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

[Michael Yourshaw]

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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