[Bioc-devel] BiocGenerics request
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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