This was a consideration. I guess I've never got much use out of them being
DNAStringSets, so I just went with the simple character vectors. It makes
sense to support DNAStringSet. I could imagine someone e.g. wanting to
represent mutations at the protein-level, and structural variants will
require more complexity, but DNA is by far the most common use case. Are
you willing to submit this as a patch?

Just out of curiosity, how are you using Biostrings in this case?


On Mon, Nov 4, 2013 at 1:12 AM, Julian Gehring <julian.gehring@embl.de>wrote:

> Hi,
>
> Would it be reasonable to (optionally) allow storing the reference and
> alternative alleles in the 'VRanges' class as a 'DNAStringSet'? Currently,
> 'character' and 'Rle' are possible.  Having a 'DNAStringSet' would make it
> more consistent with the rest of the 'VariantAnnotation' framework and make
> use of the efficient 'Biostrings' string handling infrastructure.
>
> Best wishes
> Julian
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]

