Message-ID: <8ae46555-2e5b-d70e-3620-8373d27abbe1@u.washington.edu>
Date: 2017-10-13T23:00:51Z
From: Stephanie M. Gogarten
Subject: [Bioc-devel] BiocGenerics request
In-Reply-To: <59E13F0C.4090502@fredhutch.org>
On 10/13/17 3:32 PM, Herv? Pag?s wrote:
> Hi Stephanie,
>
> Can you provide a little bit more context? Have you observed
> conflicts between VariantAnnotation:::asVCF() and other asVCF()
> functions defined elsewhere? Any reason why you can't use/import
> VariantAnnotation:::asVCF() in your package?
I would prefer to leave VariantAnnotation in "Suggests" rather than
"Imports" for performance reasons - it adds substantially to package
load time, but will be used only rarely.
>
> Alternatively, have you considered using/defining a coercion method
> to VCF instead? That should work (and would be preferred) if you
> don't need the extra arguments that an "asVCF" method would allow
> you to support.
I will look into coercion methods; thanks for the suggestion! Can one
define a coercion method where the "to" class is in a package that's not
attached until the method is called (with requireNamespace)?
thanks,
Stephanie
>
> The VCF class is defined in the VariantAnnotation package so it
> would be weird to have the asVCF() generic in BiocGenerics.
>
> Cheers,
> H.
>
>
> On 10/13/2017 01:55 PM, Stephanie M. Gogarten wrote:
>> Can we move the "asVCF" generic to BiocGenerics?
>>
>> thanks,
>> Stephanie
>>
>> _______________________________________________
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>