[ensembl-dev] Question regarding plugin behavior under fork conditions in VEP

[Will McLaren]

Hi Duarte,

Now this was a weird bug!

Somehow the $vf->{_line} was getting overwritten with some $_ value from
the forking process communication handle.

Thanks for pointing it out, I've committed a fix to branch and head (in
VEP.pm), although I'm mildly concerned I don't fully understand why it was
happening.

Regards

Will


On 16 May 2013 15:56, Duarte Molha <duartemolha at gmail.com> wrote:

> Dear Developers
>
> I have created a simple plugin for VEP and adds to the annotation output
> file a few fields from an input VCF (namely the score and the the genotype
> fields for each processed individual.
>
> It seems to work fine if I do not fork the process but using fork it dies
> complaining about line
> 86.
>
> If it isn't too much trouble could you take a look and give me some hints
> why the $split_line[8] field might be undefined in the forked script? This
> should always be there because it is the genotype field of a VCF file and
> is included in all vcf lines.
>
> Best regards
>
> Duarte
>
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