generalize Alleles to contain refBases & altBases

this PR includes indel code and some refactorings of `Pileup`s, `GenotypeAlleles`, and others to support a universal notion of an `Allele` that is determined by multiple reference bases and multiple sequence bases.

I back-ported existing callers to be more general of their handling of variants/alleles, accordingly.

This should let us reuse a lot of @arahuja's bayesian/log-odds variant-analysis/filtering code across callers more easily.