gatk3的最后一个经典版本3.8

Mark DePristo 7bf5ca51ee Major bugfix for adaptive contexts ... -- Basically I was treating the context history in the wrong direction, effectively predicting the further bases in the context based on the closer one. Totally backward. Updated the code to build the tree in the right direction. -- Added a few more useful outputs for analysis (minPenalty and maxPenalty) -- Misc. cleanup of the code -- Overall I'm not 100% certain this is even the right way to think about the problem. Clearly this is producing a reasonable output but the sum of chi2 values over the entire tree is just enormous. Perhaps a MCMC convergence / sampling criterion would be a better way to think about this problem?		2012-08-06 11:42:55 -04:00
licensing	Final final final version of the license.	2012-07-20 18:00:02 -04:00
protected/java	Merging together the computeDiploidHaplotypeLikelihoods functions in the HaplotypeCaller's LikelihoodEngine so they both benefit from the ReducedRead's RepresentativeCount	2012-08-06 11:40:07 -04:00
public	Major bugfix for adaptive contexts	2012-08-06 11:42:55 -04:00
settings	Removed Categories.	2012-07-25 13:46:24 -04:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
build.xml	Remove reference dependence in BCF2Codec	2012-07-25 08:56:38 -04:00
ivy.xml	V1 of tool to visualize the quality score information in the context covariates	2012-07-31 08:11:02 -04:00