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
..
annotator	Some significant changes to the annotator:	2010-03-18 05:38:32 +00:00
concordance	Update to VCF code to get it up to spec.	2010-03-03 06:12:42 +00:00
fasta	Fix off-by-one error in original implementation of read sharding. Tested by	2010-03-06 18:52:53 +00:00
filters	Update to VCF code to get it up to spec.	2010-03-03 06:12:42 +00:00
genotyper	Some significant changes to the annotator:	2010-03-18 05:38:32 +00:00
indels	Added test of Nway cleaning for Matt; thanks to Aaron for the help.	2010-03-10 21:00:41 +00:00
recalibration	Oops. Commented out some tests to improve performance and then checked in the commented out tests. Reverted.	2010-03-16 16:34:50 +00:00
sequenom	Hmm. I thought I removed this already.	2010-03-10 03:09:13 +00:00
varianteval	Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system.	2010-03-09 03:41:07 +00:00
DepthOfCoverageIntegrationTest.java	Fix for accumulator exception when running reduce by interval walkers without	2010-03-05 01:04:08 +00:00
PileupWalkerIntegrationTest.java	Now that we changed how deletions are represented, got to update MD5...	2009-12-30 22:00:58 +00:00
PrintReadsWalkerTest.java	adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come.	2010-03-03 15:56:44 +00:00