[ensembl-dev] errors in with incomplete_terminal_codon_variant

[Sarah Hunt]

Hi Michael,

The three issues you raised have been fixed for version 67 in CVS and
an updated API tarball should be available next week.

Thanks for reporting these problems and do let us know if you find any
other issues.

Best wishes,

Sarah

On Thu, May 24, 2012 at 7:25 AM, Sarah Hunt <seh at ebi.ac.uk> wrote:
>  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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