ebanks ee0e833616 Some significant changes to the annotator: ... 1. Annotations can now be "decorated" with any arbitrary interface description - not just standard or experimental. 2. Users can now not only specify specific annotations to use, but also the interface names from #1. Any number of them can be specified, e.g. -G Standard -G Experimental -A RankSumTest. 3. These same arguments can be used with the Unified Genotyper for when it calls into the Annotator. 4. There are now two types of annotations: those that are applied to the INFO field and those that are applied to specific genotypes (the FORMAT field) in the VCF (however, I haven't implemented any of these latter annotations just yet; coming soon). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3029 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-18 05:38:32 +00:00
..
arguments	Bug fix in variant eval 2. Preliminary (slow and buggy) support for -XL exclude lists.	2010-03-12 19:23:12 +00:00
contexts/variantcontext	add a new JEXLContext that lazy-evaluates JEXL expressions given the VariantContext.	2010-03-15 16:00:55 +00:00
datasources	Performance improvements for RODs in conjunction with new sharding system.	2010-03-16 14:54:12 +00:00
executive	Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.	2009-05-13 21:32:05 +00:00
io	Fix for problem where err stream remapped to output stream in certain cases, (hopefully) completing Matt's hat trick of fail. Thanks, unit tests.	2009-09-16 08:33:56 +00:00
iterators	Fix off-by-one error in original implementation of read sharding. Tested by	2010-03-06 18:52:53 +00:00
refdata	adding methods to get RODs by name or type in read traversals, performance improvements to RODs for Reads in general, and some more Tribble infrastructure.	2010-03-11 21:13:39 +00:00
traversals	Rework the way the MicroScheduler handles locus shards to handle intervals that span shards	2010-03-11 18:40:31 +00:00
walkers	Some significant changes to the annotator:	2010-03-18 05:38:32 +00:00