ADAMFlatGenotype is a smaller, flat version of a genotype schema

Includes a rewrite of a non-Tribble VCF parser, which parses (large) VCF files line-by-line and includes a converter into the ADAMFlatGenotype format itself.  

Also:
1. Added support for missing genotypes in the VCFLineConverter for ADAMFlatGenotype.
2. Added a ReferenceMapping for the ADAMFlatGenotype
3. the flat genotype converter uses multiple writers for smaller output files.
This should already be done, no? Is this needed because this is not a Spark command?