[med-svn] [Git][med-team/htsjdk][upstream] New upstream version 2.14.3+dfsg

[Andreas Tille]

Andreas Tille pushed to branch upstream at Debian Med / htsjdk


Commits:
26feb9cc by Andreas Tille at 2018-03-28T14:18:36+02:00
New upstream version 2.14.3+dfsg
- - - - -


30 changed files:

- .gitignore
- build.gradle
- 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
- src/main/java/htsjdk/samtools/filter/NotPrimaryAlignmentFilter.java
- src/main/java/htsjdk/samtools/filter/ReadNameFilter.java
- src/main/java/htsjdk/samtools/filter/SecondaryAlignmentFilter.java
- src/main/java/htsjdk/samtools/filter/SecondaryOrSupplementaryFilter.java
- src/main/java/htsjdk/samtools/filter/TagFilter.java
- src/main/java/htsjdk/samtools/liftover/LiftOver.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/htsjdk/commit/26feb9cc4a546debcbd8191529e4135e210b964a

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View it on GitLab: https://salsa.debian.org/med-team/htsjdk/commit/26feb9cc4a546debcbd8191529e4135e210b964a
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