Annotation changes for M2:

Build a ReferenceContext in ActiveRegionWalkers to pass in to annotation engine so we can call the TandemRepeatAnnotator from M2
Make TandemRepeatAnnotator default annotation for M2.
Setup (but don't use yet) HC-style contamination downsampling.
New HC integration test with TandemRepeatAnnotator

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/TandemRepeatAnnotator.java

@@ -52,6 +52,7 @@
 package org.broadinstitute.gatk.tools.walkers.annotator;
 
 import org.apache.log4j.Logger;
+import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
 import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
 import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
@@ -81,7 +82,7 @@ import java.util.*;
  * </ul>
  *
  */
-public class TandemRepeatAnnotator extends InfoFieldAnnotation implements StandardAnnotation {
+public class TandemRepeatAnnotator extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
     private final static Logger logger = Logger.getLogger(TandemRepeatAnnotator.class);
     private boolean walkerIdentityCheckWarningLogged = false;
 
@@ -93,15 +94,6 @@ public class TandemRepeatAnnotator extends InfoFieldAnnotation implements Standa
                                         final VariantContext vc,
                                         final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) throws UserException {
 
-        // Can not be called from HaplotypeCaller
-        if ( walker instanceof HaplotypeCaller ) {
-            if ( !walkerIdentityCheckWarningLogged ) {
-                logger.warn("Annotation will not be calculated, can not be called from HaplotypeCaller");
-                walkerIdentityCheckWarningLogged = true;
-            }
-            return null;
-        }
-
         if ( !vc.isIndel())
             return null;
 

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java

@@ -54,6 +54,7 @@ package org.broadinstitute.gatk.tools.walkers.haplotypecaller;
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import htsjdk.variant.variantcontext.*;
+import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
 import org.broadinstitute.gatk.utils.genotyper.AlleleList;
 import org.broadinstitute.gatk.utils.genotyper.IndexedAlleleList;
 import org.broadinstitute.gatk.utils.genotyper.SampleList;
@@ -272,7 +273,8 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
                     readAlleleLikelihoods = prepareReadAlleleLikelihoodsForAnnotation(readLikelihoods, perSampleFilteredReadList,
                             genomeLocParser, emitReferenceConfidence, alleleMapper, readAlleleLikelihoods, call);
 
-                    VariantContext annotatedCall = annotationEngine.annotateContextForActiveRegion(tracker,readAlleleLikelihoods, call);
+                    ReferenceContext referenceContext = new ReferenceContext(genomeLocParser, genomeLocParser.createGenomeLoc(mergedVC.getChr(), mergedVC.getStart(), mergedVC.getEnd()), refLoc, ref);
+                    VariantContext annotatedCall = annotationEngine.annotateContextForActiveRegion(referenceContext, tracker,readAlleleLikelihoods, call);
 
                     if( call.getAlleles().size() != mergedVC.getAlleles().size() )
                        annotatedCall = GATKVariantContextUtils.reverseTrimAlleles(annotatedCall);

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

@@ -443,4 +443,9 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
                                 " -o %s",
                         1, UserException.CommandLineException.class));
     }
+
+    @Test
+    public void testHaplotypeCallerTandemRepeatAnnotator() throws IOException{
+        HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "ab9907559e5b20dadbb6f24d02b8070c");
+    }
 }

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java

@@ -218,17 +218,19 @@ public class VariantAnnotatorEngine {
         return annotateDBs(tracker, annotated);
     }
 
-    public VariantContext annotateContextForActiveRegion(final RefMetaDataTracker tracker,
+    public VariantContext annotateContextForActiveRegion(final ReferenceContext referenceContext,
+                                                         final RefMetaDataTracker tracker,
                                                          final ReadLikelihoods<Allele> readLikelihoods,
                                                          final VariantContext vc) {
         //TODO we transform the read-likelihood into the Map^2 previous version for the sake of not changing of not changing annotation interface.
         //TODO should we change those interfaces?
 
         final Map<String, PerReadAlleleLikelihoodMap> annotationLikelihoods = readLikelihoods.toPerReadAlleleLikelihoodMap();
-        return annotateContextForActiveRegion(tracker, annotationLikelihoods, vc);
+        return annotateContextForActiveRegion(referenceContext, tracker, annotationLikelihoods, vc);
     }
 
-    public VariantContext annotateContextForActiveRegion(final RefMetaDataTracker tracker,
+    public VariantContext annotateContextForActiveRegion(final ReferenceContext referenceContext,
+                                                         final RefMetaDataTracker tracker,
                                                          final Map<String, PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap,
                                                          final VariantContext vc) {
         final Map<String, Object> infoAnnotations = new LinkedHashMap<>(vc.getAttributes());
@@ -238,7 +240,7 @@ public class VariantAnnotatorEngine {
             if ( !(annotationType instanceof ActiveRegionBasedAnnotation) )
                 continue;
 
-            final Map<String, Object> annotationsFromCurrentType = annotationType.annotate(perReadAlleleLikelihoodMap, vc);
+            final Map<String, Object> annotationsFromCurrentType = annotationType.annotate(referenceContext, perReadAlleleLikelihoodMap, vc);
             if ( annotationsFromCurrentType != null ) {
                 infoAnnotations.putAll(annotationsFromCurrentType);
             }

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.gatk.tools.walkers.annotator.interfaces;
 
+import org.broadinstitute.gatk.utils.GenomeLoc;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
 import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
 import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
@@ -51,6 +52,10 @@ public abstract class InfoFieldAnnotation extends VariantAnnotatorAnnotation {
         return annotate(null, null, null, null, vc, perReadAlleleLikelihoodMap);
     }
 
+    public Map<String, Object> annotate(ReferenceContext referenceContext, Map<String, PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap, VariantContext vc) {
+
+        return annotate(null, null, referenceContext, null, vc, perReadAlleleLikelihoodMap);
+    }
 
     public abstract Map<String, Object> annotate(final RefMetaDataTracker tracker,
                                                  final AnnotatorCompatible walker,