gatk3的最后一个经典版本3.8

Mark DePristo cb857d1640 AFCalcs must be made by factory method now ... -- AFCalcFactory is the only way to make AFCalcs now. There's a nice ordered enum there describing the models and their ploidy and max alt allele restrictions. The factory makes it easy to create them, and to find models that work for you given your ploidy and max alt alleles. -- AFCalc no longer has UAC constructor -- only AFCalcFactory does. Code cleanup throughout -- Enabling more unit tests, all of which almost pass now (except for IndependentAllelesDiploidExactAFCalc which will be fixed next) -- It's now possible to run the UG / HC with any of the exact models currently in the system. -- Code cleanup throughout the system, reorganizing the unit tests in particular		2012-10-15 07:53:56 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	AFCalcs must be made by factory method now	2012-10-15 07:53:56 -04:00
public	AFCalcs must be made by factory method now	2012-10-15 07:53:56 -04:00
settings	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00
.gitignore	a few more useful git ignores	2012-09-01 11:08:36 -04:00
build.xml	Proper error handling in NanoScheduler	2012-09-19 17:03:13 -04:00
ivy.xml	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00