[ensembl-dev] VEP 2.5 regex error in TranscriptVariationAllele.pm

[Sarah Hunt]

Hi Michael,

Thanks for reporting this one. It is fixed in branch 67 now.

Best wishes,

Sarah

On Tue, Jun 12, 2012 at 2:45 AM, Michael Yourshaw <myourshaw at ucla.edu> wrote:
> VCF input line:
> 19 42355761 . C CTAGAAA 2917.84 PASS
> AC=2;AF=0.0076;AN=264;DP=11854;HRun=0;set=variant3-variant GT:AD:DP:GQ:PL
> ...
>
> in TranscriptVariationAllele.pm sub _check_for_peptide_duplication{
>
> $self->{peptide} = ‘*K'
> $hgvs_notation->{alt} = ‘*K’
>
> error at line 1206 if($upstream_trans =~/$hgvs_notation->{alt}$/){
>
> Quantifier follows nothing in regex; marked by <-- HERE in m/* <-- HERE K$/
> at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 1206, <GEN1> line 127.
>
>
> ॐ
>
> Michael Yourshaw
>
> UCLA Geffen School of Medicine
> Department of Human Genetics, Nelson Lab
> 695 Charles E Young Drive S
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> myourshaw at ucla.edu
>
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>
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