[GSoC] GSoC python variant update 6
Brad Chapman
chapmanb at 50mail.com
Mon Jul 2 10:36:39 UTC 2012
Lenna;
Thanks for the updates and thoughts. I like the direction you're moving
after taking everything you've learned from the SQL experiments.
My general suggestions would be:
- Leverage PyVCF for all of the backend parsing. We want to remain
compatible with this since merging/interfacing with the work James and
everyone is doing is a primary goal. Keeping a similar code structure
is a great way to facilitate this.
- For HGVS the general idea is to not be too tied to the VCF format, so
I wouldn't worry about strict compatibility but rather use it to inform
choices where you feel that things are mirroring VCF structure rather
than more general variant representation.
> Another question that may reveal my complete ignorance of haplotypes
> and such: could a polyploid site ever be partially phased? e.g. a
> triploid genotype of 0/1|0?
It's possible but this is kind of a fringe case right now so I wouldn't
especially worry about it.
Thanks again,
Brad
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