From 478f42672737233af1ce6fb07dccda3bd55ee8a1 Mon Sep 17 00:00:00 2001 From: kiran Date: Tue, 25 Aug 2009 21:21:58 +0000 Subject: [PATCH] Fixed a missing method implementation in these two files. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1459 348d0f76-0448-11de-a6fe-93d51630548a --- .../playground/gatk/walkers/variants/VECHomopolymer.java | 4 ++-- .../gatk/walkers/variants/VECOnOffGenotypeRatio.java | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECHomopolymer.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECHomopolymer.java index 230cf8677..72f363149 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECHomopolymer.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECHomopolymer.java @@ -111,7 +111,7 @@ public class VECHomopolymer implements VariantExclusionCriterion { exclude = checkOne || checkTwo || checkThree || checkFour; } - public boolean isExcludable() { - return exclude; + public double inclusionProbability() { + return exclude ? 0.0 : 1.0; } } \ No newline at end of file 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 5d87a68e5..153e7dc3b 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 @@ -64,12 +64,12 @@ public class VECOnOffGenotypeRatio implements VariantExclusionCriterion { // ext exclude = ratio < threshold; } - public boolean useZeroQualityReads() { return false; } - - public boolean isExcludable() { - return exclude; + public double inclusionProbability() { + return exclude ? 0.0 : 1.0; } + public boolean useZeroQualityReads() { return false; } + public String getStudyHeader() { return "OnOffGenotype("+threshold+")\tOnRatio"; }