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Add test case for fix

This commit is contained in:
Laura Gauthier 2016-03-15 11:06:48 -04:00
parent 31fc64f82c
commit 9ffdfeccd5
2 changed files with 10 additions and 1 deletions
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2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
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@ -210,7 +210,7 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
* @param vc Input VC * @param vc Input VC
* @param model GL calculation model * @param model GL calculation model
* @param inheritAttributesFromInputVC Output VC will contain attributes inherited from input vc * @param inheritAttributesFromInputVC Output VC will contain attributes inherited from input vc
* @return VC with assigned genotypes * @return VC with assigned genotypes (may be null if QUAL<emit threshold or MLEAF==0)
*/ */
protected VariantCallContext calculateGenotypes(final RefMetaDataTracker tracker, final ReferenceContext refContext, protected VariantCallContext calculateGenotypes(final RefMetaDataTracker tracker, final ReferenceContext refContext,
final AlignmentContext rawContext, Map<String, AlignmentContext> stratifiedContexts, final AlignmentContext rawContext, Map<String, AlignmentContext> stratifiedContexts,

9
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
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@ -612,6 +612,15 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
executeTest("testAlleleSpecificAnnotations_elevenSamples", spec); executeTest("testAlleleSpecificAnnotations_elevenSamples", spec);
} }
@Test
public void testMonomorphicVCwithAlt() {
final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header --disableDithering -V "
+ privateTestDir + "monomorphicGVCwithAlt.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("080951cdb5d4903dd58b1e753b9378d5"));
spec.disableShadowBCF();
executeTest("testAlleleSpecificAnnotations", spec);
}
@Test @Test
public void testFractionInformativeReads() { public void testFractionInformativeReads() {
final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header -A FractionInformativeReads --disableDithering -V " final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header -A FractionInformativeReads --disableDithering -V "