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Merge pull request #367 from broadinstitute/md_hc_ref_fix 

Bugfix for ReferenceConfidenceModel
This commit is contained in:
Eric Banks 2013-08-06 20:37:08 -07:00
parent 6dfd17122f 40bc7d6a9c
commit dd0e6409c6
2 changed files with 16 additions and 3 deletions
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10
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -791,9 +791,13 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
if( DEBUG ) { logger.info("----------------------------------------------------------------------------------"); } if( DEBUG ) { logger.info("----------------------------------------------------------------------------------"); }
if ( emitReferenceConfidence() ) { if ( emitReferenceConfidence() ) {
return referenceConfidenceModel.calculateRefConfidence(assemblyResult.getRefHaplotype(), if ( calledHaplotypes.getCalls().isEmpty() ) {
calledHaplotypes.getCalledHaplotypes(), assemblyResult.paddedReferenceLoc, assemblyResult.regionForGenotyping, // no called all of the potential haplotypes
stratifiedReadMap, calledHaplotypes.getCalls()); return referenceModelForNoVariation(originalActiveRegion, false);
} else
return referenceConfidenceModel.calculateRefConfidence(assemblyResult.getRefHaplotype(),
calledHaplotypes.getCalledHaplotypes(), assemblyResult.paddedReferenceLoc, assemblyResult.regionForGenotyping,
stratifiedReadMap, calledHaplotypes.getCalls());
} else { } else {
return calledHaplotypes.getCalls(); return calledHaplotypes.getCalls();
} }

9
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
View File

@ -85,4 +85,13 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(md5)); final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(md5));
executeTest(name, spec); executeTest(name, spec);
} }
@Test
public void testERCRegionWithNoCalledHaplotypes() {
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF",
b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001");
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
spec.disableShadowBCF();
executeTest("testERCRegionWithNoCalledHaplotypes", spec);
}
} }