[med-svn] [Git][med-team/htsjdk][master] 12 commits: New upstream version 4.1.3+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / htsjdk


Commits:
386fe92f by Pierre Gruet at 2024-10-09T09:45:19+02:00
New upstream version 4.1.3+dfsg
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32e940dc by Pierre Gruet at 2024-10-09T09:46:05+02:00
Update upstream source from tag 'upstream/4.1.3+dfsg'

Update to upstream version '4.1.3+dfsg'
with Debian dir d28aea167091cac9ac94e4b8fe3b70eb30a72d9a
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9eb962a3 by Pierre Gruet at 2024-12-26T21:41:58+01:00
Refreshing patches

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05a568a1 by Pierre Gruet at 2024-12-26T21:42:55+01:00
Using libjson-java instead of mjson to replace non-free org.json

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2e64792f by Pierre Gruet at 2024-12-26T21:43:10+01:00
Updating Maven rules

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8c086fbb by Pierre Gruet at 2024-12-26T21:44:07+01:00
Removing a test file that seems to be unreadable

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095c9999 by Pierre Gruet at 2024-12-26T21:45:27+01:00
Changing date format in patch 10

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4d9a7192 by Pierre Gruet at 2024-12-26T21:48:42+01:00
Removing old mjson patch from d/p/series

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3bac8806 by Pierre Gruet at 2024-12-26T21:56:40+01:00
Polishing header of patch 171

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2f542a56 by Pierre Gruet at 2024-12-26T21:56:52+01:00
Updating changelog

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086d2014 by Pierre Gruet at 2024-12-26T23:44:52+01:00
Cleaning test file only if it is at the root currently

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4a58db42 by Pierre Gruet at 2024-12-26T23:45:04+01:00
Upload to unstable

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30 changed files:

- build.gradle
- debian/changelog
- debian/control
- debian/maven.rules
- debian/patches/10-build.xml.patch
- debian/patches/100-fix-java11
- debian/patches/150-use-rhino-as-JS-engine.patch
- − debian/patches/170-use-mjson.patch
- + debian/patches/171-use-org-kordamp-json.patch
- − debian/patches/180-ambiguous-assertions.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
- debian/rules
- gradle/wrapper/gradle-wrapper.properties
- gradlew
- scripts/install-samtools.sh
- src/main/java/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.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/BAMEncoder.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/CRAMEncoder.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/5532e2d62b6fed55df6d713bf1d753624bc8344c...4a58db4251b844adac96f61ee2c8dd6d2767318d

-- 
View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/5532e2d62b6fed55df6d713bf1d753624bc8344c...4a58db4251b844adac96f61ee2c8dd6d2767318d
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