eriqande/flockture — pull request #3 by patbarry6 (2014-11-21 04:43:06+00:00)
Title: LLOD of FLOCK does not match what I calculate based on final ref pop partitions

I rewrote the code I had initially so that it is painfully easy to follow. I have also done the calculations by hand to ensure that I wasn't doing something stupid, however there is a high probability that is still the case. Because FLOCK gets different LLOD values with only switched labels I wanted to confirm how the calculation was done. We have the final partitions that are reported from FLOCK, so we can removed each individual and calculate their LLOD pretty easily, but my results are quite different than FLOCKs. I find that I get more similar results when I don't remove the individual from the reference population before calculating the likelihood for its genotype in either group.