On 10/13/17 3:32 PM, Hervé Pagès 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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