Unified HaplotypeCaller's force-calling mode with Mutect2's

src/main/java/org/broadinstitute/hellbender/engine/FeatureCache.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.hellbender.engine;
 
+import htsjdk.samtools.util.Locatable;
 import htsjdk.tribble.Feature;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -150,7 +151,7 @@ public void fill( final Iterator<CACHED_FEATURE> featureIter, final SimpleInterv
      * @param interval the interval to check against the contents of our cache
      * @return true if all records overlapping the provided interval are already contained in our cache, otherwise false
      */
-    public boolean cacheHit( final SimpleInterval interval ) {
+    public boolean cacheHit( final Locatable interval ) {
         final boolean cacheHit = cachedInterval != null && cachedInterval.contains(interval);
 
         if ( cacheHit ) {

src/main/java/org/broadinstitute/hellbender/engine/FeatureContext.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.hellbender.engine;
 
 import com.google.common.annotations.VisibleForTesting;
+import htsjdk.samtools.util.Locatable;
 import htsjdk.tribble.Feature;
 import org.broadinstitute.hellbender.cmdline.CommandLineProgram;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
@@ -165,7 +166,7 @@ public <T extends Feature> List<T> getValues(final FeatureInput<T> featureDescri
      *         this FeatureContext's query interval as expanded by the specified number of leading/trailing bases.
      *         Empty List if there is no backing data source and/or interval.
      */
-    public <T extends Feature> List<T> getValues(final FeatureInput<T> featureDescriptor, final SimpleInterval queryInterval) {
+    public <T extends Feature> List<T> getValues(final FeatureInput<T> featureDescriptor, final Locatable queryInterval) {
         if (featureManager == null || queryInterval == null || featureDescriptor == null) {
             return Collections.emptyList();
         }

src/main/java/org/broadinstitute/hellbender/engine/FeatureDataSource.java

@@ -2,6 +2,7 @@
 
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.util.IOUtil;
+import htsjdk.samtools.util.Locatable;
 import htsjdk.tribble.*;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.VCFHeader;
@@ -509,7 +510,7 @@ public Iterator<T> query(final SimpleInterval interval) {
      * @param interval retrieve all Features overlapping this interval
      * @return a List of all Features in this data source that overlap the provided interval
      */
-    public List<T> queryAndPrefetch(final SimpleInterval interval) {
+    public List<T> queryAndPrefetch(final Locatable interval) {
         if (!supportsRandomAccess) {
             throw new UserException("Input " + featureInput.getFeaturePath() + " must support random access to enable queries by interval. " +
                     "If it's a file, please index it using the bundled tool " + IndexFeatureFile.class.getSimpleName());
@@ -540,7 +541,7 @@ public List<T> queryAndPrefetch(final SimpleInterval interval) {
      *
      * @param interval the query interval that produced a cache miss
      */
-    private void refillQueryCache(final SimpleInterval interval) {
+    private void refillQueryCache(final Locatable interval) {
         // Tribble documentation states that having multiple iterators open simultaneously over the same FeatureReader
         // results in undefined behavior
         closeOpenIterationIfNecessary();

src/main/java/org/broadinstitute/hellbender/engine/FeatureManager.java

@@ -2,6 +2,7 @@
 
 import com.google.common.annotations.VisibleForTesting;
 import htsjdk.samtools.SAMSequenceDictionary;
+import htsjdk.samtools.util.Locatable;
 import htsjdk.tribble.Feature;
 import htsjdk.tribble.FeatureCodec;
 import htsjdk.variant.vcf.VCFHeader;
@@ -342,7 +343,7 @@ public List<SAMSequenceDictionary> getAllSequenceDictionaries() {
      * @return A List of all Features in the backing data source for the provided FeatureInput that overlap
      *         the provided interval (may be empty if there are none, but never null)
      */
-    public <T extends Feature> List<T> getFeatures( final FeatureInput<T> featureDescriptor, final SimpleInterval interval ) {
+    public <T extends Feature> List<T> getFeatures( final FeatureInput<T> featureDescriptor, final Locatable interval ) {
         final FeatureDataSource<T> dataSource = lookupDataSource(featureDescriptor);
 
         // No danger of a ClassCastException here, since we verified that the FeatureDataSource for this

src/main/java/org/broadinstitute/hellbender/engine/ReferenceContext.java

@@ -2,6 +2,7 @@
 
 import htsjdk.samtools.SAMSequenceRecord;
 import htsjdk.samtools.reference.ReferenceSequence;
+import htsjdk.samtools.util.Locatable;
 import org.broadinstitute.hellbender.exceptions.GATKException;
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
@@ -30,7 +31,7 @@
  * return empty arrays / iterators. You can determine whether there is a backing source of reference
  * data via {@link #hasBackingDataSource()}, and whether there is an interval via {@link #getInterval}.
  */
-public final class ReferenceContext implements Iterable<Byte> {
+public final class ReferenceContext implements Iterable<Byte>, Locatable {
 
     /**
      * Backing data source. Null if there is no reference data.
@@ -142,6 +143,16 @@ public ReferenceContext( final ReferenceDataSource dataSource, final SimpleInter
         }
     }
 
+    @Override
+    public String getContig() { return interval.getContig(); }
+
+    @Override
+    public int getStart() { return interval.getStart(); }
+
+    @Override
+    public int getEnd() { return interval.getEnd(); }
+
+
     /**
      * Determines whether this ReferenceContext has a backing reference data source. A ReferenceContext with
      * no backing data source will always return an empty bases array from {@link #getBases()} and an

src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java

@@ -259,7 +259,7 @@ private VariantContext calculateGenotypes(VariantContext vc){
         final GenotypeLikelihoodsCalculationModel model = vc.getType() == VariantContext.Type.INDEL
                 ? GenotypeLikelihoodsCalculationModel.INDEL
                 : GenotypeLikelihoodsCalculationModel.SNP;
-        return genotypingEngine.calculateGenotypes(vc, model, null);
+        return genotypingEngine.calculateGenotypes(vc, model);
     }
 
     /**