Low level optimizations

[mortonjt]

Right now, our optimization scheme is pretty dumb - its just iterating through the microbial reads one at a time.

This can be drastically speed up (likely 100-1000x faster) if all of the reads for a single microbe were considered in a single step. This should yield identical results since the sum of Gamma/Poisson RVs is still Gamma/Poisson.