From ba07f057ac798be2c2bd955096135733f0dd61e9 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 3 Aug 2009 16:18:09 +0000
Subject: [PATCH] finish the math for RMS

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1362 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/genotype/calls/SSGGenotypeCall.java             | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/utils/genotype/calls/SSGGenotypeCall.java b/java/src/org/broadinstitute/sting/utils/genotype/calls/SSGGenotypeCall.java
index 2ea144f13..0760868cc 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/calls/SSGGenotypeCall.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/calls/SSGGenotypeCall.java
@@ -107,6 +107,8 @@ public class SSGGenotypeCall implements GenotypeCall, GenotypeOutput {
         for (SAMRecord r : pileup.getReads()) {
             rms += r.getMappingQuality() * r.getMappingQuality();
         }
+        rms /= pileup.getReads().size();
+        rms = Math.sqrt(rms);
         return rms;
     }