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Merge pull request #387 from lbergelson/lb_add_ungenotyped_case_countvariants 

adding a check for the UNAVAILABLE case of GenotypeType in CountVariants
This commit is contained in:
Eric Banks 2013-08-30 06:14:08 -07:00
parent 7479152977 4473b0065e
commit 5d79a6cbe0
2 changed files with 18 additions and 1 deletions
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17
protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -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 +

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
View File

@ -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);
}