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.
Merge pull request #13 from bigdatagenomics/new-variant

Cleaning up VCF<->ADAM pipeline