Prevent annotating start_lost if start codon is retained in case of indels

[nakib103]

ENSVAR-5777

Test

Check ticket

Update on unit test

1. atg -> atGCAg - we still retain the start codon, hence we should return start_retained beside inframe_insertion
2. CATG -> CAT - there is another G after the deleted G (see here) , so we should have start_retained beside 5_prime_UTR_variant

[nuno-agostinho]

Hi @nakib103, I tested this PR with ClinVar VCF file, but it returns this error:

Can't call method "seq" on an undefined value at /hps/software/users/ensembl/repositories/nuno/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm line 1050.

You can reproduce the issue with the command:

perl vep --id "5 14664825 1462152 CA C" --database --db_version 111

It seems the issue may be related with $utr being undefined.

[nakib103]

Hi @nakib103, I tested this PR with ClinVar VCF file, but it returns this error:

Can't call method "seq" on an undefined value at /hps/software/users/ensembl/repositories/nuno/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm line 1050.

You can reproduce the issue with the command:

perl vep --id "5 14664825 1462152 CA C" --database --db_version 111

It seems the issue may be related with $utr being undefined.

Hi @nuno-agostinho , thanks , fixed it!

[nuno-agostinho]

Thanks @nakib103, looks good to me!

I will wait for the unit tests to finish before merging.

[nuno-agostinho]

Merged to main and release/113.