From f0179109fa2ca435273d39a769cc43a5269b6972 Mon Sep 17 00:00:00 2001 From: depristo Date: Fri, 28 Aug 2009 01:04:13 +0000 Subject: [PATCH] Removing min confidence for on/off genotype git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1473 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/variants/VECOnOffGenotypeRatio.java | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECOnOffGenotypeRatio.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECOnOffGenotypeRatio.java index 25056e944..aaf03f613 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECOnOffGenotypeRatio.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECOnOffGenotypeRatio.java @@ -5,8 +5,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.utils.*; public class VECOnOffGenotypeRatio implements VariantExclusionCriterion { // extends RatioFilter { - private static final double minGenotypeConfidenceToTest = 5.0; // TODO -- must be replaced with true confidence scoore, right now assumes LOD - //final private static GenotypeFeatureData.Tail tail = GenotypeFeatureData.Tail.LeftTailed; private boolean exclude; private double threshold = 0.0; @@ -53,8 +51,7 @@ public class VECOnOffGenotypeRatio implements VariantExclusionCriterion { // ext Pair counts = scoreVariant(ref, pileup, variant); int n = counts.first + counts.second; ratio = counts.first.doubleValue() / (double)n; - boolean highGenotypeConfidence = variant.getConsensusConfidence() > minGenotypeConfidenceToTest; - exclude = ratio < threshold && highGenotypeConfidence; + exclude = ratio < threshold; } public double inclusionProbability() {