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Merge pull request #791 from broadinstitute/ldg_fixCGPbug 

Add error handling for genotypes that are called but have no PLs
This commit is contained in:
rpoplin 2015-01-05 09:40:38 -05:00
parent a4a9e73ec8 a9694951d2
commit ac10b9c3cd
1 changed files with 3 additions and 3 deletions
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6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FamilyLikelihoodsUtils.java
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@ -107,9 +107,9 @@ public class FamilyLikelihoodsUtils {
*/
public void getUpdatedGenotypes(final VariantContext vc, final Genotype motherGenotype, final Genotype fatherGenotype, final Genotype childGenotype, final ArrayList<Genotype> updatedGenotypes){
//genotypes here can be no call
boolean fatherIsCalled = fatherGenotype != null && hasCalledGT(fatherGenotype.getType());
boolean motherIsCalled = motherGenotype != null && hasCalledGT(motherGenotype.getType());
boolean childIsCalled = childGenotype != null && hasCalledGT(childGenotype.getType());
boolean fatherIsCalled = fatherGenotype != null && hasCalledGT(fatherGenotype.getType()) && fatherGenotype.hasLikelihoods();
boolean motherIsCalled = motherGenotype != null && hasCalledGT(motherGenotype.getType()) && motherGenotype.hasLikelihoods();
boolean childIsCalled = childGenotype != null && hasCalledGT(childGenotype.getType()) && childGenotype.hasLikelihoods();
//default to posteriors equal to likelihoods (flat priors) in case input genotypes are not called
double[] uninformativeLikelihoods = {ONE_THIRD, ONE_THIRD, ONE_THIRD};