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.gehr...@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]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
