Compute some transition matrix terms in log-space

Hey @mjhubisz, here is a small pull request for your changes to calculate some transition terms in log-space.  Overall, this looks good and all tests continue pass.  I just have a few comments, which I wanted to share.
Could do
```c++
double c_term = (c > 0 ? exp(lnG4[b] + lnB[c-1]) : 0.0);
```