[med-svn] [Git][med-team/htsjdk][upstream] New upstream version 2.18.2+dfsg

[Andreas Tille]

Andreas Tille pushed to branch upstream at Debian Med / htsjdk


Commits:
cfc2c703 by Andreas Tille at 2019-01-24T16:31:37Z
New upstream version 2.18.2+dfsg
- - - - -


30 changed files:

- 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
- + src/main/java/htsjdk/samtools/cram/encoding/ByteArrayLenCodec.java
- src/main/java/htsjdk/samtools/cram/encoding/ByteArrayLenEncoding.java
- + src/main/java/htsjdk/samtools/cram/encoding/CRAMCodec.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/htsjdk/commit/cfc2c703ab904b6cdca5e2b2e5b91e3a0a55ccf5

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View it on GitLab: https://salsa.debian.org/med-team/htsjdk/commit/cfc2c703ab904b6cdca5e2b2e5b91e3a0a55ccf5
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