From 29f94119d175646bb6ded1e8a5835aa80fd26cb5 Mon Sep 17 00:00:00 2001 From: depristo Date: Tue, 29 Dec 2009 18:08:41 +0000 Subject: [PATCH] Fixes git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2466 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/papergenotyper/GATKPaperGenotyper.java | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java index 3a00c282b..3695cfc54 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java @@ -51,11 +51,10 @@ public class GATKPaperGenotyper extends LocusWalker impleme if (quals[index] > 0) { double epsilon = Math.pow(10, quals[index] / -10.0); byte pileupBase = bases[index]; - for (char genotypeBase : genotype.toString().toCharArray()) - if (genotypeBase == pileupBase) - likelihoods[genotype.ordinal()] += Math.log10(0.5 * (1 - epsilon) + epsilon / 3); - else - likelihoods[genotype.ordinal()] += Math.log10(epsilon / 3); + for (char genotypeBase : genotype.toString().toCharArray()) { + double p = genotypeBase == pileupBase ? 1 - epsilon : epsilon / 3; + likelihoods[genotype.ordinal()] += Math.log10(p / 2); + } } }