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