New genotype and somaticgenotype to store more intermediate statistics

- Added new CalledGenotype and CalledSomaticGenotype (and Kryo serializers) to save more intermediate variant calling information used for filtering

This also makes a distinctions between germline and somatic calls to the filters can be applied appropriately.  Part of breaking down #147 and is dependent on #162 
Yes, comment should be changed.  Since we ADAMGenotype -> Genotype, I just this class which represents a collection of bases (1 per chromosomes) to the Alleles.  They are very closely related, the distinction to me is GenotypeAlleles is the collection of bases that make up the Genotype, while CalledGenotype is the decision that this is the allele at this position in this specific sample.