GenotypeAlleles takes referenceAllele at creation

- makes more sense than passing it in to all subsequent method calls
- will allow for generalizing to multiple alleles / multiple
  reference-base-sequences e.g. when supporting deletions
remove PileupElement.sequencedSingleBaseOpt

doesn't generalize well to an insertion-capable world, and isn't
really that useful anyway.
Merge pull request #174 from hammerlab/ga-refbase

GenotypeAlleles takes referenceAllele at creation