That's great, thanks.


On Tue, Sep 24, 2013 at 12:16 PM, Valerie Obenchain <vobencha@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
>>>
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>
>

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