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Be smarter about dealing with infinite quals for ref calls 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3024 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2010-03-17 17:35:23 +00:00
parent 1bb4394aa9
commit 5e29d0c219
1 changed files with 4 additions and 1 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
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@ -337,8 +337,11 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
phredScaledConfidence = QualityUtils.phredScaleErrorRate(PofFs[indexOfMax]);
if ( Double.isInfinite(phredScaledConfidence) ) {
double sum = 0.0;
for (int i = 1; i < frequencyEstimationPoints; i++)
for (int i = 1; i < frequencyEstimationPoints; i++) {
if ( log10PofDgivenAFi[indexOfMax][i] == VALUE_NOT_CALCULATED )
break;
sum += log10PofDgivenAFi[indexOfMax][i];
}
phredScaledConfidence = -10.0 * sum;
}
}