[med-svn] [Git][med-team/milib][master] 8 commits: routine-update: New upstream version

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / milib


Commits:
49df3ad1 by Steffen Moeller at 2020-06-13T21:31:54+02:00
routine-update: New upstream version

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03ca7e47 by Steffen Moeller at 2020-06-13T21:31:55+02:00
New upstream version 1.13
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079163b2 by Steffen Moeller at 2020-06-13T21:31:56+02:00
Update upstream source from tag 'upstream/1.13'

Update to upstream version '1.13'
with Debian dir 56d928ae73523651fb1efb8272b0dc30dac79b9f
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f9ab1e16 by Steffen Moeller at 2020-06-13T21:31:56+02:00
routine-update: Standards-Version: 4.5.0

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249c65e2 by Steffen Moeller at 2020-06-13T21:31:56+02:00
routine-update: debhelper-compat 13

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b96278bc by Steffen Moeller at 2020-06-13T21:32:30+02:00
routine-update: Add salsa-ci file

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fd519d64 by Steffen Moeller at 2020-06-13T21:32:30+02:00
routine-update: Rules-Requires-Root: no

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afc51608 by Steffen Moeller at 2020-06-13T21:40:54+02:00
Addressed FTBFS

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30 changed files:

- .gitignore
- CHANGELOG
- debian/changelog
- debian/control
- debian/patches/jaxb.patch
- + debian/patches/removeHostnameFromPomXml.patch
- debian/patches/series
- + debian/salsa-ci.yml
- init.sh
- pom.xml
- src/main/java/com/milaboratory/cli/ACommandWithSmartOverwriteWithSingleInput.java
- src/main/java/com/milaboratory/core/Range.java
- src/main/java/com/milaboratory/core/alignment/Alignment.java
- + src/main/java/com/milaboratory/core/alignment/AlignmentElement.java
- + src/main/java/com/milaboratory/core/alignment/AlignmentElementType.java
- src/main/java/com/milaboratory/core/alignment/kaligner1/KAlignerParameters.java
- src/main/java/com/milaboratory/core/sequence/AminoAcidSequence.java
- src/main/java/com/milaboratory/core/sequence/GeneticCode.java
- src/main/java/com/milaboratory/core/sequence/NucleotideSequence.java
- src/main/java/com/milaboratory/core/sequence/SequencesUtils.java
- src/main/java/com/milaboratory/core/sequence/Wildcard.java
- src/main/java/com/milaboratory/core/sequence/quality/QualityTrimmer.java
- src/main/java/com/milaboratory/core/sequence/quality/ReadTrimmerReport.java
- src/main/java/com/milaboratory/util/VersionInfo.java
- src/main/resources/parameters/kaligner_parameters.json → src/main/resources/parameters_resource/kaligner_parameters.json
- src/test/java/com/milaboratory/core/alignment/AlignmentTest.java
- src/test/java/com/milaboratory/core/motif/MotifUtilsTest.java
- + src/test/java/com/milaboratory/core/sequence/GeneticCodeTest.java
- src/test/java/com/milaboratory/core/sequence/NucleotideSequencesTest.java
- src/test/java/com/milaboratory/core/sequence/SequencesUtilsTest.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/milib/-/compare/65157c35b8cbe14928d7ff056b14cbb2ae96c779...afc51608b61ee2c15cabcf4eedbf2f9bd9ec6e9f

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View it on GitLab: https://salsa.debian.org/med-team/milib/-/compare/65157c35b8cbe14928d7ff056b14cbb2ae96c779...afc51608b61ee2c15cabcf4eedbf2f9bd9ec6e9f
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