RE: making this class private to ADAM, I think that this is a good idea, but would note one downstream concern: it is useful to expose a method for converting an RDD of GATK VariantContexts to an RDD of AdamVariants. People who are building tools downstream may need to do this conversion—the big use case is if you have to open a pipe to/from an application that needs VCF. It'd probably be best to expose that via AdamRDDFunctions.