - .../htsjdk/samtools/SAMSequenceDictionaryTest.java | 55 ++ src/test/java/htsjdk/samtools/SAMUtilsTest.java | 27 +- .../java/htsjdk/samtools/SamReaderSortTest.java | 2 +- .../{SAMFileReaderTest.java => SamReaderTest.java} | 2 +- .../samtools/util/PositionalOutputStreamTest.java | 62 ++ .../samtools/util/RelativeIso8601DateTest.java | 10 +- .../htsjdk/samtools/util/SequenceUtilTest.java | 33 +- .../java/htsjdk/samtools/util/StringUtilTest.java | 52 ++ .../java/htsjdk/tribble/FeatureReaderTest.java | 2 +- src/test/java/htsjdk/tribble/bed/BEDCodecTest.java | 11 + .../htsjdk/tribble/index/IndexFactoryTest.java | 5 + src/test/java/htsjdk/tribble/index/IndexTest.java | 47 ++ .../htsjdk/tribble/index/tabix/TabixIndexTest.java | 3 +- .../variantcontext/VariantJEXLContextUnitTest.java | 276 +++++--- .../reference_with_lower_and_uppercase.dict | 3 + .../reference_with_lower_and_uppercase.fasta | 4 + .../reference_with_lower_and_uppercase.fasta.fai | 2 + .../SequenceUtil/upper_and_lowercase_read.sam | 10 + 62 files changed, 1453 insertions(+), 1539 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/htsjdk.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
