[med-svn] [Git][med-team/htsjdk][master] 7 commits: New upstream version 3.0.5+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / htsjdk


Commits:
e0310ee7 by Pierre Gruet at 2023-06-13T22:25:49+02:00
New upstream version 3.0.5+dfsg
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52fec292 by Pierre Gruet at 2023-06-13T22:26:35+02:00
Update upstream source from tag 'upstream/3.0.5+dfsg'

Update to upstream version '3.0.5+dfsg'
with Debian dir 58426d7777d6b4d15c639d7e64eeac553979d751
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8bd01c59 by Pierre Gruet at 2023-06-13T23:46:51+02:00
Refreshing patches, grouping some of them

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c3a8d698 by Pierre Gruet at 2023-06-13T23:47:22+02:00
Refreshing patches

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78623283 by Pierre Gruet at 2023-06-14T23:45:10+02:00
Skipping more tests needing the network

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db0cbd42 by Pierre Gruet at 2023-06-14T23:45:36+02:00
Updating changelog

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1a276af4 by Pierre Gruet at 2023-06-20T14:46:20+02:00
Upload to unstable

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30 changed files:

- README.md
- build.gradle
- debian/changelog
- debian/patches/10-build.xml.patch
- debian/patches/100-fix-java11
- − debian/patches/110-debian-lib-version.patch
- − debian/patches/120-fix-build.patch
- debian/patches/13-skip_network_tests
- debian/patches/150-use-rhino-as-JS-engine.patch
- debian/patches/20-fix-version.patch
- debian/patches/30-disable-scalatest.patch
- − debian/patches/40-fix-java9
- debian/patches/60-enable-tests
- debian/patches/70-removesometests-testng.patch
- debian/patches/90-disable-testftp.patch
- debian/patches/92-disable-testhttp.patch
- − debian/patches/disable-network-tests.diff
- debian/patches/series
- gradle/spotbugs-exclude.xml
- gradle/wrapper/gradle-wrapper.properties
- gradlew
- − scripts/checkScalaAndJavaFiles.sh
- src/main/java/htsjdk/samtools/Cigar.java
- src/main/java/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.java
- src/main/java/htsjdk/variant/vcf/VCFEncoder.java
- src/test/java/htsjdk/HtsjdkTest.java
- src/test/java/htsjdk/samtools/CRAMReferencelessTest.java
- src/test/java/htsjdk/samtools/CigarTest.java
- src/test/java/htsjdk/samtools/cram/structure/CRAMRecordTestHelper.java
- src/test/java/htsjdk/variant/vcf/VCFEncoderTest.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/98fddc5949e96a26c4a13ace7e10a3ee32a5480f...1a276af47f19c0746d67e7c29fe27187a5f50171

-- 
View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/98fddc5949e96a26c4a13ace7e10a3ee32a5480f...1a276af47f19c0746d67e7c29fe27187a5f50171
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