[med-svn] [Git][med-team/htsjdk][upstream] New upstream version 3.0.2+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch upstream at Debian Med / htsjdk


Commits:
7a5fc365 by Pierre Gruet at 2022-10-31T22:04:32+01:00
New upstream version 3.0.2+dfsg
- - - - -


30 changed files:

- + .github/workflows/tests.yml
- .travis.yml
- README.md
- build.gradle
- scripts/explain_sam_flags.py
- scripts/htsget-scripts/htsget_config.json
- scripts/htsget-scripts/start-htsget-test-server.sh
- scripts/install-samtools.sh
- + src/main/java/htsjdk/annotations/BetaAPI.java
- + src/main/java/htsjdk/annotations/InternalAPI.java
- + src/main/java/htsjdk/beta/codecs/hapref/fasta/FASTACodecV1_0.java
- + src/main/java/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.java
- + src/main/java/htsjdk/beta/codecs/package-info.java
- + src/main/java/htsjdk/beta/codecs/reads/ReadsCodecUtils.java
- + src/main/java/htsjdk/beta/codecs/reads/bam/BAMCodec.java
- + src/main/java/htsjdk/beta/codecs/reads/bam/BAMDecoder.java
- + src/main/java/htsjdk/beta/codecs/reads/bam/BAMDecoderOptions.java
- + src/main/java/htsjdk/beta/codecs/reads/bam/BAMEncoder.java
- + src/main/java/htsjdk/beta/codecs/reads/bam/BAMEncoderOptions.java
- + src/main/java/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMCodecV1_0.java
- + src/main/java/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMDecoderV1_0.java
- + src/main/java/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMEncoderV1_0.java
- + src/main/java/htsjdk/beta/codecs/reads/cram/CRAMCodec.java
- + src/main/java/htsjdk/beta/codecs/reads/cram/CRAMDecoder.java
- + src/main/java/htsjdk/beta/codecs/reads/cram/CRAMDecoderOptions.java
- + src/main/java/htsjdk/beta/codecs/reads/cram/CRAMEncoder.java
- + src/main/java/htsjdk/beta/codecs/reads/cram/CRAMEncoderOptions.java
- + src/main/java/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMCodecV2_1.java
- + src/main/java/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMDecoderV2_1.java
- + src/main/java/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMEncoderV2_1.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/commit/7a5fc365f8101979b0d3763c34c6077e2cf8541e

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View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/commit/7a5fc365f8101979b0d3763c34c6077e2cf8541e
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