[Bioc-devel] seqnames as a candidate for BiocGenerics

[Nicolas Delhomme]

Hej Michael and Hervé!

Importing from GenomeInfoDb is what I do at the moment. I will have to check more extensively - adding more unit tests - but it seems to work so far, without "depending" on IRanges - thanks Michael I'll keep that in mind while testing.

I just had the understanding that if many packages needed the same generic, such generics were candidates for being ported to BiocGenerics simply because it would be more consistent to have them in BiocGenerics; that's all. But I also understand the cons and importing from GenomeInfoDb is certainly the path of least resistance ;-)

Thanks for the feedback, I'll come back to you if the point raised by Michael occurs.

Cheers,

Nico

---------------------------------------------------------------
Nicolas Delhomme

The Street Lab
Department of Plant Physiology
Umeå Plant Science Center

Tel: +46 90 786 5478
Email: nicolas.delhomme at umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
---------------------------------------------------------------

> On 27 Apr 2015, at 20:22, Michael Lawrence <lawrence.michael at gene.com> wrote:
> 
> Probably because that would mean genomeIntervals depending on IRanges. Because GenomeInfoDb needs CompressedList.
> 
> On Mon, Apr 27, 2015 at 11:14 AM, Hervé Pagès <hpages at fredhutch.org> wrote:
> Hi Nico,
> 
> On 04/26/2015 09:58 AM, Nicolas Delhomme wrote:
> Hej Hervé (I guess)!
> 
> Could it be possible to move the generic from "seqnames" and "seqnames<-" from GenomeInfoDb to BiocGenerics? I would then deprecate the "seq_name" and "seq_name<-" functions of the genomeIntervals package and import them in the easyRNASeq package.
> 
> I guess I could.
> 
> However I want to make it clear that a generic function doesn't have
> to go to BiocGenerics before it can be shared across packages. There
> are situations where this kind of move actually helps to resolve
> conflicts but it doesn't seem to be the case here. Any reason why
> you can't just import GenomeInfoDb? This is what all the packages that
> need the "seqnames" and "seqnames<-" generics currently do. Moving
> these generics to BiocGenerics will likely break many of them.
> 
> Thanks,
> H.
> 
> 
> Cheers,
> 
> Nico
> 
> ---------------------------------------------------------------
> Nicolas Delhomme
> 
> The Street Lab
> Department of Plant Physiology
> Umeå Plant Science Center
> 
> Tel: +46 90 786 5478
> Email: nicolas.delhomme at umu.se
> SLU - Umeå universitet
> Umeå S-901 87 Sweden
> ---------------------------------------------------------------
> 
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> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
> 
> 
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