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ENSVAR-6654 & ENSVAR-6381 #1149

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ENSVAR-6654 & ENSVAR-6381 #1149

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aba935b
consequence fix
olaaustine Jan 31, 2025
5a5fedf
Removing an unneccessary change
olaaustine Jan 31, 2025
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6 changes: 3 additions & 3 deletions modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -1346,10 +1346,10 @@ sub ref_eq_alt_sequence {

my $final_stop_length = length($final_stop) if defined($final_stop) ne '';

# 1 is if the ref_pep and the first letter of the alt_pep is the same and the alt_pep has * in it
# 1 is if the ref_pep and the first letter of the alt_pep is the same and the alt_pep has * in it, lot of bug complaints with this step.
# 2 is the ref_seq eq $mut_substring and the final stop length is less than 3
# 3 is * in ref_pep and the same index position exists for both the ref and alt pep
return 1 if ( ($ref_pep eq substr($alt_pep, 0, 1) && $alt_pep =~ /\*/) ||
# 3 is * in ref_pep and the same index position exists for both the ref and alt pep
return 1 if (
($ref_seq eq $mut_substring && defined($final_stop_length) && $final_stop_length < 3) || ( $ref_pep =~ /\*/ && (index($ref_pep, "*") + 1 == index($alt_pep, "*") + 1) ));
return 0;
}
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