gatk3的最后一个经典版本3.8

Menachem Fromer 449b89bd34 Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)		2012-09-10 15:08:44 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	Bug fix in HC GenotypingEngine to ensure that all the merged complex events get properly added to the priority list used by VariantContextUtils when combining multiallelic events.	2012-09-09 13:47:54 -04:00
public	The comprehensive LIBS unit test is now truly comprehensive (or it would be if LIBS wasn't busted). The test can handle a read with any arbitrary legal CIGAR and iterates over the elements/bases in time with the real LIBS, failing if there are any differences. I've left the few hard-coded CIGARs in there for now with a note to move to all possible permutations once we move to fix LIBS (otherwise the tests would fail now).	2012-09-10 15:04:06 -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	More memory for gatkdocs and extracthelp targets	2012-09-05 15:45:22 -04:00
ivy.xml	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00