Modifying conversion code to resolve #112.
Merge pull request #260 from fnothaft/sanity-check-flags

Modifying conversion code to resolve #112.
.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
Added comments to Vcf2FlatGenotype

Also, removed some extraneous imports.