gatk3的最后一个经典版本3.8

Mauricio Carneiro 67d4148b32 Fixing but reported by Thomas in the forum where reads were soft-clipped beyond the limits of the contig and ReduceReads was failing with a NoSuchElement exception. Now we hard clip anything that goes beyond the boundaries of the contig.		2012-08-09 15:58:18 -04:00
licensing	Final final final version of the license.	2012-07-20 18:00:02 -04:00
protected/java	Fixing but reported by Thomas in the forum where reads were soft-clipped beyond the limits of the contig and ReduceReads was failing with a NoSuchElement exception. Now we hard clip anything that goes beyond the boundaries of the contig.	2012-08-09 15:58:18 -04:00
public	Updating VQSR to work with the MNP and symbolic variants that are coming out of the HaplotypeCaller. Integration tests change because of the MNPs in dbSNP.	2012-08-03 10:44:36 -04:00
settings	Removed Categories.	2012-07-25 13:46:24 -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	Remove reference dependence in BCF2Codec	2012-07-25 08:56:38 -04:00
ivy.xml	Added the ability to update the Forum	2012-07-23 17:17:33 -04:00