Made the necessary changes to get SnpEff support working with the new rodbinding system.

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java

@@ -24,6 +24,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -43,8 +44,8 @@ import java.util.*;
  * (http://snpeff.sourceforge.net/).
  *
  * For each variant, chooses one of the effects of highest biological impact from the SnpEff
- * output file (which must be bound to an RMD track named "SnpEff"), and adds annotations
+ * output file (which must be provided on the command line via --snpEffFile:SnpEff <filename>),
- * on that effect.
+ * and adds annotations on that effect.
  *
  * The possible biological effects and their associated impacts are defined in the class:
  * org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants
@@ -68,28 +69,32 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
     public static final String CODON_NUM_KEY = "CODON_NUM";
     public static final String CDS_SIZE_KEY = "CDS_SIZE";
 
-    // Name of the RMD track bound to the raw SnpEff-generated output file:
-    public static final String RMD_TRACK_NAME = "SnpEff";
-
     public Map<String, Object> annotate ( RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc ) {
-        List<Object> snpEffFeatures = tracker.getReferenceMetaData(RMD_TRACK_NAME);
+        List<Feature> features = tracker.getValues(Feature.class);
 
         // Add only annotations for one of the most biologically-significant effects as defined in
         // the SnpEffConstants class:
-        SnpEffFeature mostSignificantEffect = getMostSignificantEffect(snpEffFeatures);
+        SnpEffFeature mostSignificantEffect = getMostSignificantEffect(features);
+
+        if ( mostSignificantEffect == null ) {
+            return null;
+        }
+
         return generateAnnotations(mostSignificantEffect);
     }
 
-    private SnpEffFeature getMostSignificantEffect ( List<Object> snpEffFeatures ) {
+    private SnpEffFeature getMostSignificantEffect ( List<Feature> features ) {
         SnpEffFeature mostSignificantEffect = null;
 
-        for ( Object feature : snpEffFeatures ) {
+        for ( Feature feature : features ) {
-            SnpEffFeature snpEffFeature = (SnpEffFeature)feature;
+            if ( feature instanceof SnpEffFeature ) {
+                SnpEffFeature snpEffFeature = (SnpEffFeature)feature;
 
-            if ( mostSignificantEffect == null ||
+                if ( mostSignificantEffect == null ||
-                 snpEffFeature.isHigherImpactThan(mostSignificantEffect) ) {
+                     snpEffFeature.isHigherImpactThan(mostSignificantEffect) ) {
 
-                mostSignificantEffect = snpEffFeature;
+                    mostSignificantEffect = snpEffFeature;
+                }
             }
         }
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -37,6 +37,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
+import org.broadinstitute.sting.utils.codecs.snpEff.SnpEffFeature;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
@@ -55,6 +56,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
     @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
     public RodBinding<VariantContext> variants;
 
+    @Input(fullName="snpEffFile", shortName = "snpEffFile", doc="SnpEff file", required=false)
+    public RodBinding<SnpEffFeature> snpEffFile;
+
     @Output(doc="File to which variants should be written",required=true)
     protected VCFWriter vcfWriter = null;
 

public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java

@@ -129,8 +129,8 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testSnpEffAnnotations() {
         WalkerTestSpec spec = new WalkerTestSpec(
-            "-T VariantAnnotator -R " + b37KGReference + " -NO_HEADER -o %s -A SnpEff -B:variant,VCF " +
+            "-T VariantAnnotator -R " + b37KGReference + " -NO_HEADER -o %s -A SnpEff --variants:VCF " +
-            validationDataLocation + "1000G.exomes.vcf -B:SnpEff,SnpEff " + validationDataLocation +
+            validationDataLocation + "1000G.exomes.vcf --snpEffFile:SnpEff " + validationDataLocation +
             "snpEff_1.9.6_1000G.exomes.vcf_hg37.61.out -L 1:26,000,000-26,500,000",
             1,
             Arrays.asList("c08648a078368c80530bff004b3157f1")