Fix for combining records in which one has a spanning deletion and needs a padded reference allele.

This was erroring out and not working.

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java

@@ -237,4 +237,18 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
                 Arrays.asList(""));
         executeTest("combineSymbolicVariants: ", spec);
     }
-}
+
+    @Test
+    public void combineSpanningDels() {
+        // Just checking that this does not fail, hence no output files and MD5
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T CombineVariants --no_cmdline_in_header -o %s "
+                        + " -R " + b37KGReference
+                        + " -V " + privateTestDir + "test.spanningdel.combine.1.vcf "
+                        + " -V " + privateTestDir + "test.spanningdel.combine.2.vcf "
+                        + " -genotypeMergeOptions UNIQUIFY",
+                0,
+                Arrays.asList(""));
+        executeTest("combineSpanningDels: ", spec);
+    }
+}

public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java

@@ -1468,7 +1468,9 @@ public class GATKVariantContextUtils {
                     if ( extended.equals(b) )
                         extended = b;
                 map.put(a, extended);
-            } else if ( a.isSymbolic() ) {
+            }
+            // as long as it's not a reference allele then we want to add it as is (this covers e.g. symbolic and spanning deletion alleles)
+            else if ( !a.isReference() ) {
                 map.put(a, a);
             }
         }
@@ -1477,7 +1479,7 @@ public class GATKVariantContextUtils {
     }
 
     static private boolean isUsableAlternateAllele(final Allele allele) {
-        return ! (allele.isReference() || allele.isSymbolic() );
+        return ! (allele.isReference() || allele.isSymbolic() || allele == Allele.SPAN_DEL );
     }
 
     public static List<VariantContext> sortVariantContextsByPriority(Collection<VariantContext> unsortedVCs, List<String> priorityListOfVCs, GenotypeMergeType mergeOption ) {