[ensembl-dev] Possible bug in VEP(v73)

[saurabh gupta]

Dear Fiona,

Please do let me know if I am wrong.

--
Saurabh Gupta
Ganit Labs, Bangalore


On Fri, Oct 18, 2013 at 10:12 PM, Fiona Cunningham <fiona at ebi.ac.uk> wrote:

> Dear Saurabh,
>
> Many thanks for taking the time to report this to us. We will take a look.
>
> Best regards,
> Fiona
>
>
> ---------------------------------------------------------------------------------------------------------------
> Fiona Cunningham, Ensembl Coordinator, Ensembl Variation Project Leader.
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton,  CB10 1SD, UK
> www.ensembl.org || www.lrg-sequence.org || t: +44 1223 494612
>
>
> On 18 October 2013 07:22, saurabh gupta <saurabh at ganitlabs.in> wrote:
> > Hi,
> >
> > I had downloaded the standalone version of VEP(v73) and was using it
> > offline. When I tried using --hgvs with --offline I was getting an error:
> > "ERROR: Cannot generate HGVS coordinates in offline mode without a FASTA
> > file (see --fasta)". However I had specified the --fasta option as well.
> > After going through the code it seems the condition(line 954) is
> checking if
> > $config{fasta_db} is defined or not and throwing this error. In the code
> > $config{fasta_db} is initialized at a later stage, so it throws an error.
> >
> > I changed $config{fasta_db} to $config{fasta} on line 954(where the
> > condition is checked) in variant_effect_predictor.pl and it worked.
> >
> > You guys might want to incorporate/modify this in the code.
> >
> > --
> > Saurabh Gupta
> > Ganit Labs, Bangalore
> >
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