From e5cc0f4eec541fcf5dd0c6b949efc9f5af97c941 Mon Sep 17 00:00:00 2001 From: carneiro Date: Tue, 3 May 2011 20:48:30 +0000 Subject: [PATCH] Added 'specificity' to variant eval's Validation Report evaluator. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5742 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/varianteval/evaluators/ValidationReport.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java index c51f3c398..8bf317b25 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java @@ -35,6 +35,7 @@ public class ValidationReport extends VariantEvaluator implements StandardEval { @DataPoint(description = "TN") int TN = 0; @DataPoint(description = "Sensitivity") double sensitivity = 0; + @DataPoint(description = "Specificity") double specificity = 0; @DataPoint(description = "PPV") double PPV = 0; @DataPoint(description = "FDR") double FDR = 0; @@ -90,6 +91,7 @@ public class ValidationReport extends VariantEvaluator implements StandardEval { throw new ReviewedStingException("BUG: nComp != TP + FN + FP + TN + CompFiltered!"); sensitivity = (100.0 * TP) / (TP + FN); + specificity = (TN+FP > 0) ? (100.0 * TN) / (TN + FP) : 100.0; PPV = (100.0 * TP) / (TP + FP); FDR = (100.0 * FP) / (FP + TP); }