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

java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContext.java

@@ -198,7 +198,8 @@ public class VariantContext {
         this.commonInfo = new InferredGeneticContext(name, negLog10PError, filters, attributes);
 
         if ( alleles == null ) { throw new StingException("Alleles cannot be null"); }
-        this.alleles = Collections.unmodifiableSet(alleleCollectionToSet(new HashSet<Allele>(), alleles));
+        // we need to make this a LinkedHashSet in case the user prefers a given ordering of alleles
+        this.alleles = Collections.unmodifiableSet(alleleCollectionToSet(new LinkedHashSet<Allele>(), alleles));
 
         if ( genotypes == null ) { genotypes = NO_GENOTYPES; }
         this.genotypes = Collections.unmodifiableMap(genotypes);

java/src/org/broadinstitute/sting/gatk/walkers/annotator/Alignability.java

@@ -5,12 +5,13 @@ import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.TabularROD;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.Map;
 
 
-public class Alignability implements VariantAnnotation {
+public class Alignability implements InfoFieldAnnotation {
 
     public String annotate(RefMetaDataTracker tracker, 
 						   ReferenceContext ref, 

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

@@ -4,13 +4,14 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.Map;
 
 
-public class AlleleBalance extends StandardVariantAnnotation {
+public class AlleleBalance implements InfoFieldAnnotation, StandardAnnotation {
 
     public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
 

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

@@ -4,13 +4,14 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.Map;
 
 
-public class DepthOfCoverage extends StandardVariantAnnotation {
+public class DepthOfCoverage implements InfoFieldAnnotation, StandardAnnotation {
 
     public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
         int depth = 0;

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

@@ -4,14 +4,14 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.Map;
 
 
-public class GCContent implements VariantAnnotation {
+public class GCContent implements InfoFieldAnnotation, ExperimentalAnnotation {
 
     public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
         double content = computeGCContent(ref);

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

@@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.genotype.HardyWeinbergCalculation;
 import org.broadinstitute.sting.utils.QualityUtils;
@@ -11,7 +12,7 @@ import org.broadinstitute.sting.utils.QualityUtils;
 import java.util.Map;
 
 
-public class HardyWeinberg implements VariantAnnotation {
+public class HardyWeinberg implements InfoFieldAnnotation, WorkInProgressAnnotation {
 
     private static final int MIN_SAMPLES = 10;
     private static final int MIN_GENOTYPE_QUALITY = 10;

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

@@ -4,13 +4,15 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.Map;
 
 
-public class HomopolymerRun extends StandardVariantAnnotation {
+public class HomopolymerRun implements InfoFieldAnnotation, StandardAnnotation {
 
     public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
 

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

@@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
@@ -11,7 +12,7 @@ import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 import java.util.Map;
 
 
-public class LowMQ implements VariantAnnotation {
+public class LowMQ implements InfoFieldAnnotation {
 
     public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
         double mq0 = 0;

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

@@ -4,6 +4,8 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
@@ -11,7 +13,7 @@ import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 import java.util.Map;
 
 
-public class MappingQualityZero extends StandardVariantAnnotation {
+public class MappingQualityZero implements InfoFieldAnnotation, StandardAnnotation {
 
     public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
         int mq0 = 0;

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

@@ -4,13 +4,15 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.Map;
 import java.util.ArrayList;
 
 
-public class QualByDepth extends StandardVariantAnnotation {
+public class QualByDepth implements InfoFieldAnnotation, StandardAnnotation {
 
     public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
         final Map<String, Genotype> genotypes = vc.getGenotypes();

java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualityAdjustedSecondBaseLod.java

@@ -4,18 +4,12 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.Map;
 
-/**
+public class QualityAdjustedSecondBaseLod implements InfoFieldAnnotation, ExperimentalAnnotation {
- * Created by IntelliJ IDEA.
- * User: Ghost
- * Date: Dec 19, 2009
- * Time: 1:02:09 AM
- * To change this template use File | Settings | File Templates.
- */
-public class QualityAdjustedSecondBaseLod implements VariantAnnotation {
     private final String KEY_NAME = "Qual_Adjusted_2blod";
     private final double CHI_LOD_MAX = -1000.0;
     private final SecondBaseSkew skewCalc = new SecondBaseSkew();

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

@@ -4,6 +4,8 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
@@ -14,7 +16,7 @@ import java.util.Map;
 import java.util.ArrayList;
 
 
-public class RMSMappingQuality extends StandardVariantAnnotation {
+public class RMSMappingQuality implements InfoFieldAnnotation, StandardAnnotation {
 
     public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
         ArrayList<Integer> qualities = new ArrayList<Integer>();

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

@@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
@@ -12,7 +13,7 @@ import java.util.ArrayList;
 import java.util.Map;
 
 
-public abstract class RankSumTest implements VariantAnnotation {
+public abstract class RankSumTest implements InfoFieldAnnotation, WorkInProgressAnnotation {
     private final static boolean DEBUG = false;
     private static final double minPValue = 1e-10;
 

java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java

@@ -9,18 +9,12 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 
 import java.util.Map;
 
 
-/**
+public class SecondBaseSkew implements InfoFieldAnnotation, ExperimentalAnnotation {
- * Created by IntelliJ IDEA.
- * User: chartl
- * Date: Nov 16, 2009
- * Time: 11:25:51 AM
- * To change this template use File | Settings | File Templates.
- */
-public class SecondBaseSkew implements VariantAnnotation {
     private final static double epsilon = Math.pow(10.0,-12.0);
     private final static String KEY_NAME = "2b_Chi";
     private final static double[] UNIFORM_ON_OFF_RATIO = {1.0/3.0, 2.0/3.0};

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

@@ -4,13 +4,15 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.Map;
 
 
-public class SpanningDeletions extends StandardVariantAnnotation {
+public class SpanningDeletions implements InfoFieldAnnotation, StandardAnnotation {
 
     public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
         int deletions = 0;

java/src/org/broadinstitute/sting/gatk/walkers/annotator/StandardVariantAnnotation.java

@@ -1,6 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers.annotator;
-
-
-public abstract class StandardVariantAnnotation implements VariantAnnotation {
-
-}

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

@@ -2,10 +2,11 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.contexts.*;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.MutableVariantContext;
 import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 import org.broadinstitute.sting.utils.genotype.Genotype;
@@ -27,12 +28,12 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
     protected File VCF_OUT;
     @Argument(fullName="sampleName", shortName="sample", doc="The sample (NA-ID) corresponding to the variant input (for non-VCF input only)", required=false)
     protected String sampleName = null;
-    @Argument(fullName="annotations", shortName="A", doc="Annotation types to apply to variant calls", required=false)
+    @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
-    protected String[] ANNOTATIONS;
+    protected String[] annotationsToUse = {};
-    @Argument(fullName="includeExperimentalAnnotations", shortName="exp", doc="Use all possible annotations, including experimental ones", required=false)
+    @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
+    protected String[] annotationClassesToUse = { };
+    @Argument(fullName="useAllAnnotations", shortName="all", doc="Use all possible annotations (not for the faint of heart)", required=false)
     protected Boolean USE_ALL_ANNOTATIONS = false;
-    @Argument(fullName="useStandardAnnotations", shortName="standard", doc="Use all standard annotations", required=false)
-    protected Boolean USE_STANDARD_ANNOTATIONS = false;
     @Argument(fullName="list", shortName="ls", doc="List the available annotations and exit")
     protected Boolean LIST = false;
 
@@ -40,43 +41,19 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
 
     private HashMap<String, String> nonVCFsampleName = new HashMap<String, String>();
 
-    private ArrayList<VariantAnnotation> requestedAnnotations;
+    private VariantAnnotatorEngine engine;
-
-    // should we annotate dbsnp?
-    private boolean annotateDbsnp = false;
-    // how about hapmap2?
-    private boolean annotateHapmap2 = false;
-    // how about hapmap3?
-    private boolean annotateHapmap3 = false;
-
-    // mapping from class name to class
-    private static HashMap<String, VariantAnnotation> allAnnotations = null;
-    private static HashMap<String, VariantAnnotation> standardAnnotations = null;
 
 
-    private static void determineAllAnnotations() {
+    private void listAnnotationsAndExit() {
-        allAnnotations = new HashMap<String, VariantAnnotation>();
+        List<Class<? extends InfoFieldAnnotation>> infoAnnotationClasses = PackageUtils.getClassesImplementingInterface(InfoFieldAnnotation.class);
-        standardAnnotations = new HashMap<String, VariantAnnotation>();
+        out.println("\nAvailable annotations for the VCF INFO field:");
-        List<Class<? extends VariantAnnotation>> annotationClasses = PackageUtils.getClassesImplementingInterface(VariantAnnotation.class);
+        for (int i = 0; i < infoAnnotationClasses.size(); i++)
-        for ( Class c : annotationClasses ) {
+            out.println("\t" + infoAnnotationClasses.get(i).getSimpleName());
-            try {
+        out.println();
-                VariantAnnotation annot = (VariantAnnotation) c.newInstance();
+        List<Class<? extends GenotypeAnnotation>> genotypeAnnotationClasses = PackageUtils.getClassesImplementingInterface(GenotypeAnnotation.class);
-                allAnnotations.put(c.getSimpleName().toUpperCase(), annot);
+        out.println("\nAvailable annotations for the VCF FORMAT field:");
-                if ( annot instanceof StandardVariantAnnotation )
+        for (int i = 0; i < genotypeAnnotationClasses.size(); i++)
-                    standardAnnotations.put(c.getSimpleName().toUpperCase(), annot);
+            out.println("\t" + genotypeAnnotationClasses.get(i).getSimpleName());
-            } catch (InstantiationException e) {
-                throw new StingException(String.format("Cannot instantiate annotation class '%s': must be concrete class", c.getSimpleName()));
-            } catch (IllegalAccessException e) {
-                throw new StingException(String.format("Cannot instantiate annotation class '%s': must have no-arg constructor", c.getSimpleName()));
-            }
-        }
-    }
-
-    private void listFiltersAndExit() {
-        List<Class<? extends VariantAnnotation>> annotationClasses = PackageUtils.getClassesImplementingInterface(VariantAnnotation.class);
-        out.println("\nAvailable annotations:");
-        for (int i = 0; i < annotationClasses.size(); i++)
-            out.println("\t" + annotationClasses.get(i).getSimpleName());
         out.println();
         System.exit(0);
     }
@@ -87,7 +64,7 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
     public void initialize() {
 
         if ( LIST )
-            listFiltersAndExit();
+            listAnnotationsAndExit();
 
         // get the list of all sample names from the various VCF input rods
         TreeSet<String> samples = new TreeSet<String>();
@@ -104,53 +81,17 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
             logger.warn("There are no samples input at all; use the --sampleName argument to specify one if desired.");
         }
 
-        determineAllAnnotations();
+        if ( USE_ALL_ANNOTATIONS )
-
+            engine = new VariantAnnotatorEngine(getToolkit());
-        if ( USE_STANDARD_ANNOTATIONS ) {
+        else
-            requestedAnnotations = new ArrayList<VariantAnnotation>(standardAnnotations.values());
+            engine = new VariantAnnotatorEngine(getToolkit(), annotationClassesToUse, annotationsToUse);
-        } else if ( USE_ALL_ANNOTATIONS ) {
-            requestedAnnotations = new ArrayList<VariantAnnotation>(allAnnotations.values());
-        } else {
-            requestedAnnotations = new ArrayList<VariantAnnotation>();
-            if ( ANNOTATIONS != null ) {
-                for ( String requested : ANNOTATIONS ) {
-
-                    VariantAnnotation annot = allAnnotations.get(requested.toUpperCase());
-                    if ( annot == null )
-                        throw new StingException("Unknown annotation '" + requested + "'.  Issue the '-ls' argument to list available annotations.");
-
-                    requestedAnnotations.add(annot);
-                }
-            }
-        }
-
-        // check to see whether a dbsnp rod was included
-        List<ReferenceOrderedDataSource> dataSources = getToolkit().getRodDataSources();
-        for ( ReferenceOrderedDataSource source : dataSources ) {
-            ReferenceOrderedData rod = source.getReferenceOrderedData();
-            if ( rod.getType().equals(rodDbSNP.class) ) {
-                annotateDbsnp = true;
-            }
-            if ( rod.getName().equals("hapmap2") ) {
-                annotateHapmap2 = true;
-            }
-            if ( rod.getName().equals("hapmap3") ) {
-                annotateHapmap3 = true;
-            }
-        }
 
         // setup the header fields
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
         hInfo.add(new VCFHeaderLine("source", "VariantAnnotator"));
         hInfo.add(new VCFHeaderLine("annotatorReference", getToolkit().getArguments().referenceFile.getName()));
-        hInfo.addAll(getVCFAnnotationDescriptions(requestedAnnotations));
+        hInfo.addAll(engine.getVCFAnnotationDescriptions());
-        if ( annotateDbsnp )
-            hInfo.add(new VCFInfoHeaderLine(VCFRecord.DBSNP_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "dbSNP membership"));
-        if ( annotateHapmap2 )
-            hInfo.add(new VCFInfoHeaderLine(VCFRecord.HAPMAP2_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Hapmap 2 membership"));
-        if ( annotateHapmap3 )
-            hInfo.add(new VCFInfoHeaderLine(VCFRecord.HAPMAP3_KEY,1,VCFInfoHeaderLine.INFO_TYPE.Integer, "Hapmap 3 membership"));
 
         vcfWriter = new VCFWriter(VCF_OUT);
         VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
@@ -189,120 +130,31 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
         if ( rods == null || rods.size() == 0 )
             return 0;
 
-        Map<String, String> annotations = new HashMap<String, String>();
         ReferenceOrderedDatum variant = rods.get(0);
         VariantContext vc = VariantContextAdaptors.toVariantContext("variant", variant);
         if ( vc == null )
             return 0;
 
+        MutableVariantContext mvc = new MutableVariantContext(vc);
+
         // if the reference base is not ambiguous, we can annotate
         if ( BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 ) {
             Map<String, StratifiedAlignmentContext> stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup());
-            if ( stratifiedContexts != null )
+            if ( stratifiedContexts != null ) {
-                annotations = getAnnotations(tracker, ref, stratifiedContexts, vc, requestedAnnotations, annotateDbsnp, annotateHapmap2, annotateHapmap3);
+                engine.annotateContext(tracker, ref, stratifiedContexts, mvc);
+            }
         }
 
-        VCFRecord record;
+        if ( variant instanceof RodVCF ) {
-        if ( variant instanceof RodVCF )
+            RodVCF vcf = (RodVCF)variant;
-            record = ((RodVCF)variant).mCurrentRecord;
+            vcfWriter.addRecord(VariantContextAdaptors.toVCF(mvc, ref.getBase(), Arrays.asList(vcf.getRecord().getGenotypeFormatString().split(VCFRecord.GENOTYPE_FIELD_SEPERATOR)), vcf.getFilterString() != null));
-        else
+        } else {
-            record = VariantContextAdaptors.toVCF(vc, ref.getBase());
+            vcfWriter.addRecord(VariantContextAdaptors.toVCF(mvc, ref.getBase()));
-
+        }
-        record.addInfoFields(annotations);
-        writeVCF(tracker, record);
 
         return 1;
     }
 
-    // option #1: don't specify annotations to be used: standard annotations are used by default
-    public static Set<VCFHeaderLine> getVCFAnnotationDescriptions() {
-        if ( standardAnnotations == null )
-            determineAllAnnotations();
-
-        TreeSet<VCFHeaderLine> descriptions = new TreeSet<VCFHeaderLine>();
-        for ( VariantAnnotation annotation : standardAnnotations.values() )
-            descriptions.add(annotation.getDescription());
-
-        return descriptions;
-    }
-
-    // option #2: specify that all possible annotations be used
-    public static Set<VCFHeaderLine> getAllVCFAnnotationDescriptions() {
-        if ( standardAnnotations == null )
-            determineAllAnnotations();
-
-        TreeSet<VCFHeaderLine> descriptions = new TreeSet<VCFHeaderLine>();
-        for ( VariantAnnotation annotation : allAnnotations.values() )
-            descriptions.add(annotation.getDescription());
-
-        return descriptions;
-    }
-
-    // option #3: specify the exact annotations to be used
-    public static Set<VCFHeaderLine> getVCFAnnotationDescriptions(Collection<VariantAnnotation> annotations) {
-
-        TreeSet<VCFHeaderLine> descriptions = new TreeSet<VCFHeaderLine>();
-        for ( VariantAnnotation annotation : annotations )
-            descriptions.add(annotation.getDescription());
-
-        return descriptions;
-    }
-
-    // option #1: don't specify annotations to be used: standard annotations are used by default
-    public static Map<String, String> getAnnotations(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc, boolean annotateDbsnp, boolean annotateHapmap2, boolean annotateHapmap3) {
-        if ( standardAnnotations == null )
-            determineAllAnnotations();
-        return getAnnotations(tracker, ref, stratifiedContexts, vc, standardAnnotations.values(), annotateDbsnp, annotateHapmap2, annotateHapmap3);
-    }
-
-    // option #2: specify that all possible annotations be used
-    public static Map<String, String> getAllAnnotations(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc, boolean annotateDbsnp, boolean annotateHapmap2, boolean annotateHapmap3) {
-        if ( allAnnotations == null )
-            determineAllAnnotations();
-        return getAnnotations(tracker, ref, stratifiedContexts, vc, allAnnotations.values(), annotateDbsnp, annotateHapmap2, annotateHapmap3);
-    }
-
-    // option #3: specify the exact annotations to be used
-    public static Map<String, String> getAnnotations(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc, Collection<VariantAnnotation> annotations, boolean annotateDbsnp, boolean annotateHapmap2, boolean annotateHapmap3) {
-
-        HashMap<String, String> results = new HashMap<String, String>();
-
-        // annotate dbsnp occurrence
-        if ( annotateDbsnp ) {
-            rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getTrackData("dbsnp", null));
-            results.put(VCFRecord.DBSNP_KEY, dbsnp == null ? "0" : "1");
-        }
-
-        if ( annotateHapmap2 ) {
-            RODRecordList hapmap2 = tracker.getTrackData("hapmap2",null);
-            results.put(VCFRecord.HAPMAP2_KEY, hapmap2 == null? "0" : "1");
-        }
-
-        if ( annotateHapmap3 ) {
-            RODRecordList hapmap3 = tracker.getTrackData("hapmap3",null);
-            results.put( VCFRecord.HAPMAP3_KEY, hapmap3 == null ? "0" : "1");
-        }
-
-        for ( VariantAnnotation annotator : annotations) {
-            String annot = annotator.annotate(tracker, ref, stratifiedContexts, vc);
-            if ( annot != null ) {
-                results.put(annotator.getKeyName(), annot);
-            }
-        }
-
-        return results;
-    }
-
-    private void writeVCF(RefMetaDataTracker tracker, VCFRecord record) {
-        // annotate dbsnp id if available and not already there
-        if ( annotateDbsnp && (record.getID() == null || record.getID().equals(VCFRecord.EMPTY_ID_FIELD)) ) {
-            rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getTrackData("dbsnp", null));
-            if ( dbsnp != null )
-                record.setID(dbsnp.getRS_ID());
-        }
-        vcfWriter.addRecord(record);
-    }
-
     /**
      * Increment the number of loci processed.
      *

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

@@ -0,0 +1,169 @@
+package org.broadinstitute.sting.gatk.walkers.annotator;
+
+import org.broadinstitute.sting.gatk.contexts.*;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.MutableVariantContext;
+import org.broadinstitute.sting.gatk.refdata.*;
+import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
+import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.genotype.vcf.*;
+
+import java.util.*;
+
+
+public class VariantAnnotatorEngine {
+
+    private ArrayList<InfoFieldAnnotation> requestedInfoAnnotations;
+    private ArrayList<GenotypeAnnotation> requestedGenotypeAnnotations;
+
+    // should we annotate dbsnp?
+    private boolean annotateDbsnp = false;
+    // how about hapmap2?
+    private boolean annotateHapmap2 = false;
+    // how about hapmap3?
+    private boolean annotateHapmap3 = false;
+
+
+    // use this constructor if you want all possible annotations
+    public VariantAnnotatorEngine(GenomeAnalysisEngine engine) {
+        List<Class<? extends InfoFieldAnnotation>> infoAnnotationClasses = PackageUtils.getClassesImplementingInterface(InfoFieldAnnotation.class);
+        requestedInfoAnnotations = getInstances(infoAnnotationClasses);
+        List<Class<? extends GenotypeAnnotation>> genotypeAnnotationClasses = PackageUtils.getClassesImplementingInterface(GenotypeAnnotation.class);
+        requestedGenotypeAnnotations = getInstances(genotypeAnnotationClasses);
+
+        initialize(engine);
+    }
+
+    // use this constructor if you want to select specific annotations (and/or interfaces)
+    public VariantAnnotatorEngine(GenomeAnalysisEngine engine, String[] annotationClassesToUse, String[] annotationsToUse) {
+        // create a map for all annotation classes which implement our top-level interfaces
+        HashMap<String, Class> classMap = new HashMap<String, Class>();
+        for ( Class c : PackageUtils.getClassesImplementingInterface(InfoFieldAnnotation.class) )
+            classMap.put(c.getSimpleName(), c);
+        for ( Class c : PackageUtils.getClassesImplementingInterface(GenotypeAnnotation.class) )
+            classMap.put(c.getSimpleName(), c);
+        for ( Class c : PackageUtils.getInterfacesExtendingInterface(AnnotationType.class) )
+            classMap.put(c.getSimpleName(), c);
+
+        HashSet<Class> classes = new HashSet<Class>();
+        // get the classes from the provided groups (interfaces)
+        for ( String group : annotationClassesToUse ) {
+            Class interfaceClass = classMap.get(group);
+            if ( interfaceClass == null )
+                interfaceClass = classMap.get(group + "Annotation");
+            if ( interfaceClass == null )
+                throw new StingException("Class " + group + " is not found; please check that you have specified the class name correctly");
+            classes.addAll(PackageUtils.getClassesImplementingInterface(interfaceClass));
+        }
+        // get the specific classes provided
+        for ( String annotation : annotationsToUse ) {
+            Class annotationClass = classMap.get(annotation);
+            if ( annotationClass == null )
+                annotationClass = classMap.get(annotation + "Annotation");
+            if ( annotationClass == null )
+                throw new StingException("Class " + annotation + " is not found; please check that you have specified the class name correctly");
+            classes.add(annotationClass);
+        }
+
+        // get the instances
+        requestedInfoAnnotations = new ArrayList<InfoFieldAnnotation>();
+        requestedGenotypeAnnotations = new ArrayList<GenotypeAnnotation>();
+
+        for ( Class c : classes ) {
+            if ( InfoFieldAnnotation.class.isAssignableFrom(c) )
+                requestedInfoAnnotations.add((InfoFieldAnnotation)getInstance(c));
+            else if ( GenotypeAnnotation.class.isAssignableFrom(c) )
+                requestedGenotypeAnnotations.add((GenotypeAnnotation)getInstance(c));
+        }
+
+        initialize(engine);
+    }
+
+    private static <T> ArrayList<T> getInstances(List<Class<? extends T>> classes) {
+        ArrayList<T> objects = new ArrayList<T>();
+        for ( Class c : classes )
+            objects.add((T)getInstance(c));
+        return objects;
+    }
+
+    private static <T> T getInstance(Class<T> c) {
+        try {
+            return c.newInstance();
+        } catch (InstantiationException e) {
+            throw new StingException(String.format("Cannot instantiate annotation class '%s': must be concrete class", c.getSimpleName()));
+        } catch (IllegalAccessException e) {
+            throw new StingException(String.format("Cannot instantiate annotation class '%s': must have no-arg constructor", c.getSimpleName()));
+        }
+    }
+
+    private void initialize(GenomeAnalysisEngine engine) {
+
+        // check to see whether a dbsnp rod was included
+        List<ReferenceOrderedDataSource> dataSources = engine.getRodDataSources();
+        for ( ReferenceOrderedDataSource source : dataSources ) {
+            ReferenceOrderedData rod = source.getReferenceOrderedData();
+            if ( rod.getType().equals(rodDbSNP.class) ) {
+                annotateDbsnp = true;
+            }
+            if ( rod.getName().equals("hapmap2") ) {
+                annotateHapmap2 = true;
+            }
+            if ( rod.getName().equals("hapmap3") ) {
+                annotateHapmap3 = true;
+            }
+        }
+    }
+
+    public Set<VCFHeaderLine> getVCFAnnotationDescriptions() {
+
+        Set<VCFHeaderLine> descriptions = new HashSet<VCFHeaderLine>();
+
+        for ( InfoFieldAnnotation annotation : requestedInfoAnnotations )
+            descriptions.add(annotation.getDescription());
+        for ( GenotypeAnnotation annotation : requestedGenotypeAnnotations )
+            descriptions.add(annotation.getDescription());
+        if ( annotateDbsnp )
+            descriptions.add(new VCFInfoHeaderLine(VCFRecord.DBSNP_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "dbSNP membership"));
+        if ( annotateHapmap2 )
+            descriptions.add(new VCFInfoHeaderLine(VCFRecord.HAPMAP2_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Hapmap 2 membership"));
+        if ( annotateHapmap3 )
+            descriptions.add(new VCFInfoHeaderLine(VCFRecord.HAPMAP3_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Hapmap 3 membership"));
+
+        return descriptions;
+    }
+
+    public void annotateContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, MutableVariantContext vc) {
+
+        // annotate dbsnp occurrence
+        if ( annotateDbsnp ) {
+            rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getTrackData("dbsnp", null));
+            vc.putAttribute(VCFRecord.DBSNP_KEY, dbsnp == null ? "0" : "1");
+            // annotate dbsnp id if available and not already there
+            if ( dbsnp != null && !vc.hasAttribute("ID") )
+                vc.putAttribute("ID", dbsnp.getRS_ID());
+        }
+
+        if ( annotateHapmap2 ) {
+            RODRecordList hapmap2 = tracker.getTrackData("hapmap2",null);
+            vc.putAttribute(VCFRecord.HAPMAP2_KEY, hapmap2 == null? "0" : "1");
+        }
+
+        if ( annotateHapmap3 ) {
+            RODRecordList hapmap3 = tracker.getTrackData("hapmap3",null);
+            vc.putAttribute(VCFRecord.HAPMAP3_KEY, hapmap3 == null ? "0" : "1");
+        }
+
+        for ( InfoFieldAnnotation annotation : requestedInfoAnnotations ) {
+            String annot = annotation.annotate(tracker, ref, stratifiedContexts, vc);
+            if ( annot != null ) {
+                vc.putAttribute(annotation.getKeyName(), annot);
+            }
+        }
+
+        for ( GenotypeAnnotation annotation : requestedGenotypeAnnotations ) {
+            annotation.annotateContext(tracker, ref, stratifiedContexts, vc);
+        }
+    }
+}

java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java

@@ -0,0 +1,3 @@
+package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+
+public interface AnnotationType {}

java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java

@@ -0,0 +1,3 @@
+package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+
+public interface ExperimentalAnnotation extends AnnotationType {}

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

@@ -0,0 +1,22 @@
+package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFFormatHeaderLine;
+
+import java.util.Map;
+
+public interface GenotypeAnnotation {
+
+    // annotate the given record for the given variation and context split by sample
+    public void annotateContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc);
+
+    // return the FORMAT key
+    public String getKeyName();
+
+    // return the description used for the VCF FORMAT meta field
+    public VCFFormatHeaderLine getDescription();
+   
+}

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

@@ -1,15 +1,14 @@
-package org.broadinstitute.sting.gatk.walkers.annotator;
+package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.Map;
 
-
+public interface InfoFieldAnnotation {
-public interface VariantAnnotation {
 
     // return the annotation for the given variation and context split by sample (return null for no annotation)
     public String annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc);

java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java

@@ -0,0 +1,3 @@
+package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+
+public interface StandardAnnotation extends AnnotationType {}

java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java

@@ -0,0 +1,3 @@
+package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+
+public interface WorkInProgressAnnotation extends AnnotationType {}

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java

@@ -53,9 +53,6 @@ public class UnifiedArgumentCollection {
     @Argument(fullName = "noSLOD", shortName = "nsl", doc = "If provided, we will not calculate the SLOD", required = false)
     public boolean NO_SLOD = false;
 
-    @Argument(fullName = "include_experimental_annotations", shortName = "exp", doc = "Annotate calls with all annotations, including experimental ones", required = false)
-    public boolean ALL_ANNOTATIONS = false;
-
 
     // control the error modes
     @Argument(fullName = "assume_single_sample_reads", shortName = "single_sample", doc = "The single sample that we should assume is represented in the input bam (and therefore associate with all reads regardless of whether they have read groups)", required = false)

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

@@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.*;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator;
+import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.cmdLine.*;
 import org.broadinstitute.sting.utils.genotype.*;
@@ -59,9 +59,18 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
     @Argument(fullName = "beagle_file", shortName = "beagle", doc = "File to print BEAGLE-specific data for use with imputation", required = false)
     public PrintStream beagleWriter = null;
 
+    @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
+    protected String[] annotationsToUse = {};
+
+    @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
+    protected String[] annotationClassesToUse = { "Standard" };
+
     // the calculation arguments
     private UnifiedGenotyperEngine UG_engine = null;
 
+    // the annotation engine
+    private VariantAnnotatorEngine annotationEngine;
+
     // enable deletions in the pileup
     public boolean includeReadsWithDeletionAtLoci() { return true; }
 
@@ -95,7 +104,8 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
      **/
     public void initialize() {
 
-        UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, writer, verboseWriter, beagleWriter);
+        annotationEngine = new VariantAnnotatorEngine(getToolkit(), annotationClassesToUse, annotationsToUse);
+        UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, writer, verboseWriter, beagleWriter, annotationEngine);
 
         // initialize the writers
         if ( verboseWriter != null ) {
@@ -129,11 +139,8 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         headerInfo.add(new VCFHeaderLine("source", "UnifiedGenotyper"));
         headerInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
 
-        // annotation (INFO) fields from VariantAnnotator
+        // all annotation fields from VariantAnnotatorEngine
-        if ( UAC.ALL_ANNOTATIONS )
+        headerInfo.addAll(annotationEngine.getVCFAnnotationDescriptions());
-            headerInfo.addAll(VariantAnnotator.getAllVCFAnnotationDescriptions());
-        else
-            headerInfo.addAll(VariantAnnotator.getVCFAnnotationDescriptions());
 
         // annotation (INFO) fields from UnifiedGenotyper
         headerInfo.add(new VCFInfoHeaderLine(VCFRecord.ALLELE_FREQUENCY_KEY, 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Allele Frequency"));

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java

@@ -32,7 +32,7 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.MutableVariantConte
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
-import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator;
+import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.pileup.*;
 import org.broadinstitute.sting.utils.genotype.*;
@@ -57,6 +57,9 @@ public class UnifiedGenotyperEngine {
     // the unified argument collection
     protected UnifiedArgumentCollection UAC = null;
 
+    // the annotation engine
+    protected VariantAnnotatorEngine annotationEngine;
+
     // the model used for calculating genotypes
     protected ThreadLocal<GenotypeCalculationModel> gcm = new ThreadLocal<GenotypeCalculationModel>();
 
@@ -71,20 +74,21 @@ public class UnifiedGenotyperEngine {
 
 
     public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC) {
-        initialize(toolkit, UAC, null, null, null, null);
+        initialize(toolkit, UAC, null, null, null, null, null);
     }
 
-    public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, Logger logger, GenotypeWriter genotypeWriter, PrintStream verboseWriter, PrintStream beagleWriter) {
+    public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, Logger logger, GenotypeWriter genotypeWriter, PrintStream verboseWriter, PrintStream beagleWriter, VariantAnnotatorEngine engine) {
-        initialize(toolkit, UAC, logger, genotypeWriter, verboseWriter, beagleWriter);
+        initialize(toolkit, UAC, logger, genotypeWriter, verboseWriter, beagleWriter, engine);
 
     }
 
-    private void initialize(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, Logger logger, GenotypeWriter genotypeWriter, PrintStream verboseWriter, PrintStream beagleWriter) {
+    private void initialize(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, Logger logger, GenotypeWriter genotypeWriter, PrintStream verboseWriter, PrintStream beagleWriter, VariantAnnotatorEngine engine) {
         this.UAC = UAC;
         this.logger = logger;
         this.genotypeWriter = genotypeWriter;
         this.verboseWriter = verboseWriter;
         this.beagleWriter = beagleWriter;
+        this.annotationEngine = engine;
 
         // deal with input errors
         if ( UAC.genotypeModel == GenotypeCalculationModel.Model.INDELS && !(genotypeWriter instanceof VCFGenotypeWriter) ) {
@@ -223,13 +227,7 @@ public class UnifiedGenotyperEngine {
             if ( call != null && call.vc != null ) {
                 // first off, we want to use the *unfiltered* context for the annotations
                 stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(rawContext.getBasePileup());
-
+                annotationEngine.annotateContext(tracker, refContext, stratifiedContexts, (MutableVariantContext)call.vc);
-                Map<String, String> annotations;
-                if ( UAC.ALL_ANNOTATIONS )
-                    annotations = VariantAnnotator.getAllAnnotations(tracker, refContext, stratifiedContexts, call.vc, annotateDbsnp, annotateHapmap2, annotateHapmap3);
-                else
-                    annotations = VariantAnnotator.getAnnotations(tracker, refContext, stratifiedContexts, call.vc, annotateDbsnp, annotateHapmap2, annotateHapmap3);
-                ((MutableVariantContext)call.vc).putAttributes(annotations);
             }
         }
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfNonrefBasesSupportingSNP.java

@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.oneoffprojects.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.BaseUtils;
@@ -19,7 +19,7 @@ import java.util.Map;
  * Time: 2:48:15 PM
  * To change this template use File | Settings | File Templates.
  */
-public class ProportionOfNonrefBasesSupportingSNP implements VariantAnnotation {
+public class ProportionOfNonrefBasesSupportingSNP implements InfoFieldAnnotation {
     private String KEY_NAME = "prop_nonref_that_are_snp";
 
     public String getKeyName() { return KEY_NAME; }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfRefSecondBasesSupportingSNP.java

@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.oneoffprojects.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
@@ -20,7 +20,7 @@ import java.util.Map;
  * Time: 2:18:43 PM
  * To change this template use File | Settings | File Templates.
  */
-public class ProportionOfRefSecondBasesSupportingSNP implements VariantAnnotation {
+public class ProportionOfRefSecondBasesSupportingSNP implements InfoFieldAnnotation {
     private String KEY_NAME = "ref_2bb_snp_prop";
     private boolean USE_MAPQ0_READS = false;
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ProportionOfSNPSecondBasesSupportingRef.java

@@ -4,7 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.BaseUtils;
@@ -20,7 +20,7 @@ import java.util.Map;
  * Time: 2:42:05 PM
  * To change this template use File | Settings | File Templates.
  */
-public class ProportionOfSNPSecondBasesSupportingRef implements VariantAnnotation {
+public class ProportionOfSNPSecondBasesSupportingRef implements InfoFieldAnnotation {
     public String KEY_NAME = "SNP_2B_SUPPORT_REF";
     public boolean USE_MAPQ0_READS = false;
     public String debug_file = "/humgen/gsa-scr1/chartl/temporary/ProportionOfRefSecondBasesSupportingSNP.debug.txt";

java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ThousandGenomesAnnotator.java

@@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotation;
+import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.oneoffprojects.refdata.HapmapVCFROD;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
@@ -17,7 +17,7 @@ import java.util.Map;
  * @author chartl
  * @date Feb 1, 2010
  */
-public class ThousandGenomesAnnotator implements VariantAnnotation {
+public class ThousandGenomesAnnotator implements InfoFieldAnnotation {
 
     public String getKeyName() {
         return "1KG";

java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java

@@ -27,7 +27,6 @@ import java.util.*;
 // todo -- write a simple column table system and have the evaluators return this instead of the list<list<string>> objects
 
 // todo -- site frequency spectrum eval (freq. of variants in eval as a function of their AC and AN numbers)
-// todo -- allele freqeuncy discovery tool (FREQ in true vs. discovery counts in eval).  Needs to process subset of samples in true (pools)
 // todo -- clustered SNP counter
 // todo -- HWEs
 // todo -- indel metrics [count of sizes in/del should be in CountVariants]
@@ -84,12 +83,10 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
     //
     // --------------------------------------------------------------------------------------------------------------
 
-    // todo -- add doc string
+    @Argument(shortName="select", doc="One or more stratifications to use when evaluating the data", required=false)
-    @Argument(shortName="select", doc="", required=false)
     protected String[] SELECT_EXPS = {"QUAL > 500.0", "HARD_TO_VALIDATE==1", "GATK_STANDARD==1"};
 
-    // todo -- add doc string
+    @Argument(shortName="selectName", doc="Names to use for the list of stratifications (must be a 1-to-1 mapping)", required=false)
-    @Argument(shortName="selectName", doc="", required=false)
     protected String[] SELECT_NAMES = {"q500plus", "low_mapq", "gatk_std_filters"};
 
     @Argument(shortName="known", doc="Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets", required=false)

java/src/org/broadinstitute/sting/utils/PackageUtils.java

@@ -52,4 +52,22 @@ public class PackageUtils {
 
         return concreteTypes;
     }
+
+    /**
+     * Return the interface classes that extend the specified interface.
+     *
+     * @param iface  the interface which returned classes should extend.
+     * @return       the list of interface classes that implement the interface.
+     */
+    public static <T> List<Class<? extends T>> getInterfacesExtendingInterface(Class<T> iface) {
+        // Load all classes extending the given interface, then filter out any class that is concrete.
+        Set<Class<? extends T>> allTypes = reflections.getSubTypesOf(iface);
+        List<Class<? extends T>> nonConcreteTypes = new ArrayList<Class<? extends T>>();
+        for( Class<? extends T> type: allTypes ) {
+            if( !JVMUtils.isConcrete(type) )
+                nonConcreteTypes.add(type);
+        }
+
+        return nonConcreteTypes;
+    }
 }

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java

@@ -85,9 +85,6 @@ public class VCFGenotypeRecord {
         // make sure the GT field isn't being set
         if ( key.equals(GENOTYPE_KEY) )
             throw new IllegalArgumentException("Setting the GT field is not allowed as that's done internally");
-        // we need to be backwards compatible
-        if ( key.equals(OLD_DEPTH_KEY) )
-             key = DEPTH_KEY;
         mFields.put(key, value);
     }
 

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java

@@ -172,6 +172,8 @@ public class VCFRecord {
                 case INFO:
                     String vals[] = columnValues.get(val).split(";");
                     for (String alt : vals) {
+                        if ( alt.equals(EMPTY_INFO_FIELD) )
+                            continue;
                         String keyVal[] = alt.split("=");
                         if ( keyVal.length == 1 )
                             addInfoField(keyVal[0], "");
@@ -391,11 +393,6 @@ public class VCFRecord {
      * @return a map, of the info key-value pairs
      */
     public final Map<String, String> getInfoValues() {
-        if (mInfoFields.size() < 1) {
-            Map<String, String> map = new HashMap<String, String>();
-            map.put(".", "");
-            return map;
-        }
         return mInfoFields;
     }
 
@@ -497,10 +494,6 @@ public class VCFRecord {
     public void addInfoField(String key, String value) {
         //System.out.printf("Adding info field %s=%s%n", key, value);
         mInfoFields.put(key, value);
-
-        // remove the empty token if it's present
-        if ( mInfoFields.containsKey(".") )
-            mInfoFields.remove(".");
     }
 
     public void printInfoFields() {
@@ -587,15 +580,18 @@ public class VCFRecord {
      * @return a string representing the infomation fields
      */
     protected String createInfoString() {
-        String info = "";
+        StringBuffer info = new StringBuffer();
-        for (String str : getInfoValues().keySet()) {
+        boolean isFirst = true;
-
+        for (String str : mInfoFields.keySet()) {
-            if (str.equals(EMPTY_INFO_FIELD))
+            if ( isFirst )
-                return EMPTY_INFO_FIELD;
+                isFirst = false;
             else
-                info += str + "=" + getInfoValues().get(str) + INFO_FIELD_SEPERATOR;
+                info.append(INFO_FIELD_SEPERATOR);
+            info.append(str);
+            info.append("=");
+            info.append(mInfoFields.get(str));
         }
-        return (info.contains(INFO_FIELD_SEPERATOR)) ? info.substring(0, info.lastIndexOf(INFO_FIELD_SEPERATOR)) : info;
+        return info.length() == 0 ? EMPTY_INFO_FIELD : info.toString();
     }
 
     /**

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

@@ -65,7 +65,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testHasAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("98bcbd4dd9d0edc5aa1ae97877a7e8f8"));
         executeTest("test file has annotations, asking for annotations, #1", spec);
     }
@@ -73,7 +73,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testHasAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
+                baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
                 Arrays.asList("74d1dc2a65f4398cd8c11b294917dfe5"));
         executeTest("test file has annotations, asking for annotations, #2", spec);
     }
@@ -97,7 +97,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testNoAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
+                baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
                 Arrays.asList("437b45d2ee1a150f15c4479cb2cb5e8f"));
         executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
     }
@@ -105,7 +105,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testNoAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
+                baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
                 Arrays.asList("857875a3234112bcd047cf31683aa331"));
         executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
     }

java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -22,7 +22,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testPooled1() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,000-10,024,000 -bm empirical -gm POOLED -ps 60 -confidence 30", 1,
-                Arrays.asList("c30af5d192661abd77b05a316f1d8923"));
+                Arrays.asList("c91f44a198cd7222520118726ea806ca"));
         executeTest("testPooled1", spec);
     }
 
@@ -35,7 +35,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot1Joint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("882b2fae1cd1ba65cac3cadacec0ce2b"));
+                Arrays.asList("d8af2cb687aa89d21c5492c98f100b5f"));
         executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
     }
 
@@ -43,7 +43,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot2Joint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("aa0cff414e6623c36465726a987a645d"));
+                Arrays.asList("724bc2b640e111df82b9ebd261ddb5d9"));
         executeTest("testMultiSamplePilot2 - Joint Estimate", spec);
     }
 
@@ -51,7 +51,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testSingleSamplePilot2Joint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("53df224164083cc7d8ad85f3d16ba38f"));
+                Arrays.asList("304ec09a459705f5738a9a82b603ae1f"));
         executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
     }
 
@@ -64,7 +64,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testParallelization() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,400,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30 -nt 4", 1,
-                Arrays.asList("3ade750c0d261594ea549db7b127a1e3"));
+                Arrays.asList("33e9fe3b8c1ed729c22196d5db3e0d11"));
         executeTest("test parallelization", spec);
     }
 
@@ -77,11 +77,11 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testParameter() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "-genotype", "bee9fa71d70fdde094ab30785d4fa84e" );
+        e.put( "-genotype", "fb3ffa0f101cf9f8ffc6892b0acab414" );
-        e.put( "-all_bases", "410cff9d97cd017becd1f6260c7abeeb" );
+        e.put( "-all_bases", "3888d0856370f9a5b18c078e2caaec2a" );
-        e.put( "--min_base_quality_score 26", "85e1c35d3926afc68761aefea3f41332" );
+        e.put( "--min_base_quality_score 26", "66f729d1948dc057486832731278c226" );
-        e.put( "--min_mapping_quality_score 26", "1c49a7d5e6ad295c0450b8a35053050f" );
+        e.put( "--min_mapping_quality_score 26", "80a7fca199b899a3d0bc1293eb7bf7e5" );
-        e.put( "--max_mismatches_in_40bp_window 5", "7e7db5a0d859704e12a4b89d35065682" );
+        e.put( "--max_mismatches_in_40bp_window 5", "c6f8846865dcd9021372df917f6c962b" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -95,7 +95,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testConfidence() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -bm empirical -gm JOINT_ESTIMATE -confidence 10 ", 1,
-                Arrays.asList("c67dd3e97cb188b117074d2c4692fcfa"));
+                Arrays.asList("7854c02fcc0c8fcc879f6e35fef2e11f"));
         executeTest("testConfidence", spec);
     }
 
@@ -106,7 +106,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     // --------------------------------------------------------------------------------------------------------------
     @Test
     public void testOtherOutput() {
-        String[] md5s = {"ce0024816a092af9f998a7561ffb4fb2", "8cba0b8752f18fc620b4697840bc7291"};
+        String[] md5s = {"5f3b9abe1b2c30c2ede0007c43e1934c", "8cba0b8752f18fc620b4697840bc7291"};
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper" +
                         " -R " + oneKGLocation + "reference/human_b36_both.fasta" +