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

[Duarte Molha]

BTW Will

I was thinking it would be very useful to create a plugin that could output to the annotation file, any fields from the input VCF file by declaring it explicitly as parameters.

Something like

--plugin vcf_fields_retrieval,INFO,FORMAT
Or
Less neatly
--plugin vcf_fields_retrieval,5,6,7

But in order to achieve this I would like to be able to:
In the 1st example, determine the field index position from the input name
Or in the 2nd example, determine the field name from the index position given and add that info in the get_header_info method

How to you think this would best be achieved?

Thank you

Duarte



From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Duarte Molha
Sent: 17 May 2013 13:34
To: Ensembl developers list
Subject: Re: [ensembl-dev] Question regarding plugin behavior under fork conditions in VEP

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> [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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