Ryan Poplin 5dbd3625cd Initial algorithm for choosing best alternate haplotypes to genotype based on the likelihoods from all samples instead of choosing for each sample independently. Simple tradeoff of penalty for increasing model complexity and likelihood of the data.		2012-03-27 13:38:52 -04:00
..
config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Initial algorithm for choosing best alternate haplotypes to genotype based on the likelihoods from all samples instead of choosing for each sample independently. Simple tradeoff of penalty for increasing model complexity and likelihood of the data.	2012-03-27 13:38:52 -04:00
test	Significant restructuring of the Exact model, as discussed within the dev group last week. There is no more marginalizing over alternate alleles, and we now keep track of the MLE and MAP. Important notes: 1) integration tests change because the previous marginalization wasn't done correctly (as pointed out by Guillermo) and our confidences were too high for many multi-allelic sites; 2) there is a major TO-DO item that needs to be discussed within the dev group (so they should expect a follow up email); 3) this code is still in flux as I am awaiting feedback from Ryan now on its performance with the Haplotype Caller (the good news, Ryan, is that we recover that site that we were losing previously).	2012-03-27 00:27:44 -05:00