# This is a combination of 3 commits.
# The first commit's message is:
Cleaning up VCF<->ADAM pipeline. Added internal ADAM variant context, that handles the unification of the core variant standard with additional variant/genotype annotations. This variant context also handles the unification of unnested variant and genotype info. In addition to this, the VCF<->ADAM conversion pipeline was upgraded to use Hadoop-BAM/GATK's VariantContext code, to eliminate text parsing. Also, an adam2vcf command was added.

# This is the 2nd commit message:

Converting some of the Option() calls to Some(), where they look like they can be converted.

Carl and I ran into problems with this before, were the use of Option() actually broke other code, which was using an implicit ordering defined ... somewhere else now, I forget.  (Carl, do you remember?)

# This is the 3rd commit message:

Adding ability to convert genotypes to variants. Upgrading tests for rest of variant/genotype infrastructure.
Cleaning up VCF<->ADAM pipeline. Added internal ADAM variant context, that handles the unification of the core variant standard with additional variant/genotype annotations. This variant context also handles the unification of unnested variant and genotype info. In addition to this, the VCF<->ADAM conversion pipeline was upgraded to use Hadoop-BAM/GATK's VariantContext code, to eliminate text parsing. Also, an adam2vcf command was added to do conversion back. A feature to generate variant data from genotype data was suggested and implemented, along with a command.