Ryan Poplin d665a8ba0c The Bayesian calculation of Qemp in the BQSR is now hierarchical. This fixes issues in which the covariate bins were very sparse and the prior estimate being used was the original quality score. This resulted in large correction factors for each covariate which breaks the equation. There is also now a new option, qlobalQScorePrior, which can be used to ignore the given (very high) quality scores and instead use this value as the prior.		2013-01-28 15:56:33 -05:00
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BQSRArgumentSet.java	The Bayesian calculation of Qemp in the BQSR is now hierarchical. This fixes issues in which the covariate bins were very sparse and the prior estimate being used was the original quality score. This resulted in large correction factors for each covariate which breaks the equation. There is also now a new option, qlobalQScorePrior, which can be used to ignore the given (very high) quality scores and instead use this value as the prior.	2013-01-28 15:56:33 -05:00
BQSRMode.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
EventType.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00