[med-svn] [Git][med-team/snpeff][master] 2 commits: Import Upstream version 5.2.b+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / snpeff


Commits:
42370782 by Pierre Gruet at 2024-05-12T21:14:28+02:00
Import Upstream version 5.2.b+dfsg
- - - - -
50acaa15 by Andreas Tille at 2024-05-12T21:14:30+02:00
Import Debian changes 5.2.b+dfsg-1

snpeff (5.2.b+dfsg-1) unstable; urgency=medium
.
  [ Pierre Gruet ]
  * New upstream version
  * Refreshing patches
  * Changing the path to tests in the autopkgtest
  * Alleviating d/rules and correcting paths in the patches as build-time
    test .java files are now conveniently located under src/test
  * Removing now unused Lintian override
.
  [ Andreas Tille ]
  * Remove trailing whitespace in debian/copyright (routine-update)
  * Lintian-override for all source-is-missing issues
  * d/watch: fix download name

- - - - -


30 changed files:

- .vscode/launch.json
- + config/snpEff.ENSEMBL_110.config
- + config/snpEff.ENSEMBL_BFMPP_57.config
- + config/snpEff.bundles.ENSEMBL_BFMPP_57.config
- config/snpEff.config
- config/snpEff.dbs.config
- config/snpEff.test.config
- debian/changelog
- debian/patches/update_launching_script_and_config_file_for_Debian.patch
- debian/source/lintian-overrides
- debian/watch
- docs/download/index.html
- + docs/images/coverage_hitogram.png
- docs/index.html
- docs/sitemap.xml.gz
- docs/snpeff/faq/index.html
- docs/snpeff/inputoutput/index.html
- docs/snpeff/outputsummary/index.html
- docs/versions.txt
- galaxy/tool-data/snpEff_genomes.loc
- galaxy/tool-data/snpEff_genomes.loc.sample
- − pcingola_cleanup.xml
- − pcingola_formatter.xml
- src/bds/download/downloadEnsemblBulk.bds
- src/bds/download/downloadGenome.bds
- src/bds/download/downloadMane.bds
- src/bds/make.bds
- src/docs/download.md
- + src/docs/images/coverage_hitogram.png
- src/docs/index.md


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/compare/7db0d55baee06c00358acacdb7cd864cba604c33...50acaa15c4ab990f51f8e1cc4f31bdf99aebddbf

-- 
View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/compare/7db0d55baee06c00358acacdb7cd864cba604c33...50acaa15c4ab990f51f8e1cc4f31bdf99aebddbf
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