[med-svn] [Git][med-team/htsjdk][master] 8 commits: New upstream version 2.14.3+dfsg

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / htsjdk


Commits:
26feb9cc by Andreas Tille at 2018-03-28T14:18:36+02:00
New upstream version 2.14.3+dfsg
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0c4c86ec by Andreas Tille at 2018-03-28T14:18:54+02:00
Update upstream source from tag 'upstream/2.14.3+dfsg'

Update to upstream version '2.14.3+dfsg'
with Debian dir f3cb3f9088d070b7bd9c7562139c0c4a17af8e82
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afe5dc32 by Andreas Tille at 2018-03-28T14:22:08+02:00
New upstream version

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f2dd84b2 by Andreas Tille at 2018-03-28T14:22:17+02:00
Update pom files

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39dd500d by Andreas Tille at 2018-03-28T14:22:46+02:00
Standards-Version: 4.1.3

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7e7b3488 by Andreas Tille at 2018-03-28T14:31:01+02:00
Adapt quilt patches

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b29ccd1b by Andreas Tille at 2018-03-28T14:33:21+02:00
Drop warning and upload to experimental until picard-tools will catch up

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0fa566a1 by Andreas Tille at 2018-03-28T14:54:02+02:00
Make sure the package will not incidentally uploaded to unstable

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30 changed files:

- .gitignore
- build.gradle
- debian/changelog
- debian/control
- debian/htsjdk.pom
- debian/htsjdk.pom.asc
- debian/patches/13-skip_network_tests
- debian/patches/30-disable-scalatest.patch
- src/main/java/htsjdk/samtools/BAMFileWriter.java
- src/main/java/htsjdk/samtools/Defaults.java
- src/main/java/htsjdk/samtools/DownsamplingIteratorFactory.java
- src/main/java/htsjdk/samtools/NotPrimarySkippingIterator.java
- src/main/java/htsjdk/samtools/SAMFileHeader.java
- src/main/java/htsjdk/samtools/SAMFileWriterFactory.java
- src/main/java/htsjdk/samtools/SAMFlag.java
- src/main/java/htsjdk/samtools/SAMRecord.java
- src/main/java/htsjdk/samtools/SAMRecordQueryNameComparator.java
- src/main/java/htsjdk/samtools/SAMRecordSetBuilder.java
- − src/main/java/htsjdk/samtools/SAMRecordUtil.java
- src/main/java/htsjdk/samtools/SAMUtils.java
- src/main/java/htsjdk/samtools/SAMValidationError.java
- src/main/java/htsjdk/samtools/SamFileValidator.java
- src/main/java/htsjdk/samtools/SamFlagField.java
- src/main/java/htsjdk/samtools/SamInputResource.java
- src/main/java/htsjdk/samtools/SamReaderFactory.java
- + src/main/java/htsjdk/samtools/SecondaryAlignmentSkippingIterator.java
- src/main/java/htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.java
- src/main/java/htsjdk/samtools/cram/build/Cram2SamRecordFactory.java
- src/main/java/htsjdk/samtools/cram/build/Sam2CramRecordFactory.java
- src/main/java/htsjdk/samtools/cram/ref/EnaRefService.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/htsjdk/compare/8ec0970c1170e86972bbfa88f0bc513e96950c51...0fa566a17784405b9a78b7fdc1a673f2fccba59b

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View it on GitLab: https://salsa.debian.org/med-team/htsjdk/compare/8ec0970c1170e86972bbfa88f0bc513e96950c51...0fa566a17784405b9a78b7fdc1a673f2fccba59b
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