Debugging

Instead of only adding to the veterbi most-likely sequence, now
adds to each output function proportional to liklihood of being
in that state
Debugging

Changed the initialization again. Corrected the "old way" to account for
sequences rather than just the total set of samples. Also added
a line to the biohmm_parameter_Iteration_*.txt output that gives the
loglike at that iteration. This modification should be compatible with
previous parameter file parsing.