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bug fix: forgot to uncomment code to compute genotype likelihoods 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4397 348d0f76-0448-11de-a6fe-93d51630548a
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delangel 2010-09-30 21:38:22 +00:00
parent ece694d0af
commit eb67aee732
1 changed files with 6 additions and 6 deletions
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12
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -208,25 +208,25 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
if (bestGTguess == 0) { if (bestGTguess == 0) {
myAlleles.add(alleleA); myAlleles.add(alleleA);
myAlleles.add(alleleA); myAlleles.add(alleleA);
//qual = posteriors[0] - Math.max(posteriors[1],posteriors[2]); qual = posteriors[0] - Math.max(posteriors[1],posteriors[2]);
} else if(bestGTguess == 1) { } else if(bestGTguess == 1) {
myAlleles.add(alleleA); myAlleles.add(alleleA);
myAlleles.add(alleleB); myAlleles.add(alleleB);
//qual = posteriors[1] - Math.max(posteriors[0],posteriors[2]); qual = posteriors[1] - Math.max(posteriors[0],posteriors[2]);
} else { } else {
myAlleles.add(alleleB); myAlleles.add(alleleB);
myAlleles.add(alleleB); myAlleles.add(alleleB);
// qual = posteriors[2] - Math.max(posteriors[1],posteriors[0]); qual = posteriors[2] - Math.max(posteriors[1],posteriors[0]);
} }
/*
if (qual <= 0.0) { if (qual <= 0.0) {
qual = 0.0; qual = 0.0;
myAlleles.clear(); myAlleles.clear();
myAlleles.add(Allele.NO_CALL); myAlleles.add(Allele.NO_CALL);
// myAlleles.add(Allele.NO_CALL); myAlleles.add(Allele.NO_CALL);
} }
*/
attributes.put(VCFConstants.GENOTYPE_QUALITY_KEY,String.format("%4.2f", 10*qual)); attributes.put(VCFConstants.GENOTYPE_QUALITY_KEY,String.format("%4.2f", 10*qual));
GenotypeLikelihoods likelihoods = new GenotypeLikelihoods(GL.getLikelihoods()); GenotypeLikelihoods likelihoods = new GenotypeLikelihoods(GL.getLikelihoods());