From 471c18054f7b5376241301585b0c72a742053933 Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 15 Oct 2010 17:51:18 +0000 Subject: [PATCH] Fix for SB calculation: the best overall AF might not have any mass when just looking at reads from a single strand. We need to compute the best AF for each stratification. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4505 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index c86a9c357..57e67764c 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -236,6 +236,7 @@ public class UnifiedGenotyperEngine { clearAFarray(log10AlleleFrequencyPosteriors.get()); afcm.get().getLog10PNonRef(tracker, refContext, GLs, log10AlleleFrequencyPriors, log10AlleleFrequencyPosteriors.get()); double forwardLog10PofNull = log10AlleleFrequencyPosteriors.get()[0]; + bestAFguess = MathUtils.maxElementIndex(log10AlleleFrequencyPosteriors.get()); double forwardLog10PofF = log10AlleleFrequencyPosteriors.get()[bestAFguess]; //System.out.println("forwardLog10PofNull=" + forwardLog10PofNull + ", forwardLog10PofF=" + forwardLog10PofF); @@ -245,6 +246,7 @@ public class UnifiedGenotyperEngine { clearAFarray(log10AlleleFrequencyPosteriors.get()); afcm.get().getLog10PNonRef(tracker, refContext, GLs, log10AlleleFrequencyPriors, log10AlleleFrequencyPosteriors.get()); double reverseLog10PofNull = log10AlleleFrequencyPosteriors.get()[0]; + bestAFguess = MathUtils.maxElementIndex(log10AlleleFrequencyPosteriors.get()); double reverseLog10PofF = log10AlleleFrequencyPosteriors.get()[bestAFguess]; //System.out.println("reverseLog10PofNull=" + reverseLog10PofNull + ", reverseLog10PofF=" + reverseLog10PofF);