adamnovak/sequence-graphs — pull request #4 by fnothaft (2014-01-23 01:11:04+00:00)
Title: Adding exporter from sequence graph to VCF.

Added Graph->VCF exporter. I'm not 100% sure if this exporter handles all AlleleGroup situations properly. I need to double check that, but figured that it'd be better to get _mostly working_ code out in the wild earlier. Also, I noticed a few things from the import side:

* It seems like there may be an off-by error when numbering positions-I've noticed that we seem to be _slightly_ off when compared to the original VCF.
* If a sample is homozygous reference at a site, we don't need to create AlleleGroups for that site; we can instead prune those genotypes.
* We should look at how the reference data is stored in non-reference alleles. I added a bit in the schema for this, but don't think it is the best possible implementation.