gatk3的最后一个经典版本3.8

David Roazen e740977994 GATK Engine: do not merge FilePointers that span multiple contigs ... This affects both the non-experimental and experimental engine paths, and so may break tests, but this is a necessary change.		2012-09-27 18:02:25 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	RR bug: when determining the most common base at a position, break ties by which base has the highest sum of base qualities. Otherwise, sites with 1 Q2 N and 1 Q30 C are ending up as Ns in the consensus. I think perhaps we don't even care about which base has the most observations - it should just be determined by which has the highest sum of base qualities - but I'm not sure that's what users would expect.	2012-09-24 21:46:14 -04:00
public	GATK Engine: do not merge FilePointers that span multiple contigs	2012-09-27 18:02:25 -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