zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
This commit is contained in:
carneiro 2011-05-03 20:48:30 +00:00
parent b88dec387c
commit e5cc0f4eec
1 changed files with 2 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
View File

@ -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);
}