Apply reference base read quality to Deletions

also some misc cleanups
I think I was actually interested in handling the case where normal has a mutation and tumor doesn't as a somatic variant, hence I didn't want to only operate when tumor had a variant.

Since that's probably exceedingly rare, I'll put the optimization back in, unless you feel otherwise.

If we add a first pass that restricts to loci where only one of the two has a variant, then we could remove the tumor-variant restriction without adding work.