[WIP] Avoid computing the reference base and hanging on to md tag

This builds on #220.

Right now we keep the referenceBases and mdTag even though they contain the same information - if we have computed the referenceBase we no longer need the mdTag and the mdTag can be fairly large memory-wise.  However, it is useful currently to quickly check whether a pileup element is a match.  Instead we should pass in a reference base to each pileup a and pileup element

This is a bit clunky right now but wanted to hear thoughts on doing this or not.
hrm, so this is still just inferring the reference base somewhat arbitrarily from one of the reads each time, right?