[ensembl-dev] errors in with incomplete_terminal_codon_variant

[Sarah Hunt]

 Hi Michael,

 Thanks for your detailed bug reports - we will investigate and get
back to you on each of them.

 Best wishes,

 Sarah


 On 5/23/12, Michael Yourshaw <myourshaw at ucla.edu> wrote:
> With Ensembl version 67, cvs download 2012-05-22 and VEP v 2.5, I’m getting
> a lot of errors in TranscriptVariationAllele.pm
>
> This is an example of an offending input VCF record:
> 5       96232565        incomplete_terminal_codon_variant       A       ACC
>    .       .       .       GT:AB:AD:DP:GQ:PL
> 0/1:0.88:36,5:41:77.58:78,0,611 1/1:.:0,5:5:12.01:111,12,0
>
> This record has 5 transcripts
>       ENST00000513084.1:c.1501_1502insCC
>       ENST00000379904.4:c.1366_1367insCC
>       ENST00000508077.1:c.488_489insCC
>       ENST00000510373.1:c.1501_1502insCC
>       ENST00000437043.3:c.1501_1502insCC
>
> All five transcripts cause this error:
>       Use of uninitialized value in numeric lt (<) at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 980, <GEN9> line 3.
>
> It looks like the error is actually caused by line 986
>       elsif( length($self->codon()) < 3 && $hgvs_notation->{type} ne "fs”){
> because $self->codon() returns undef when $allele_len=2 and $vf_nt_len=0
>
> Transcript ENST00000508077.1:c.488_489insCC causes two additional errors:
>       Use of uninitialized value in substitution (s///) at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 997, <GEN9> line 3.
>       Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 761, <GEN9> line 3.
>
> For this transcript, $hgvs_notation->{ref} = '' and $hgvs_notation->{alt}  =
> undef, which seems to cause these errors.
>
>
>
> ॐ
>
> Michael Yourshaw
> UCLA Geffen School of Medicine
> Department of Human Genetics, Nelson Lab
> 695 Charles E Young Drive S
> Gonda 5554
> Los Angeles CA 90095-8348 USA
> myourshaw at ucla.edu
> 970.691.8299
>
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