That's great, thanks.
On Tue, Sep 24, 2013 at 12:16 PM, Valerie Obenchain <voben...@fhcrc.org>wrote: > Michael, > > This is implemented in 1.7.48. AD is expanded as a list matrix where each > list element holds a REF,ALT pair. > > Val > > > > On 09/05/2013 07:36 AM, Valerie Obenchain wrote: > >> Hi, >> >> On 09/04/2013 04:23 PM, Michael Lawrence wrote: >> >>> Hi, Val, >>> >>> I just fixed expand,VCF to support multiple 'A' columns in info. Looks >>> like >>> expand,DataFrame does a cartesian product of list columns, which is not >>> what we want in that case. >>> >> >> Thanks. >> >> >>> Ran up against another hurdle though: the conventional AD genotype field >>> has a (virtual) Number of 'A+1', but since VCF does not have such a >>> thing, >>> it's Number is typically missing. Should we special case this one and >>> have >>> it keep yield a ref,alt pair for each alt? Opinions? >>> >> >> At the moment I can't think of a better option. Looking around the 1000 >> Genomes page I didn't find other fields that had this 'ref + alt' >> length. So, implementing an option for the user to specify a field name >> and expansion type ... etc. seems like overkill. >> >> I'm fine with special casing it until more fields of this type come up. >> >> Val >> >> >>> Michael >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________**_________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/**listinfo/bioc-devel<https://stat.ethz.ch/mailman/listinfo/bioc-devel> >>> >>> >> ______________________________**_________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/**listinfo/bioc-devel<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
