[ensembl-dev] bugs in TranscriptVariationAllele.pm and Conservation.pm plugin

[Will McLaren]

Hi Michael,

Thanks as always for the detailed bug report.

These are all fixed on CVS (for the API stuff) and GitHub (for the plugin).

Will
Ensembl Variation

On 13 September 2012 04:02, Michael Yourshaw <myourshaw at ucla.edu> wrote:
> Apologies for a possible duplicated message; the first version was bounced
> for being too long. This version omits output files.
>
> 1. In TranscriptVariationAllele.pm (CVS version of 2012-09-12) it is
> possible to have an undefined $hgvs_transcript-{type}, which causes this
> series of errors:
>
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 909, <GEN1> line 305.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 914, <GEN1> line 305.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 932, <GEN1> line 305.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 946, <GEN1> line 305.
> Use of uninitialized value in string eq at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 950, <GEN1> line 305.
>
> In the attached VCF file, 5:96101028 is an example of this error.
>
> 2. Also in TranscriptVariationAllele.pm
> $self->transcript_variation->cds_end() can be undefined, causing this error:
>
> Use of uninitialized value in substr at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
> line 1121, <GEN1> line 452.
>
> In the attached VCF file, 17:7186959 is an example of this error.
>
> 3. In the Conservation.pm VEP plugin with default parameters, @$scores == 0
> causes this error:
>
> Plugin 'Conservation' went wrong: Illegal division by zero at
> /share/apps/myourshaw/VEP_plugins/Conservation.pm line 168, <GEN1> line 137.
>
> In the attached VCF file, 21:34948695 is an example of this error.
>
>
>
> 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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