Precompute pairhmm cell probs

[johanneskoester]

This PR introduces precomputed miscall probabilities into pairHMM computation. By that, we should save maybe 20 cycles in the innermost loop of the HMM. @dlaehnemann since you have the setup already, can you please create a flamegraph of this vs master branch? You can use test09 in lib.rs for that.

[dlaehnemann]

Here come the flamegraphs for master vs. the current head of the precompute-pairhmm-cell-probs branch. The Emission part you changed seems to have gone from almost 13% to almost 8% of cputime.

Master branch

perf record --call-graph dwarf,16384 -e cpu-clock -F 997 target/release/deps/lib-d3feb2225a97a416 test09

https://gist.github.com/dlaehnemann/054604c0d9b8ffac9dc211f4f9d4263f (to view the interactive and searchable SVG, right-click the preview in the gist and select View Image)

Precompute pairhmm cell probs

perf record --call-graph dwarf,16384 -e cpu-clock -F 997 target/release/deps/lib-d3feb2225a97a416 test09

https://gist.github.com/dlaehnemann/b452366c468a89d7fe1ef7e0f1c03e3b (to view the interactive and searchable SVG, right-click the preview in the gist and select View Image)

[johanneskoester]

Thank you so much!

[johanneskoester]

Closing in favor of #53, which contains the changes from this branch.