[ensembl-dev] VEP (ver78) TranscriptVariationAllele.pm unitialized value error with --hgvs enabled

[Sarah Hunt]

Hi Oliver,

Thanks for the detailed report. This was a similar issue with a stop 
inserted before the stop not being handled well. It is fixed in branch78 
so the consequence of the variant has changed from 'stop_gained' to 
'stop_retained'. The HGVS string reflects the synonymous status.

Best wishes,

Sarah


On 03/02/2015 16:52, Homann, Oliver wrote:
>
> Apologies, forgot to clarify that the error occurs in line 1221 of the 
> new version of TranscriptVariationAllele.pm:
>
>    1221 unless( $hgvs_notation->{ref} eq "-"){
>
>    1222 $hgvs_notation->{ref}  = 
> Bio::SeqUtils->seq3(Bio::PrimarySeq->new(-seq => 
> $hgvs_notation->{ref}, -id => 'ref',  -alphabet => 'protein')) || "";
>
>    1223   }
>
> Regards,
>
> Oliver
>
> *From:*dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] *On 
> Behalf Of *Homann, Oliver
> *Sent:* Tuesday, February 03, 2015 8:50 AM
> *To:* Ensembl developers list
> *Subject:* Re: [ensembl-dev] VEP (ver78) TranscriptVariationAllele.pm 
> unitialized value error with --hgvs enabled
>
> Hello Sarah,
>
> Your fix worked for all but one of my ‘uninitialized value’ errors.  
> Would you mind trying to track down the issue with this remaining 
> problematic entry?
>
> #CHROM POS        ID            REF         ALT         QUAL FILTER   
> INFO      FORMAT              SAMPLENAME
>
> 19 42355761             rs374945441       C CTAGAAA            
> 885.10   . 
> AC=1;AF=5.556e-03;AN=180;BaseQRankSum=-1.922e+00;DB;DP=2670;FS=2.561;GQ_MEAN=75.28;GQ_STDDEV=91.16;InbreedingCoeff=-0.0056;MLEAC=1;MLEAF=5.556e-03;MQ=60.00;MQ0=0;MQRankSum=-2.160e-01;NCC=0;QD=9.83;ReadPosRankSum=0.353;SOR=0.669 
> GT:AD:DP:GQ:PL              0/0:17,0:17:34:0,34,505
>
> Thanks,
>
> Oliver
>
>
>
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