Is c_pos suppose to match negative numbers in vcf2maf.pl ?
kimin0402 opened this issue · 0 comments
kimin0402 commented
Hi, I'm not a perl expert, but was looking through the script and found this part to be a little bit odd.
In the script vcf2maf.pl line 755-759 it goes
# Fix HGVSp_Short, CDS_position, and Protein_position for splice acceptor/donor variants
if( $effect{One_Consequence} =~ m/^(splice_acceptor_variant|splice_donor_variant)$/ ) {
my ( $c_pos ) = $effect{HGVSc} =~ m/^c.(\d+)/;
if( defined $c_pos ) {
$c_pos = 1 if( $c_pos < 1 ); # Handle negative cDNA positions used in 5' UTRs
I think c_pos is suppose to match both positive and negative numbers but it seems like it can only match positive numbers. Shouldn't it be something like c.(-?\d+)
?
I was trying to process HGVSc output like "c.-64+1G>A", and ended up in this github repo.
I'm sorry if my question was out from my ignorance of perl.
Thank you.