Eric Banks bdb1da30fd Better interface for getting RodBindings to the VariantAnnotatorEngine and its annotations: pass around an AnnotatorCompatibleWalker (interface) object. Updating VA to use the new rod system.		2011-08-10 22:43:08 -04:00
..
alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	GATK now does dynamic type determination for VCF files	2011-08-08 14:45:46 -04:00
gatk	Better interface for getting RodBindings to the VariantAnnotatorEngine and its annotations: pass around an AnnotatorCompatibleWalker (interface) object. Updating VA to use the new rod system.	2011-08-10 22:43:08 -04:00
jna	Memory limits changed from Int to Double.	2011-07-21 22:57:18 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
utils	More tools moved over. Fixed the VariantContextIntegrationTest which was not useful because the md5s were all removed. In the future, instead of removing md5s (putting it in 'parameterization' mode), you should instead use @Test{enabled=false} since it's easier to track.	2011-08-10 14:24:40 -04:00
BaseTest.java	Added b37dbSNP129, needed for Queue	2011-08-07 11:26:07 -04:00
MD5DB.java	Go for global integrationtest path first, if possible.	2011-07-26 17:35:30 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Walker test system refactoring. All MD5DB related functions are now in MD5DB.java.	2011-07-18 10:46:01 -04:00