diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index d695f2d13..9b5290dee 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/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 + diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java index 33a5a9fc9..63c34586e 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java +++ b/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); }