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

[Will McLaren]

Hi Duarte,

VCF headers are cached on $config->{headers}, which you should be able to
access in your plugin as $self->{config}->{headers}.

>From that you should be able to work out everything you need.

See the dbNSFP.pm plugin for an example of doing something similar.

Will


On 17 May 2013 13:46, Duarte Molha <Duarte.Molha at ogt.com> wrote:

> BTW Will****
>
> ** **
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> 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****
>
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>
> --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****
>
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> How to you think this would best be achieved?****
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> Thank you****
>
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>
> Duarte****
>
> ****
>
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> *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
> J****
>
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>
> Thanks for the fix****
>
> ** **
>
> Duarte****
>
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>
> ** **
>
> *From:* dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org<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.****
>
> ** **
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> 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.****
>
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>
> 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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>
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