bigdatagenomics/avocado — pull request #23 by arahuja (2014-03-10 04:32:21+00:00)
Title: [WIP] Genotype likelihood calc was flipped

Genotype likelihood calc was incorrect as g = 0 should not refer to homozygous reference but homozygous alternate (equivalently g = # of reference bases in allele) (at least according to the algorithm implemented)

The tests were passing because of a bug in the floating point equals function where the threshold was 1e6 instead of 1e-6

There are still some issues in the test on floating point accuracy as the order of operations affects the outcome and tests are written as multiplication of error probabilities which not the same as the probability of the average of two quality scores.

This can be cleaned up some more probably but I wanted to bring the issue to get some feedback