gatk3的最后一个经典版本3.8

Guillermo del Angel e29469eeeb Forgot to update 2 integration test md5's (in this cases, changes are legit because of the code revamp of AD, it's simpler if AD is not output when a site is not variant, as genotype DP conveys the same information)		2012-08-22 15:53:33 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	Final step (for now) in VA refactoring: update MD5's because, a) since it's not guaranteed that we'll iterate through reads/pileups in the same order, the rank sum dithering will change annotations, b) FS uses new generic threshold to distinguish uninformative reads (it used to use ad-hoc thresholds), c) AD definition changed and throws away uninformative reads, d) shortened general ploidy integration tests for quicker debugging. May have missed some MD5's in the update so there may be lingering test failures still	2012-08-22 11:38:51 -04:00
public	Forgot to update 2 integration test md5's (in this cases, changes are legit because of the code revamp of AD, it's simpler if AD is not output when a site is not variant, as genotype DP conveys the same information)	2012-08-22 15:53:33 -04:00
settings	Updating cofoja to the latest version	2012-08-09 16:36:18 -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	Convert external.build.dir and external.dist.dir back to paths	2012-08-15 23:04:10 -04:00
ivy.xml	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00