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
..
alignment	oops - didn't mean to check this in	2010-03-02 20:28:22 +00:00
gatk	Some significant changes to the annotator:	2010-03-18 05:38:32 +00:00
oneoffprojects/walkers	Fixing broken integration tests	2010-03-14 23:18:49 +00:00
playground	-Pushed base quals back down into SAMRecord; if -OQ is used, the SAMRecord quals get updated automatically	2010-03-17 16:00:10 +00:00
utils	Unit tests for -XL arguments; expt. annotation calculating the GC content within 100 bp of the current SNP	2010-03-14 21:08:14 +00:00
BaseTest.java	added root GATKData variable	2010-02-12 15:25:34 +00:00
TrivialInstrumenter.java	fixed a bunch of comments and license headers.	2009-06-10 14:10:46 +00:00
WalkerTest.java	another test-with-multiple outputs fix	2010-03-04 22:46:15 +00:00