[med-svn] [Git][med-team/htsjdk][master] 12 commits: New upstream version 4.0.2+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / htsjdk


Commits:
0c5275b1 by Pierre Gruet at 2023-12-01T11:11:26+01:00
New upstream version 4.0.2+dfsg
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7b628377 by Pierre Gruet at 2023-12-01T11:12:03+01:00
Update upstream source from tag 'upstream/4.0.2+dfsg'

Update to upstream version '4.0.2+dfsg'
with Debian dir ef4fac6250e82a4d46952420f42906b7ec4351ea
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b7d9fcce by Pierre Gruet at 2023-12-14T09:36:30+01:00
Adding nashorn to maven.ignoreRules

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fff4e3dc by Pierre Gruet at 2023-12-14T09:38:28+01:00
Using mjson instead of unpackaged, non-DFSG-free org.json

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acdd91f9 by Pierre Gruet at 2023-12-14T09:44:55+01:00
Solving ambiguous assertions in the unit tests

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ebadccd8 by Pierre Gruet at 2023-12-14T09:45:17+01:00
Deactivating the tests for VCF 4.4 as this version of htsjdk does not handle them

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bdc3e0cc by Pierre Gruet at 2023-12-14T09:45:29+01:00
Refreshing patches

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404ae653 by Pierre Gruet at 2023-12-14T09:46:38+01:00
Updating changelog

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9debcd7e by Pierre Gruet at 2023-12-14T09:50:46+01:00
Forwarding patch

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fd067032 by Pierre Gruet at 2023-12-14T10:11:09+01:00
Adding getDebianVersion definition, deleted by mistake

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00c7f631 by Pierre Gruet at 2023-12-14T10:11:16+01:00
Refreshing patches

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23fb7f55 by Pierre Gruet at 2023-12-14T10:11:28+01:00
Upload to unstable

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30 changed files:

- .github/workflows/tests.yml
- README.md
- build.gradle
- debian/changelog
- + debian/maven.ignoreRules
- debian/maven.rules
- debian/patches/10-build.xml.patch
- debian/patches/100-fix-java11
- debian/patches/13-skip_network_tests
- debian/patches/150-use-rhino-as-JS-engine.patch
- + debian/patches/170-use-mjson.patch
- + debian/patches/180-ambiguous-assertions.patch
- + debian/patches/190-newest-vcf.patch
- debian/patches/20-fix-version.patch
- debian/patches/30-disable-scalatest.patch
- debian/patches/60-enable-tests
- debian/patches/90-disable-testftp.patch
- debian/patches/92-disable-testhttp.patch
- debian/patches/series
- src/main/java/htsjdk/beta/io/bundle/BundleJSON.java
- src/main/java/htsjdk/samtools/BamFileIoUtils.java
- src/main/java/htsjdk/samtools/Defaults.java
- src/main/java/htsjdk/samtools/SAMReadGroupRecord.java
- src/main/java/htsjdk/samtools/SAMRecord.java
- src/main/java/htsjdk/samtools/SAMRecordIterator.java
- src/main/java/htsjdk/samtools/SAMRecordSetBuilder.java
- src/main/java/htsjdk/samtools/SAMUtils.java
- src/main/java/htsjdk/samtools/SamFileValidator.java
- src/main/java/htsjdk/samtools/TextTagCodec.java
- src/main/java/htsjdk/samtools/cram/structure/Slice.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/1c6d7d612079f339f38df5a92ed15cce1a12fe47...23fb7f554be415c197b50701b6ed589aa483c672

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View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/1c6d7d612079f339f38df5a92ed15cce1a12fe47...23fb7f554be415c197b50701b6ed589aa483c672
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