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

Duarte Molha Duarte.Molha at ogt.com
Fri May 17 13:34:04 BST 2013


Well ... At least I am glad it is not my plugin coding ineptitude causing it :)

Thanks for the fix

Duarte


From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
Sent: 17 May 2013 12:43
To: Ensembl developers list
Subject: Re: [ensembl-dev] Question regarding plugin behavior under fork conditions in VEP

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<mailto: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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