.gitignore should _not_ ignore .vcf files
ADAMFlatGenotype is a smaller, flat, simpler version of a genotype schema.

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.
Changed the argument 'bamFile' to 'vcfFile' in Vcf2FlatGenotype