[med-svn] [Git][med-team/htsjdk][master] 7 commits: New upstream version 2.18.2+dfsg

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / htsjdk


Commits:
cfc2c703 by Andreas Tille at 2019-01-24T16:31:37Z
New upstream version 2.18.2+dfsg
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7c0ed1d7 by Andreas Tille at 2019-01-24T16:31:54Z
Update upstream source from tag 'upstream/2.18.2+dfsg'

Update to upstream version '2.18.2+dfsg'
with Debian dir ca808595f9f055f14050c5b580336d07292c24c3
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a45660a7 by Andreas Tille at 2019-01-24T16:31:54Z
New upstream version

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e04f60b1 by Andreas Tille at 2019-01-24T16:31:54Z
debhelper 12

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2a8bb89c by Andreas Tille at 2019-01-24T16:31:56Z
Standards-Version: 4.3.0

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012f16c3 by Andreas Tille at 2019-01-24T16:31:58Z
Remove trailing whitespace in debian/changelog

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3b36bbcf by Andreas Tille at 2019-01-24T16:48:40Z
Cleanup changelog

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30 changed files:

- debian/changelog
- debian/compat
- debian/control
- src/main/java/htsjdk/samtools/BAMFileReader.java
- + src/main/java/htsjdk/samtools/BAMSBIIndexer.java
- src/main/java/htsjdk/samtools/CRAMIterator.java
- src/main/java/htsjdk/samtools/SAMSequenceRecord.java
- src/main/java/htsjdk/samtools/SAMUtils.java
- + src/main/java/htsjdk/samtools/SBIIndex.java
- + src/main/java/htsjdk/samtools/SBIIndexWriter.java
- src/main/java/htsjdk/samtools/SamReaderFactory.java
- src/main/java/htsjdk/samtools/SamStreams.java
- src/main/java/htsjdk/samtools/apps/TimeChannel.java
- src/main/java/htsjdk/samtools/apps/TimeRandomAccessFile.java
- src/main/java/htsjdk/samtools/cram/build/CompressionHeaderFactory.java
- src/main/java/htsjdk/samtools/cram/build/ContainerFactory.java
- src/main/java/htsjdk/samtools/cram/build/CramIO.java
- src/main/java/htsjdk/samtools/cram/io/ExternalCompression.java → src/main/java/htsjdk/samtools/cram/compression/ExternalCompression.java
- src/main/java/htsjdk/samtools/cram/encoding/ExternalCompressor.java → src/main/java/htsjdk/samtools/cram/compression/ExternalCompressor.java
- src/main/java/htsjdk/samtools/cram/encoding/rans/Constants.java → src/main/java/htsjdk/samtools/cram/compression/rans/Constants.java
- src/main/java/htsjdk/samtools/cram/encoding/rans/D04.java → src/main/java/htsjdk/samtools/cram/compression/rans/D04.java
- src/main/java/htsjdk/samtools/cram/encoding/rans/D14.java → src/main/java/htsjdk/samtools/cram/compression/rans/D14.java
- src/main/java/htsjdk/samtools/cram/encoding/rans/Decoding.java → src/main/java/htsjdk/samtools/cram/compression/rans/Decoding.java
- src/main/java/htsjdk/samtools/cram/encoding/rans/E04.java → src/main/java/htsjdk/samtools/cram/compression/rans/E04.java
- src/main/java/htsjdk/samtools/cram/encoding/rans/E14.java → src/main/java/htsjdk/samtools/cram/compression/rans/E14.java
- src/main/java/htsjdk/samtools/cram/encoding/rans/Encoding.java → src/main/java/htsjdk/samtools/cram/compression/rans/Encoding.java
- src/main/java/htsjdk/samtools/cram/encoding/rans/Frequencies.java → src/main/java/htsjdk/samtools/cram/compression/rans/Frequencies.java
- src/main/java/htsjdk/samtools/cram/encoding/rans/RANS.java → src/main/java/htsjdk/samtools/cram/compression/rans/RANS.java
- src/main/java/htsjdk/samtools/cram/encoding/rans/Utils.java → src/main/java/htsjdk/samtools/cram/compression/rans/Utils.java
- − src/main/java/htsjdk/samtools/cram/encoding/BitCodec.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/htsjdk/compare/d98b433135cf59e0060288b4075bfa3ed55f9d13...3b36bbcfc8c0e131f5292530a2da483803aa9b88

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View it on GitLab: https://salsa.debian.org/med-team/htsjdk/compare/d98b433135cf59e0060288b4075bfa3ed55f9d13...3b36bbcfc8c0e131f5292530a2da483803aa9b88
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