Merge pull request #387 from lbergelson/lb_add_ungenotyped_case_countvariants

adding a check for the UNAVAILABLE case of GenotypeType in CountVariants

protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java

@@ -48,8 +48,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval;
 
 import org.broadinstitute.sting.WalkerTest;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.testng.annotations.Test;
 import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -376,6 +376,21 @@ public class VariantEvalIntegrationTest extends WalkerTest {
         executeTestParallel("testEvalTrackWithoutGenotypes",spec);
     }
 
+    @Test
+    public void testEvalTrackWithoutGenotypesWithSampleFields() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                buildCommandLine(
+                        "-T VariantEval",
+                        "-R " + b37KGReference,
+                        "-eval " + variantEvalTestDataRoot + "noGenotypes.vcf",
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList("")); //There is no md5 because we only care that this completes without an exception.
+        executeTest("testEvalTrackWithoutGenotypesWithSampleFields", spec);
+
+    }
+
     @Test
     public void testMultipleEvalTracksWithoutGenotypes() {
         String extraArgs = "-T VariantEval -R " + b37KGReference +

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java

@@ -197,6 +197,8 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
                     break;
                 case MIXED:
                     break;
+                case UNAVAILABLE:
+                    break;
                 default:
                     throw new ReviewedStingException("BUG: Unexpected genotype type: " + g);
             }