gatk3的最后一个经典版本3.8

Mark DePristo f6a2ca6e7f Fixes / TODOs for meaningful results with AFCalculationResult ... -- Right now the state of the AFCaclulationResult can be corrupt (ie, log10 likelihoods can be -Infinity). Forced me to disable reasonable contracts. Needs to be thought through -- exactCallsLog should be optional -- Update UG integration tests as the calculation of the normalized posteriors is done in a marginally different way so the output is rounded slightly differently.		2012-10-03 19:55:12 -07:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	Count the number of evaluations in AFResult; expand unit tests	2012-10-03 19:55:11 -07:00
public	Fixes / TODOs for meaningful results with AFCalculationResult	2012-10-03 19:55:12 -07:00
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