This commit consists of the rebase of all the work we've done for the va...

...riant schema, including:

1) New nested variant & annotation schema
2) Changes to generate VCF ADAM files with our schema from Neal
3) More comprehensive VCF conversion, including INFO fields from Michael
4) Output ADAMGenotypes, and not ADAMVariant from Neal
5) Sent varIsFiltered appropriately if FILTER is PASS or "." from Michael

Among many others