[med-svn] [Git][med-team/snpeff][upstream] New upstream version 5.4.b+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch upstream at Debian Med / snpeff


Commits:
1b65ffe4 by Pierre Gruet at 2026-02-21T12:20:37+01:00
New upstream version 5.4.b+dfsg
- - - - -


65 changed files:

- .classpath
- + CLAUDE.md
- + TO_DO.md
- config/snpEff.config
- config/snpEff.core.config
- + config/v5.4a/covid.txt
- + config/v5.4a/md5.txt
- + config/v5.4a/sars_covid_genome_ids.txt
- + config/v5.4a/snpEff.ENSEMBL_105.config
- + config/v5.4a/snpEff.ENSEMBL_110.config
- config/snpEff.ENSEMBL_112.config → config/v5.4a/snpEff.ENSEMBL_112.config
- + config/v5.4a/snpEff.ENSEMBL_75.config
- + config/v5.4a/snpEff.ENSEMBL_99.config
- + config/v5.4a/snpEff.ENSEMBL_BFMPP_46.config
- + config/v5.4a/snpEff.ENSEMBL_BFMPP_52.config
- + config/v5.4a/snpEff.ENSEMBL_BFMPP_57.config
- + config/v5.4a/snpEff.FLYBASE_FB2021_06.config
- + config/v5.4a/snpEff.FLYBASE_FB2022_02.config
- + config/v5.4a/snpEff.NCBI.empty.config
- + config/v5.4a/snpEff.UCSC.config
- + config/v5.4a/snpEff.bundles.ENSEMBL_BFMPP_57.config
- + config/v5.4a/snpEff.config
- + config/v5.4a/snpEff.core.config
- + config/v5.4a/snpEff.covid19.config
- + config/v5.4a/snpEff.custom_requests.config
- + config/v5.4a/snpEff.dbs.config
- + config/v5.4a/snpEff.test.config
- + config/v5.4a/snpEff.version.5.0.config
- docs/download/index.html
- docs/examples/index.html
- docs/index.html
- docs/snpeff/additionalann/index.html
- docs/snpeff/build_db/index.html
- docs/snpeff/commands/index.html
- docs/snpeff/introduction/index.html
- docs/snpeff/running/index.html
- docs/snpsift/dbnsfp/index.html
- docs/versions.txt
- galaxy/tool-data/snpEff_genomes.loc
- galaxy/tool-data/snpEff_genomes.loc.sample
- + papers/.DS_Store
- + papers/aws-open-data/aws-open-data-agreement-signed.png
- + papers/aws-open-data/snpeff.yaml
- pom.xml
- scripts_build/make.sh
- src/bds/config.bds
- src/bds/dbNsfp.bds
- src/bds/download/download.bds
- src/bds/download/downloadHumanDb.bds
- src/bds/make.bds
- src/docs/download.md
- src/docs/examples.md
- src/docs/index.md
- src/docs/snpeff/additionalann.md
- src/docs/snpeff/build_db.md
- src/docs/snpeff/commands.md
- src/docs/snpeff/introduction.md
- src/docs/snpeff/running.md
- src/docs/snpsift/dbnsfp.md
- src/main/java/org/snpeff/SnpEff.java
- src/main/java/org/snpeff/snpEffect/Config.java
- src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdDownload.java
- src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java
- − test_04_TestCasesEff.csv
- − test_04_TestCasesEff.genes.txt


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/commit/1b65ffe42141368ab90c98f61fa444f5efb891dd

-- 
View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/commit/1b65ffe42141368ab90c98f61fa444f5efb891dd
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20260221/af35b518/attachment.htm>