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.
Can this be simplified to
```c++
matrix->lnB[b] = C[2*b-1] + log(bval);
```