Bugfix for ReferenceConfidenceModel

-- In the case where there's some variation to assembly and evaluate but the resulting haplotypes don't result in any called variants, the reference model would exception out with "java.lang.IllegalArgumentException: calledHaplotypes must contain the refHaplotype".  Now we detect this case and emit the standard no variation output.
-- [delivers #54625060]

protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java

@@ -791,9 +791,13 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         if( DEBUG ) { logger.info("----------------------------------------------------------------------------------"); }
 
         if ( emitReferenceConfidence() ) {
-            return referenceConfidenceModel.calculateRefConfidence(assemblyResult.getRefHaplotype(),
+            if ( calledHaplotypes.getCalls().isEmpty() ) {
-                    calledHaplotypes.getCalledHaplotypes(), assemblyResult.paddedReferenceLoc, assemblyResult.regionForGenotyping,
+                // no called all of the potential haplotypes
-                    stratifiedReadMap, calledHaplotypes.getCalls());
+                return referenceModelForNoVariation(originalActiveRegion, false);
+            } else
+                return referenceConfidenceModel.calculateRefConfidence(assemblyResult.getRefHaplotype(),
+                        calledHaplotypes.getCalledHaplotypes(), assemblyResult.paddedReferenceLoc, assemblyResult.regionForGenotyping,
+                        stratifiedReadMap, calledHaplotypes.getCalls());
         } else {
             return calledHaplotypes.getCalls();
         }

protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java

@@ -85,4 +85,13 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(md5));
         executeTest(name, spec);
     }
+
+    @Test
+    public void testERCRegionWithNoCalledHaplotypes() {
+        final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF",
+                b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001");
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
+        spec.disableShadowBCF();
+        executeTest("testERCRegionWithNoCalledHaplotypes", spec);
+    }
 }