Eric Banks c112e0824a I was adding verbose output to the Pileup output for a one-off and decided that I might as well commit it as an option. Updated deprecated calls while I was in there.		2012-03-27 11:09:03 -05:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	I was adding verbose output to the Pileup output for a one-off and decided that I might as well commit it as an option. Updated deprecated calls while I was in there.	2012-03-27 11:09:03 -05:00
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