[med-svn] [Git][med-team/milib][master] 8 commits: New upstream version 2.1.0+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / milib


Commits:
81930900 by Pierre Gruet at 2022-11-14T21:02:10+01:00
New upstream version 2.1.0+dfsg
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4bc5dd0a by Pierre Gruet at 2022-11-14T21:02:13+01:00
Update upstream source from tag 'upstream/2.1.0+dfsg'

Update to upstream version '2.1.0+dfsg'
with Debian dir abb268cfde3c40f694dc94a9624435d35548f53d
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124991fb by Pierre Gruet at 2022-11-14T21:06:15+01:00
Refreshing patches

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85e2b12e by Pierre Gruet at 2022-11-14T21:09:02+01:00
Refreshing d/copyright

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96d28ff6 by Pierre Gruet at 2022-11-14T21:10:29+01:00
Updating changelog

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8eb7a1ba by Pierre Gruet at 2022-11-14T21:11:07+01:00
Trim trailing whitespace.

Changes-By: lintian-brush
Fixes: lintian: trailing-whitespace
See-also: https://lintian.debian.org/tags/trailing-whitespace.html

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1fad29fb by Pierre Gruet at 2022-11-14T21:57:39+01:00
Patching out a flaky assertion in a test

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e638e10b by Pierre Gruet at 2022-11-14T21:57:56+01:00
Upload to unstable

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30 changed files:

- + .mi-ci/hooks/test-unit-before.sh
- build.gradle.kts
- debian/changelog
- debian/copyright
- debian/patches/build_gradle.patch
- + debian/patches/flaky_test.patch
- debian/patches/series
- init.sh
- − src/main/java/com/milaboratory/cli/ABaseCommand.java
- − src/main/java/com/milaboratory/cli/ACommand.java
- − src/main/java/com/milaboratory/cli/ACommandSimpleExport.java
- − src/main/java/com/milaboratory/cli/ACommandWithOutput.java
- − src/main/java/com/milaboratory/cli/ACommandWithSmartOverwrite.java
- − src/main/java/com/milaboratory/cli/ACommandWithSmartOverwriteWithSingleInput.java
- − src/main/java/com/milaboratory/cli/ActionConfiguration.java
- − src/main/java/com/milaboratory/cli/BinaryFileInfo.java
- − src/main/java/com/milaboratory/cli/BinaryFileInfoExtractor.java
- − src/main/java/com/milaboratory/cli/PipelineConfiguration.java
- − src/main/java/com/milaboratory/cli/PipelineConfigurationReader.java
- − src/main/java/com/milaboratory/cli/PipelineConfigurationWriter.java
- − src/main/java/com/milaboratory/cli/ValidationException.java
- src/main/java/com/milaboratory/core/PairedEndReadsLayout.java
- src/main/java/com/milaboratory/core/alignment/AffineGapAlignmentScoring.java
- src/main/java/com/milaboratory/core/alignment/AlignmentUtils.java
- src/main/java/com/milaboratory/core/alignment/BandedAffineAligner.java
- src/main/java/com/milaboratory/core/io/binary/AlignmentSerializer.java
- src/main/java/com/milaboratory/core/io/sequence/SequenceRead.java
- src/main/java/com/milaboratory/core/io/sequence/SingleRead.java
- src/main/java/com/milaboratory/core/io/sequence/fastq/SingleFastqReader.java
- src/main/java/com/milaboratory/core/merger/MismatchOnlyPairedReadMerger.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/milib/-/compare/6136ec0724f9953ca53fa355745534d35d049484...e638e10b9b48db2e7358e27827b3803987483c24

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View it on GitLab: https://salsa.debian.org/med-team/milib/-/compare/6136ec0724f9953ca53fa355745534d35d049484...e638e10b9b48db2e7358e27827b3803987483c24
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