Hi Michael, Sure, I'll try to dig into it and construct a patch that adds this feature.
I stumbled upon this after converting data between the 'VCF' and 'VRanges' class. The primary use case I had in mind is having a more efficient storing and processing for short InDels, or defining variants by ref/alt alleles also with respect to the sequence context.
Best wishes Julian On 11/04/2013 12:56 PM, Michael Lawrence wrote:
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 <mailto: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 <mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/__listinfo/bioc-devel <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
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