Swap over to real pair hmm

Which is what we want, in any case. Only difference now is I don't have
to specify the two sequences on separate tracks.

Ended up nuking the multi track emissions stuff, which was how I did it
before... ain't gonna use it any time soon, anyway.

To run do eg

./stochhmm -seq bcell/seq.fa -model bcell/bcell.hmm -stochastic viterbi
-repetitions 1000