From ba8a8febc69b1c2a4ca0bc62bbe216b58cdbc0ad Mon Sep 17 00:00:00 2001 From: ebanks Date: Wed, 2 Dec 2009 01:59:03 +0000 Subject: [PATCH] Thanks to Steve Hershman for finding this bug: getNegLog10PError() does not equal the confidence score (you need to multiply by 10 as confidence is traditionally phred scaled). Probably we should change the method to be getNeg10Log10PError(). Anyone have strong feelings on this? git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2207 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/varianteval/VariantEvalWalker.java | 2 +- .../walkers/varianteval/VariantEvalWalkerIntegrationTest.java | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java index 762854a05..8fc813085 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java @@ -247,7 +247,7 @@ public class VariantEvalWalker extends RefWalker { eval = null; if (eval != null) - if (eval.getNegLog10PError() < minConfidenceScore) eval = null; + if (eval.getNegLog10PError() * 10.0 < minConfidenceScore) eval = null; if ( eval != null && (eval instanceof RodVCF) && ((RodVCF)eval).mCurrentRecord.isFiltered() ) { //System.out.printf("Rejecting filtered record %s%n", eval); diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java index 5d5d1e58c..a703e3245 100644 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java @@ -75,10 +75,10 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { " -L 1:10,000,000-11,000,000" + " --outerr %s" + " --supressDateInformation" + - " -minConfidenceScore 6", + " -minConfidenceScore 60", 1, // just one output file md5); - List result = executeTest("testEvalVariantRODConfSix", spec).getFirst(); + List result = executeTest("testEvalVariantRODConfSixty", spec).getFirst(); } @Test