From 36600fd8e92e3353b585310e1a3e0114f26b4133 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Tue, 1 Nov 2011 17:46:12 -0400
Subject: [PATCH] added MQ of low MQ/BQ to consensus RMS

Bases that were excluded for MQ and BQ filters are now contributing to the MQ RMS (but not to consensus base counts and variant/not variant region triggers).
---
 public/java/src/org/broadinstitute/sting/utils/MathUtils.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
index 17e74c4f1..17f458f31 100644
--- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
@@ -408,12 +408,12 @@ public class MathUtils {
         return Math.sqrt(rms);
     }
 
-    public static double rms(Collection<Double> l) {
+    public static double rms(Collection<Integer> l) {
         if (l.size() == 0)
             return 0.0;
 
         double rms = 0.0;
-        for (Double i : l)
+        for (int i : l)
             rms += i*i;
         rms /= l.size();
         return Math.sqrt(rms);