added ReferenceMapping for Genotype, filterByOverlappingRegion for GenotypeRDDFunctions

Also, variants are not nullable in the [genotype schema](https://github.com/bigdatagenomics/bdg-formats/blob/master/src/main/resources/avro/bdg.avdl):

```
record Genotype {
  /**
   The variant called at this site.
   */
  Variant variant;
```