From b705d9cf15c2a0d39b5c0e589f45dec6d122f641 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Thu, 11 Aug 2011 13:17:16 -0400
Subject: [PATCH] Oops, these VariantAnnotator input bindings aren't needed
 during the UG

---
 .../walkers/genotyper/UnifiedGenotyper.java   | 32 ++-----------------
 1 file changed, 3 insertions(+), 29 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 5202d97d0..cbda870aa 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -66,35 +66,9 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
       */
     @ArgumentCollection protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
     public RodBinding<VariantContext> getDbsnpRodBinding() { return dbsnp.dbsnp; }
-
-    /**
-     * The INFO field will be annotated with information on the most biologically-significant effect
-     * listed in the SnpEff output file for each variant.
-     */
-    @Input(fullName="snpEffFile", shortName = "snpEffFile", doc="SnpEff file", required=false)
-    public RodBinding<SnpEffFeature> snpEffFile;
-    public RodBinding<SnpEffFeature> getSnpEffRodBinding() { return snpEffFile; }
-
-    /**
-      * If a record in the 'variant' track overlaps with a record from the provided comp track, the INFO field will be annotated
-      *  as such in the output with the track name (e.g. -comp:FOO will have 'FOO' in the INFO field).  Records that are filtered in the comp track will be ignored.
-      *  Note that 'dbSNP' has been special-cased (see the --dbsnp argument).
-      */
-    @Input(fullName="comp", shortName = "comp", doc="comparison VCF file", required=false)
-    public List<RodBinding<VariantContext>> comps = Collections.emptyList();
-    public List<RodBinding<VariantContext>> getCompRodBindings() { return comps; }
-
-    /**
-      * An external resource VCF file or files from which to annotate.
-      *
-      * One can add annotations from one of the resource VCFs to the output.
-      * For example, if you want to annotate your 'variant' VCF with the AC field value from the rod bound to 'resource',
-      * you can specify '-E resource.AC' and records in the output VCF will be annotated with 'resource.AC=N' when a record exists in that rod at the given position.
-      * If multiple records in the rod overlap the given position, one is chosen arbitrarily.
-      */
-    @Input(fullName="resource", shortName = "resource", doc="external resource VCF file", required=false)
-    public List<RodBinding<VariantContext>> resources = Collections.emptyList();
-    public List<RodBinding<VariantContext>> getResourceRodBindings() { return resources; }
+    public RodBinding<SnpEffFeature> getSnpEffRodBinding() { return null; }
+    public List<RodBinding<VariantContext>> getCompRodBindings() { return Collections.emptyList(); }
+    public List<RodBinding<VariantContext>> getResourceRodBindings() { return Collections.emptyList(); }
 
     // control the output
     @Output(doc="File to which variants should be written",required=true)