[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.
Yea.... so this doesn't really solve your comment so I should leave in some place - this was just to MakeItWork so we aren't rebuilding it on every read.  I would rather something like the SlidingWindow was monitoring the reference region it covered.