CombineVariants no longer adds PASS to unfiltered records

-- [Delivers #49876703]
-- Add integration test and test file
-- Update SymbolicAlleles combine variant tests, which was turning unfiltered records into PASS!

protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java

@@ -189,4 +189,15 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
                  Arrays.asList("aa926eae333208dc1f41fe69dc95d7a6"));
          cvExecuteTest("combineDBSNPDuplicateSites:", spec, true);
     }
+
+    @Test
+    public void combineLeavesUnfilteredRecordsUnfiltered() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T CombineVariants --no_cmdline_in_header -o %s "
+                        + " -R " + b37KGReference
+                        + " -V " + privateTestDir + "combineVariantsLeavesRecordsUnfiltered.vcf",
+                1,
+                Arrays.asList("f8c014d0af7e014475a2a448dc1f9cef"));
+        cvExecuteTest("combineLeavesUnfilteredRecordsUnfiltered: ", spec, false);
+    }
 }

public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java

@@ -697,6 +697,7 @@ public class GATKVariantContextUtils {
         int maxAC = -1;
         final Map<String, Object> attributesWithMaxAC = new LinkedHashMap<String, Object>();
         double log10PError = CommonInfo.NO_LOG10_PERROR;
+        boolean anyVCHadFiltersApplied = false;
         VariantContext vcWithMaxAC = null;
         GenotypesContext genotypes = GenotypesContext.create();
 
@@ -729,6 +730,7 @@ public class GATKVariantContextUtils {
                 log10PError =  vc.getLog10PError();
 
             filters.addAll(vc.getFilters());
+            anyVCHadFiltersApplied |= vc.filtersWereApplied();
 
             //
             // add attributes
@@ -841,7 +843,9 @@ public class GATKVariantContextUtils {
         builder.alleles(alleles);
         builder.genotypes(genotypes);
         builder.log10PError(log10PError);
-        builder.filters(filters.isEmpty() ? filters : new TreeSet<String>(filters));
+        if ( anyVCHadFiltersApplied ) {
+            builder.filters(filters.isEmpty() ? filters : new TreeSet<>(filters));
+        }
         builder.attributes(new TreeMap<String, Object>(mergeInfoWithMaxAC ? attributesWithMaxAC : attributes));
 
         // Trim the padded bases of all alleles if necessary

public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java

@@ -57,7 +57,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(b36KGReference, "symbolic_alleles_2.vcf"),
                 1,
-                Arrays.asList("bf5a09f783ab1fa44774c81f91d10921"));
+                Arrays.asList("30f66a097987330d42e87da8bcd6be21"));
         executeTest("Test symbolic alleles mixed in with non-symbolic alleles", spec);
     }
 }