Fixes to all the HMM implementation and cleanup

* HMMs are now called Logless and Log10. These are the only two implementations.
* Logless should be the reference implementation for the CUDA/FPGA/Rootbeer implementation
* Log10 is the 'exact' implementation for comparison
* FourMatrices hmm had wrong transition probabilities (they weren't adding to one) because Tau was dependent on Di and Dd.
   * fixed it by moving Di and Dd to emission probabilities and reassigning all transition probabilities with no preference to any state.
* NoDel hmm was ignoring the case where a read's most likely alignment would end before the end of the haplotype. In fact it was ignoring all alignments that fell into that category (no matter how likely).
   * fixed it by summing over all independent observations of alignments that end in matches and insertions. They are now independent because they are no longer receiving the contribution from the deletion matrix.

Fixes to all implementation and code cleanup