Make HaplotypeCaller genotype and output spanning deletions

src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java

@@ -281,6 +281,13 @@ && noAllelesOrFirstAlleleIsNotNonRef(outputAlternativeAlleles.alleles)) {
             return limitedContext ? null : estimateReferenceConfidence(vc, stratifiedContexts, AFpriors[INDEX_FOR_AC_EQUALS_1], true, probOfAtLeastOneAltAllele);
         }
 
+        // return a null call if we aren't forcing site emission and the only alt allele is a spanning deletion
+        if (! forceSiteEmission()
+                && outputAlternativeAlleles.alleles.size() == 1
+                && Allele.SPAN_DEL.equals(outputAlternativeAlleles.alleles.get(0))) {
+            return null;
+        }
+
         // start constructing the resulting VC
         final List<Allele> outputAlleles = outputAlternativeAlleles.outputAlleles(vc.getReference());
         final VariantContextBuilder builder = new VariantContextBuilder(callSourceString(), vc.getContig(), vc.getStart(), vc.getEnd(), outputAlleles);
@@ -508,8 +515,8 @@ protected final VariantCallContext emptyCallContext(final FeatureContext feature
         VariantContext vc;
 
         if ( configuration.genotypingOutputMode == GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES ) {
-            final VariantContext ggaVc = GenotypingGivenAllelesUtils.composeGivenAllelesVariantContextFromRod(features,
-                    rawContext.getLocation(), false, configuration.genotypeFilteredAlleles, logger, configuration.alleles);
+            final VariantContext ggaVc = GenotypingGivenAllelesUtils.composeGivenAllelesVariantContextFromVariantList(features,
+                    rawContext.getLocation(), configuration.genotypeFilteredAlleles, configuration.alleles);
             if (ggaVc == null) {
                 return null;
             }

src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingGivenAllelesUtils.java

@@ -1,54 +1,65 @@
 package org.broadinstitute.hellbender.tools.walkers.genotyper;
 
+import com.google.common.annotations.VisibleForTesting;
 import htsjdk.samtools.util.Locatable;
 import htsjdk.variant.variantcontext.VariantContext;
-import org.apache.logging.log4j.Logger;
 import org.broadinstitute.hellbender.engine.FeatureContext;
 import org.broadinstitute.hellbender.engine.FeatureInput;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.Utils;
+import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+import static org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED;
+import static org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.FilteredRecordMergeType.KEEP_UNCONDITIONAL;
 
 /**
  * Compendium of utils to work in GENOTYPE_GIVEN_ALLELES mode.
  */
 public final class GenotypingGivenAllelesUtils {
 
     /**
-     * Composes the given allele variant-context providing information about the rods and reference location.
+     * Composes the given allele variant-context providing information about the given variant alleles and reference location.
      * @param tracker the meta data tracker.
      * @param loc the query location.
-     * @param snpsOnly whether we only should consider SNP variation.
      * @param keepFiltered whether to include filtered variants
-     * @param logger where to output warnings.
      * @param allelesBinding the target variation context binding containing the given alleles.
      * @return never {@code null}
      */
-    public static VariantContext composeGivenAllelesVariantContextFromRod(final FeatureContext tracker,
-                                                                          final Locatable loc,
-                                                                          final boolean snpsOnly,
-                                                                          final boolean keepFiltered,
-                                                                          final Logger logger,
-                                                                          final FeatureInput<VariantContext> allelesBinding) {
+    public static VariantContext composeGivenAllelesVariantContextFromVariantList(final FeatureContext tracker,
+                                                                                  final Locatable loc,
+                                                                                  final boolean keepFiltered,
+                                                                                  final FeatureInput<VariantContext> allelesBinding) {
         Utils.nonNull(tracker, "tracker may not be null");
         Utils.nonNull(loc, "location may not be null");
         Utils.nonNull(allelesBinding, "alleles binding may not be null");
-        VariantContext vc = null;
-
-        // search for usable record
-        for ( final VariantContext rodVc : tracker.getValues(allelesBinding, new SimpleInterval(loc)) ) {
-            if ( rodVc != null && (keepFiltered || rodVc.isNotFiltered()) && (! snpsOnly || rodVc.isSNP() )) {
-                if ( vc == null ) {
-                    vc = rodVc;
-                } else {
-                    if (logger != null) {
-                        logger.warn("Multiple valid VCF records detected in the alleles input file at site "
-                                + loc + ", only considering the first record");
-                    }
-                }
-            }
+
+        final List<VariantContext> variantContextsInFeatureContext = tracker.getValues(allelesBinding, new SimpleInterval(loc));
+        return composeGivenAllelesVariantContextFromVariantList(variantContextsInFeatureContext, loc, keepFiltered);
+    }
+
+    @VisibleForTesting
+    protected static VariantContext composeGivenAllelesVariantContextFromVariantList(final List<VariantContext> variantContextsInFeatureContext,
+                                                                                     final Locatable loc,
+                                                                                     final boolean keepFiltered) {
+        final List<VariantContext> vcsAtLoc = variantContextsInFeatureContext
+                .stream()
+                .filter(vc -> vc.getStart() == loc.getStart() &&
+                        (keepFiltered || vc.isNotFiltered()))
+                .collect(Collectors.toList());
+
+
+        if (vcsAtLoc.isEmpty()) {
+            return null;
         }
+        final List<String> haplotypeSources = vcsAtLoc.stream().map(VariantContext::getSource).collect(Collectors.toList());
+        final VariantContext mergedVc = GATKVariantContextUtils.simpleMerge(vcsAtLoc, haplotypeSources,
+                keepFiltered ? KEEP_UNCONDITIONAL : KEEP_IF_ANY_UNFILTERED,
+                GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false);
 
-        return vc;
+        return mergedVc;
     }
 
 }