[med-svn] [Git][med-team/milib][upstream] New upstream version 2.1.0+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch upstream at Debian Med / milib


Commits:
81930900 by Pierre Gruet at 2022-11-14T21:02:10+01:00
New upstream version 2.1.0+dfsg
- - - - -


30 changed files:

- + .mi-ci/hooks/test-unit-before.sh
- build.gradle.kts
- 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
- src/main/java/com/milaboratory/core/merger/PairedReadMergingResult.java
- src/main/java/com/milaboratory/core/sequence/IO.java
- + src/main/java/com/milaboratory/core/sequence/NSQTuple.java
- src/main/java/com/milaboratory/core/sequence/ShortSequenceSet.java
- src/main/java/com/milaboratory/core/sequence/quality/ReadTrimmerListener.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/milib/-/commit/81930900082229fc582f7871cca7e357807c94c0

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View it on GitLab: https://salsa.debian.org/med-team/milib/-/commit/81930900082229fc582f7871cca7e357807c94c0
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