gatk3的最后一个经典版本3.8

Mark DePristo b4841548f1 Bug fixes and misc. improvements to running the adaptive context tools ... -- Better output file name defaults -- Fixed nasty bug where I included non-existant quals in the contexts to process because they showed up in the Cycle covariate -- Data is processed in qual order now, so it's easier to see progress -- Logger messages explaining where we are in the process -- When in UPDATE mode we still write out the information for an equivalent prune by depth for post analysis		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	Bug fixes and misc. improvements to running the adaptive context tools	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