[med-svn] [htsjdk] branch upstream updated (00ff79c -> 1c8643b)

[Vincent Danjean]

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vdanjean pushed a change to branch upstream
in repository htsjdk.

      from  00ff79c   New upstream version 2.6.1+dfsg
      adds  1c8643b   New upstream version 2.7.0+dfsg

No new revisions were added by this update.

Summary of changes:
 .../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 +-
 .../util/PositionalOutputStream.java}              |  52 +-
 .../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, 1416 insertions(+), 1563 deletions(-)
 delete mode 100644 src/main/java/htsjdk/samtools/SAMFileReader.java
 delete mode 100644 src/main/java/htsjdk/samtools/SAMFileTruncatedReader.java
 copy src/main/java/htsjdk/{variant/vcf/VCFInfoHeaderLine.java => samtools/util/PositionalOutputStream.java} (53%)
 delete mode 100644 src/test/java/htsjdk/samtools/SAMRecordUtilTest.java
 rename src/test/java/htsjdk/samtools/{SAMFileReaderTest.java => SamReaderTest.java} (99%)
 create mode 100644 src/test/java/htsjdk/samtools/util/PositionalOutputStreamTest.java
 create mode 100644 src/test/resources/htsjdk/samtools/SequenceUtil/reference_with_lower_and_uppercase.dict
 create mode 100644 src/test/resources/htsjdk/samtools/SequenceUtil/reference_with_lower_and_uppercase.fasta
 create mode 100644 src/test/resources/htsjdk/samtools/SequenceUtil/reference_with_lower_and_uppercase.fasta.fai
 create mode 100644 src/test/resources/htsjdk/samtools/SequenceUtil/upper_and_lowercase_read.sam

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