From 3b1aad4f1731125d67b51e6681a812f4c2a59a6d Mon Sep 17 00:00:00 2001 From: Christopher Hartl Date: Fri, 20 Jan 2012 23:43:51 -0500 Subject: [PATCH] After a minor and abject freakout, alter the T2D script to seek out truth sensitivities between 80 and 100, rather than between 0.8 and 1. Also, don't consider a genotype "changed by beagle" if the initial genotype is a no-call. --- .../gatk/walkers/beagle/BeagleOutputToVCFWalker.java | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java index 4f115b46e..ec67563dc 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java @@ -320,8 +320,7 @@ public class BeagleOutputToVCFWalker extends RodWalker { og = a1+"/"+a2; // See if Beagle switched genotypes - if (!((bglAlleleA.equals(originalAlleleA) && bglAlleleB.equals(originalAlleleB) || - (bglAlleleA.equals(originalAlleleB) && bglAlleleB.equals(originalAlleleA))))){ + if (! originalAlleleA.equals(Allele.NO_CALL) && beagleSwitchedGenotypes(bglAlleleA,originalAlleleA,bglAlleleB,originalAlleleB)){ originalAttributes.put("OG",og); numGenotypesChangedByBeagle++; } @@ -364,6 +363,11 @@ public class BeagleOutputToVCFWalker extends RodWalker { return 1; } + private boolean beagleSwitchedGenotypes(Allele bglAlleleA, Allele originalAlleleA, Allele bglAlleleB, Allele originalAlleleB) { + return !((bglAlleleA.equals(originalAlleleA) && bglAlleleB.equals(originalAlleleB) || + (bglAlleleA.equals(originalAlleleB) && bglAlleleB.equals(originalAlleleA)))); + } + public Integer reduceInit() { return 0; // Nothing to do here }