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