added ReferenceMapping for Genotype, filterByOverlappingRegion for GenotypeRDDFunctions

I think the general direction we're moving in (e.g., #469) is to require the API caller to provide input with valid mappings.

From a practical standpoint though, variants are meaningless without being anchored to a reference position. If you get to the point where you have variants without mappings attached to them, you've done something wrong.