8008235832
57%

Ran 22 Feb 2024 05:23PM UTC

Jobs 1

Files 76

Run time 7s

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Committed 22 Feb 2024 05:03PM UTC coverage: 80.998% (+0.2%) from 80.842%

Build # 8008235832

Build Type

push

github

Committed by

web-flow

Commit Message

update  agat_sp_add_start_and_stop.pl (#429)

* avoid disturbing AGAT message when codon table is not set by bioperl (Use of uninitialized value)

* deal with GTF stop out of CDS. Add option ni/na to avoid to interpret IUPAC code in codons. Add option to extend the sequence to find the next start/stop codon in the sequence if absent from the CDS

* update test to reflect add of option na/ni and -e/--extend

* OmniscientI: allow to parse omniscient (config sub-hash was not handled)

* OmniscientI: fix bug in check_exons where exon location was not necessarly updated if needed because the test @ was wrong because was not the number of location but the size of the location object. I took the opportunity to update that part of the code to be more concise and efficient

* avoid message [[ not found during CI

---------

Co-authored-by: Jacques Dainat <jacques.dainat@ird.fr>

Run Details

12131 of 14977 relevant lines covered (81.0%)

2134.96 hits per line

Jobs

ID	Job ID	Ran	Files	Coverage
1	8008235832.1	22 Feb 2024 05:23PM UTC	76	81.0	GitHub Action Run

NBISweden / AGAT / 8008235832
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