Currently, asking for HGVSg using offline and without FASTA, returns HGVSg using Ns as reference sequence. The correct behaviour would be to mimic what is done with HGVS and error out.
When accessing the database to retrieve sequence for HGVSg, a warning should be printed informing the user of such (like done for HGVS).
When retrieving sequence from database using --hgvs, the message is printed three times:
2024-09-03 13:25:00 - INFO: Database will be accessed when using --hgvs
2024-09-03 13:25:00 - INFO: Database will be accessed when using --hgvsc
2024-09-03 13:25:00 - INFO: Database will be accessed when using --hgvsp
As --hgvsc and --hgvsp are internal parameters (not VEP arguments), they should be omitted from the message.
Testing
vep --hgvsg --offline --cache $vep_cache --id "1 230710048 rs699 A G" --force should raise an error:
MSG: ERROR: Cannot generate HGVS coordinates (--hgvs and --hgvsg) in offline mode without a FASTA file (see --fasta)
vep --hgvsg --cache $vep_cache --id "1 230710048 rs699 A G" --force should warn that the database will be accessed to retrieve the sequence:
2024-09-03 13:21:27 - INFO: Database will be accessed when using --hgvsg
vep --hgvs --cache $vep_cache --id "1 230710048 rs699 A G" --force should only warn that the database is accessed to retrieve the sequence for --hgvs.
ENSVAR-3174
Changelog
Ns as reference sequence. The correct behaviour would be to mimic what is done with HGVS and error out.--hgvs, the message is printed three times:As
--hgvscand--hgvspare internal parameters (not VEP arguments), they should be omitted from the message.Testing
vep --hgvsg --offline --cache $vep_cache --id "1 230710048 rs699 A G" --forceshould raise an error:vep --hgvsg --cache $vep_cache --id "1 230710048 rs699 A G" --forceshould warn that the database will be accessed to retrieve the sequence:vep --hgvs --cache $vep_cache --id "1 230710048 rs699 A G" --forceshould only warn that the database is accessed to retrieve the sequence for--hgvs.