Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

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

@@ -25,6 +25,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -44,7 +46,7 @@ import java.util.Map;
 
 public class AlleleBalance extends InfoFieldAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
         

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

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -17,7 +19,7 @@ import java.util.*;
 
 public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
         Double ratio = annotateSNP(stratifiedContext, vc, g);
         if (ratio == null)
             return null;

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

@@ -31,6 +31,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -48,7 +50,7 @@ import java.util.Map;
 
 public class BaseCounts extends InfoFieldAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 

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

@@ -25,6 +25,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -50,7 +52,7 @@ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnn
             new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"),
             new VCFInfoHeaderLine(VCFConstants.ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of alleles in called genotypes") };
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( ! vc.hasGenotypes() )
             return null;
         

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

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -18,7 +20,7 @@ import java.util.Map;
 
 public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 

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

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -28,7 +30,7 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
 
     private static String DEL = "DEL"; // constant, for speed: no need to create a key string for deletion allele every time
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
         if ( g == null || !g.isCalled() )
             return null;
 

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

@@ -25,6 +25,8 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import cern.jet.math.Arithmetic;
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -46,7 +48,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
     private static final String FS = "FS";
     private static final double MIN_PVALUE = 1E-320;
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( ! vc.isVariant() || vc.isFiltered() )
             return null;
 

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

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -18,7 +20,7 @@ import java.util.Map;
 
 public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         double content = computeGCContent(ref);
         Map<String, Object> map = new HashMap<String, Object>();
         map.put(getKeyNames().get(0), String.format("%.2f", content));

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

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -27,7 +29,7 @@ public class GLstats extends InfoFieldAnnotation implements StandardAnnotation {
 
     private static final int MIN_SAMPLES = 10;
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
 
         final Map<String, Genotype> genotypes = vc.getGenotypes();
         if ( genotypes == null || genotypes.size() < MIN_SAMPLES )

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

@@ -25,6 +25,8 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import net.sf.samtools.SAMRecord;
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -54,7 +56,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
     private final static int MAX_CONSENSUS_HAPLOTYPES_TO_CONSIDER = 50;
     private final static char REGEXP_WILDCARD = '.';
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if (stratifiedContexts.size() == 0 ) // size 0 means that call was made by someone else and we have no data here
             return null;
 

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

@@ -1,6 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
 import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -24,7 +26,7 @@ public class HardyWeinberg extends InfoFieldAnnotation implements WorkInProgress
     private static final int MIN_GENOTYPE_QUALITY = 10;
     private static final int MIN_NEG_LOG10_PERROR = MIN_GENOTYPE_QUALITY / 10;
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
 
         final Map<String, Genotype> genotypes = vc.getGenotypes();
         if ( genotypes == null || genotypes.size() < MIN_SAMPLES )

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

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -20,7 +22,7 @@ public class HomopolymerRun extends InfoFieldAnnotation implements StandardAnnot
 
     private boolean ANNOTATE_INDELS = true;
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
 
         if ( !vc.isBiallelic() )
             return null;

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

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -21,7 +23,7 @@ import java.util.*;
  */
 public class IndelType extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
 
          int run;
         if (vc.isMixed()) {

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

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -18,7 +20,7 @@ import java.util.Map;
 
 public class LowMQ extends InfoFieldAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 

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

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -20,7 +22,7 @@ import java.util.Map;
 
 public class MappingQualityZero extends InfoFieldAnnotation implements StandardAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 

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

@@ -25,6 +25,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -50,8 +52,8 @@ import java.util.Map;
  * To change this template use File | Settings | File Templates.
  */
 public class MappingQualityZeroBySample extends GenotypeAnnotation {
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref,
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings,
-                                        AlignmentContext context, VariantContext vc, Genotype g) {
+                                        ReferenceContext ref, AlignmentContext context, VariantContext vc, Genotype g) {
         if ( g == null || !g.isCalled() )
             return null;
 

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

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -20,7 +22,7 @@ import java.util.Map;
 
 public class MappingQualityZeroFraction extends InfoFieldAnnotation implements ExperimentalAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 

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

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -22,7 +24,7 @@ import java.util.Map;
  */
 
 public class NBaseCount extends InfoFieldAnnotation {
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if( stratifiedContexts.size() == 0 )
             return null;
 

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

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -18,7 +20,7 @@ import java.util.Map;
 
 public class QualByDepth extends AnnotationByDepth implements StandardAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 

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

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -22,7 +24,7 @@ import java.util.Map;
 
 public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 

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

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -25,7 +27,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
     static final double INDEL_LIKELIHOOD_THRESH = 0.1;
     static final boolean DEBUG = false;
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
          

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

@@ -25,6 +25,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -58,7 +60,7 @@ public class ReadDepthAndAllelicFractionBySample extends GenotypeAnnotation {
 
         private static String DEL = "DEL"; // constant, for speed: no need to create a key string for deletion allele every time
 
-        public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref,
+        public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref,
                                             AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
             if ( g == null || !g.isCalled() )
                 return null;

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

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -18,7 +20,7 @@ import java.util.Map;
 
 public class SBByDepth extends AnnotationByDepth {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 

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

@@ -25,6 +25,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -43,7 +45,7 @@ import java.util.Map;
 
 public class SampleList extends InfoFieldAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( vc.isMonomorphic() || !vc.hasGenotypes() )
             return null;
 

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

@@ -25,6 +25,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -69,8 +70,11 @@ 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";
 
-    public Map<String, Object> annotate ( RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc ) {
+    public static final String SNPEFF_ROD_NAME = "snpEffFile";
-        List<Feature> features = tracker.getValues(Feature.class);
+
+    public Map<String, Object> annotate ( RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc ) {
+        RodBinding<SnpEffFeature> snpEffRodBinding = (RodBinding<SnpEffFeature>)rodBindings.get(SNPEFF_ROD_NAME);
+        List<SnpEffFeature> features = tracker.getValues(snpEffRodBinding);
 
         // Add only annotations for one of the most biologically-significant effects as defined in
         // the SnpEffConstants class:
@@ -83,18 +87,14 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
         return generateAnnotations(mostSignificantEffect);
     }
 
-    private SnpEffFeature getMostSignificantEffect ( List<Feature> features ) {
+    private SnpEffFeature getMostSignificantEffect ( List<SnpEffFeature> snpEffFeatures ) {
         SnpEffFeature mostSignificantEffect = null;
 
-        for ( Feature feature : features ) {
+        for ( SnpEffFeature snpEffFeature : snpEffFeatures ) {
-            if ( feature instanceof SnpEffFeature ) {
+            if ( mostSignificantEffect == null ||
-                SnpEffFeature snpEffFeature = (SnpEffFeature)feature;
+                 snpEffFeature.isHigherImpactThan(mostSignificantEffect) ) {
 
-                if ( mostSignificantEffect == null ||
+                mostSignificantEffect = snpEffFeature;
-                     snpEffFeature.isHigherImpactThan(mostSignificantEffect) ) {
-
-                    mostSignificantEffect = snpEffFeature;
-                }
             }
         }
 

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

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -18,7 +20,7 @@ import java.util.Map;
 
 public class SpanningDeletions extends InfoFieldAnnotation implements StandardAnnotation {
 
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 

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

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -29,7 +31,7 @@ public class TechnologyComposition extends InfoFieldAnnotation implements Experi
     private String n454 ="Num454";
     private String nSolid = "NumSOLiD";
     private String nOther = "NumOther";
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    public Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( stratifiedContexts.size() == 0 )
             return null;
 

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

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
@@ -59,8 +60,14 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
     @ArgumentCollection
     protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
 
+    /**
+     * A SnpEff output file from which to add annotations.
+     *
+     * 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> snpEffFile = RodBinding.makeUnbound(SnpEffFeature.class);
 
     /**
       * A dbSNP VCF file from which to annotate.
@@ -115,6 +122,8 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
 
     private Collection<VariantContext> indelBufferContext;
 
+    private Map<String, RodBinding<? extends Feature>> rodBindings = new HashMap<String, RodBinding<? extends Feature>>();
+
 
     private void listAnnotationsAndExit() {
         List<Class<? extends InfoFieldAnnotation>> infoAnnotationClasses = new PluginManager<InfoFieldAnnotation>(InfoFieldAnnotation.class).getPlugins();
@@ -157,10 +166,12 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
             logger.warn("There are no samples input at all; use the --sampleName argument to specify one if desired.");
         }
 
+        initializeRodBindingMap();
+
         if ( USE_ALL_ANNOTATIONS )
-            engine = new VariantAnnotatorEngine(getToolkit());
+            engine = new VariantAnnotatorEngine(getToolkit(), rodBindings);
         else
-            engine = new VariantAnnotatorEngine(getToolkit(), annotationGroupsToUse, annotationsToUse);
+            engine = new VariantAnnotatorEngine(getToolkit(), annotationGroupsToUse, annotationsToUse, rodBindings);
         engine.initializeExpressions(expressionsToUse);
 
         // setup the header fields
@@ -180,6 +191,13 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
         }
     }
 
+    private void initializeRodBindingMap() {
+        rodBindings.put(variantCollection.variants.getName(), variantCollection.variants);
+        rodBindings.put(snpEffFile.getName(), snpEffFile);
+        rodBindings.put(dbsnp.dbsnp.getName(), dbsnp.dbsnp);
+        rodBindings.put(comps.getName(), comps);
+    }
+
     public static boolean isUniqueHeaderLine(VCFHeaderLine line, Set<VCFHeaderLine> currentSet) {
         if ( !(line instanceof VCFCompoundHeaderLine) )
             return true;

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

@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -55,7 +56,7 @@ public class VariantAnnotatorEngine {
     private List<VAExpression> requestedExpressions = new ArrayList<VAExpression>();
 
     private HashMap<String, String> dbAnnotations = new HashMap<String, String>();
-
+    private Map<String, RodBinding<? extends Feature>> rodBindings;
 
     private static class VAExpression {
         public String fullName, bindingName, fieldName;
@@ -72,16 +73,18 @@ public class VariantAnnotatorEngine {
     }
 
     // use this constructor if you want all possible annotations
-    public VariantAnnotatorEngine(GenomeAnalysisEngine engine) {
+    public VariantAnnotatorEngine(GenomeAnalysisEngine engine, Map<String, RodBinding<? extends Feature>> rodBindings) {
         requestedInfoAnnotations = AnnotationInterfaceManager.createAllInfoFieldAnnotations();
         requestedGenotypeAnnotations = AnnotationInterfaceManager.createAllGenotypeAnnotations();
         initializeDBs(engine);
+        this.rodBindings = rodBindings;
     }
 
     // use this constructor if you want to select specific annotations (and/or interfaces)
-    public VariantAnnotatorEngine(GenomeAnalysisEngine engine, List<String> annotationGroupsToUse, List<String> annotationsToUse) {
+    public VariantAnnotatorEngine(GenomeAnalysisEngine engine, List<String> annotationGroupsToUse, List<String> annotationsToUse, Map<String, RodBinding<? extends Feature>> rodBindings) {
         initializeAnnotations(annotationGroupsToUse, annotationsToUse);
         initializeDBs(engine);
+        this.rodBindings = rodBindings;
     }
 
     // select specific expressions to use
@@ -137,7 +140,7 @@ public class VariantAnnotatorEngine {
 
         // go through all the requested info annotationTypes
         for ( InfoFieldAnnotation annotationType : requestedInfoAnnotations ) {
-            Map<String, Object> annotationsFromCurrentType = annotationType.annotate(tracker, ref, stratifiedContexts, vc);
+            Map<String, Object> annotationsFromCurrentType = annotationType.annotate(tracker, rodBindings, ref, stratifiedContexts, vc);
             if ( annotationsFromCurrentType != null )
                 infoAnnotations.putAll(annotationsFromCurrentType);
         }
@@ -202,7 +205,7 @@ public class VariantAnnotatorEngine {
 
             Map<String, Object> genotypeAnnotations = new HashMap<String, Object>(genotype.getAttributes());
             for ( GenotypeAnnotation annotation : requestedGenotypeAnnotations ) {
-                Map<String, Object> result = annotation.annotate(tracker, ref, context, vc, genotype);
+                Map<String, Object> result = annotation.annotate(tracker, rodBindings, ref, context, vc, genotype);
                 if ( result != null )
                     genotypeAnnotations.putAll(result);
             }

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -13,7 +15,8 @@ import java.util.Map;
 public abstract class GenotypeAnnotation extends VariantAnnotatorAnnotation {
 
     // return annotations for the given contexts/genotype split by sample
-    public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g);
+    public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings,
+                                                 ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g);
 
     // return the descriptions used for the VCF FORMAT meta field
     public abstract List<VCFFormatHeaderLine> getDescriptions();

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java

@@ -1,11 +1,11 @@
 package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 
+import org.broad.tribble.Feature;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.List;
@@ -13,7 +13,8 @@ import java.util.Map;
 
 public abstract class InfoFieldAnnotation extends VariantAnnotatorAnnotation {
     // return annotations for the given contexts split by sample
-    public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc);
+    public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, Map<String, RodBinding<? extends Feature>> rodBindings,
+                                                 ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc);
 
     // return the descriptions used for the VCF INFO meta field
     public abstract List<VCFInfoHeaderLine> getDescriptions();

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -25,9 +25,11 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
+import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.DownsampleType;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -138,7 +140,8 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         if ( verboseWriter != null )
             verboseWriter.println("AFINFO\tLOC\tREF\tALT\tMAF\tF\tAFprior\tAFposterior\tNormalizedPosterior");
 
-        annotationEngine = new VariantAnnotatorEngine(getToolkit(), Arrays.asList(annotationClassesToUse), annotationsToUse);
+        // TODO: Fill in the final argument with actual RodBinding map
+        annotationEngine = new VariantAnnotatorEngine(getToolkit(), Arrays.asList(annotationClassesToUse), annotationsToUse, new HashMap<String, RodBinding<? extends Feature>>());
         UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples);
 
         // initialize the header

public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java

@@ -27,11 +27,16 @@ package org.broadinstitute.sting.utils.codecs.snpEff;
 import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.TribbleException;
+import org.broad.tribble.readers.AsciiLineReader;
 import org.broad.tribble.readers.LineReader;
+import org.broadinstitute.sting.gatk.refdata.SelfScopingFeatureCodec;
+
 import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.EffectType;
 import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.ChangeType;
 import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.Zygosity;
 
+import java.io.File;
+import java.io.FileInputStream;
 import java.io.IOException;
 
 /**
@@ -68,7 +73,7 @@ import java.io.IOException;
  *
  * @author David Roazen
  */
-public class SnpEffCodec implements FeatureCodec {
+public class SnpEffCodec implements FeatureCodec, SelfScopingFeatureCodec {
 
     public static final int EXPECTED_NUMBER_OF_FIELDS = 23;
     public static final String FIELD_DELIMITER_PATTERN = "\\t";
@@ -255,4 +260,16 @@ public class SnpEffCodec implements FeatureCodec {
             }
         }
     }
+
+    public boolean canDecode ( final File potentialInput ) {
+        try {
+            LineReader reader = new AsciiLineReader(new FileInputStream(potentialInput));
+            readHeader(reader);
+        }
+        catch ( Exception e ) {
+            return false;
+        }
+
+        return true;
+    }
 }

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 --variant:VCF " +
+            "-T VariantAnnotator -R " + b37KGReference + " -NO_HEADER -o %s -A SnpEff --variant " +
-            validationDataLocation + "1000G.exomes.vcf --snpEffFile:SnpEff " + validationDataLocation +
+            validationDataLocation + "1000G.exomes.vcf --snpEffFile  " + validationDataLocation +
             "snpEff_1.9.6_1000G.exomes.vcf_hg37.61.out -L 1:26,000,000-26,500,000",
             1,
             Arrays.asList("c08648a078368c80530bff004b3157f1")