[med-svn] [Git][med-team/htsjdk][master] 22 commits: New upstream version 3.0.2+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / htsjdk


Commits:
7a5fc365 by Pierre Gruet at 2022-10-31T22:04:32+01:00
New upstream version 3.0.2+dfsg
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f11d315c by Pierre Gruet at 2022-10-31T22:05:22+01:00
Update upstream source from tag 'upstream/3.0.2+dfsg'

Update to upstream version '3.0.2+dfsg'
with Debian dir 4cbaa96de4b65c671f27165093a63e0f0592d5e3
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38c0a6f4 by Pierre Gruet at 2022-10-31T22:06:05+01:00
Refreshing patches

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83e969e3 by Pierre Gruet at 2022-10-31T22:06:57+01:00
Installing the javadoc in /usr/share/doc/libhtsjdk-java/

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b890d4b6 by Pierre Gruet at 2022-10-31T22:07:53+01:00
Updating the Lintian override related to embedded JS after a change in Lintian syntax

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538406b2 by Pierre Gruet at 2022-10-31T22:09:48+01:00
Updating the POM file and its signature

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c9287029 by Pierre Gruet at 2022-10-31T22:10:42+01:00
Depending on libmjson-java

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12037018 by Pierre Gruet at 2022-10-31T22:11:38+01:00
Patching for json-simple is not needed anymore

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5f7d2bf0 by Pierre Gruet at 2022-10-31T22:13:17+01:00
Passing long instead of int in HtsCRAMCodec30And21QueryTest

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b4b82f65 by Pierre Gruet at 2022-10-31T22:15:32+01:00
Excluding new tests requiring the network

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b142879e by Pierre Gruet at 2022-10-31T22:15:43+01:00
Refreshing patches

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034b9e8e by Pierre Gruet at 2022-10-31T22:17:02+01:00
Refreshing changelog

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10d705e7 by Pierre Gruet at 2022-11-01T17:17:24+01:00
Deactivating testFlushNotSpammed which seems to be GC-dependent

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b71473c1 by Pierre Gruet at 2022-11-01T17:17:43+01:00
Using rhino instead of nashorn as JS engine, to build against openjdk-17

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75a2158d by Pierre Gruet at 2022-11-01T17:18:14+01:00
Updating changelog

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f81d35ef by Pierre Gruet at 2022-11-01T17:19:02+01:00
Raising Standards version to 4.6.1

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67b9b998 by Pierre Gruet at 2022-11-01T17:19:50+01:00
Reordering changelog

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21811dc2 by Pierre Gruet at 2022-11-01T17:38:05+01:00
Upload to experimental

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91def6a7 by Pierre Gruet at 2022-11-01T21:00:25+01:00
Adding missing DEP-3 headers to patches

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6790144c by Pierre Gruet at 2022-11-01T21:01:15+01:00
Updating changelog

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99d0f9e2 by Pierre Gruet at 2022-11-03T20:52:51+01:00
Forwarding patches

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c3c6a7c7 by Pierre Gruet at 2022-11-03T20:55:06+01:00
Upload to unstable

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30 changed files:

- + .github/workflows/tests.yml
- .travis.yml
- README.md
- build.gradle
- debian/changelog
- debian/control
- debian/htsjdk.pom
- debian/htsjdk.pom.asc
- debian/libhtsjdk-java-doc.javadoc
- debian/libhtsjdk-java-doc.lintian-overrides
- debian/libhtsjdk-java.classpath
- debian/patches/120-fix-build.patch
- + debian/patches/130-data-types-in-tests.patch
- − debian/patches/130-use-json-simple-instead-of-mjson.patch
- + debian/patches/140-skip-testFlushNotSpammed.patch
- + debian/patches/150-use-rhino-as-JS-engine.patch
- − debian/patches/80-2to3.patch
- debian/patches/92-disable-testhttp.patch
- debian/patches/series
- 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


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/9c637b681a18bc9b953179d4447094eb45285b70...c3c6a7c73a8a1fa346070651ff23fe8885aa439b

-- 
View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/9c637b681a18bc9b953179d4447094eb45285b70...c3c6a7c73a8a1fa346070651ff23fe8885aa439b
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