[Bioc-devel] VariantAnnotation: DNAStringSets for ref/alt alleles in 'VRanges' class

Julian Gehring julian.gehring at embl.de
Mon Nov 4 14:24:46 CET 2013

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

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.gehring at embl.de
> <mailto:julian.gehring at 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
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