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 
Hm, I do agree it should be alternateBase_s_ 

Could be referenceBase_s_ as well, but that might be more involved?  Want to bring that in with the indel stuff then?