[ensembl-dev] VEP - TranscriptVariationAllele.pm errors

[Sarah Hunt]

Hi Stuart,

Hope all goes well with you! Do you have any input you can share to help
debug this one?

Sarah

On Wed, May 8, 2013 at 12:02 PM, Stuart Meacham <sm766 at cam.ac.uk> wrote:

> Hi,
>
> When using the VEP (Ensembl 71) with apparently well formed data I am
> getting some errors generated by the above mentioned module. It appears
> $hgvs_notation->{type} is queried when not defined at several locations in
> the module. I am using the 'ensembl' data format as input and outputting a
> vcf with the --everything flag. The VEP is producing output for all 715
> records provided. The errors are for locations on ch1 and chrX.
>
> For reference:
>
> Use of uninitialized value in string eq at /home/sm766/src/vep/variant_**
> effect_predictor/Bio/EnsEMBL/**Variation/**TranscriptVariationAllele.pm
> line 934.
> Use of uninitialized value in string eq at /home/sm766/src/vep/variant_**
> effect_predictor/Bio/EnsEMBL/**Variation/**TranscriptVariationAllele.pm
> line 938.
> Use of uninitialized value in string eq at /home/sm766/src/vep/variant_**
> effect_predictor/Bio/EnsEMBL/**Variation/**TranscriptVariationAllele.pm
> line 976.
> Use of uninitialized value in string eq at /home/sm766/src/vep/variant_**
> effect_predictor/Bio/EnsEMBL/**Variation/**TranscriptVariationAllele.pm
> line 984.
> Use of uninitialized value in string eq at /home/sm766/src/vep/variant_**
> effect_predictor/Bio/EnsEMBL/**Variation/**TranscriptVariationAllele.pm
> line 753.
> Use of uninitialized value in string eq at /home/sm766/src/vep/variant_**
> effect_predictor/Bio/EnsEMBL/**Variation/**TranscriptVariationAllele.pm
> line 769.
> Use of uninitialized value in string eq at /home/sm766/src/vep/variant_**
> effect_predictor/Bio/EnsEMBL/**Variation/**TranscriptVariationAllele.pm
> line 775.
> Use of uninitialized value in string eq at /home/sm766/src/vep/variant_**
> effect_predictor/Bio/EnsEMBL/**Variation/**TranscriptVariationAllele.pm
> line 775.
> Use of uninitialized value in string eq at /home/sm766/src/vep/variant_**
> effect_predictor/Bio/EnsEMBL/**Variation/**TranscriptVariationAllele.pm
> line 806.
> Use of uninitialized value in string eq at /home/sm766/src/vep/variant_**
> effect_predictor/Bio/EnsEMBL/**Variation/**TranscriptVariationAllele.pm
> line 825.
>
> Thanks
>
> Stuart
>
>
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