From 3dd6a1f96272a6794108d88ac14ab8f892996ae4 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Wed, 1 Feb 2012 19:35:09 -0500
Subject: [PATCH] Adding some generic sum and average functions to MathUtils

---
 .../broadinstitute/sting/utils/MathUtils.java | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
index 2f2dbd47e..814cb2765 100644
--- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
@@ -137,6 +137,10 @@ public class MathUtils {
 
         return size;
     }
+    
+    public static double average(Collection<Integer> x) {
+        return (double) sum(x) / x.size();
+    }
 
     public static double average(Collection<Number> numbers, boolean ignoreNan) {
         if (ignoreNan) {
@@ -176,6 +180,13 @@ public class MathUtils {
         return s;
     }
 
+    public static long sum(int[] x) {
+        long total = 0;
+        for (int v : x)
+            total += v;
+        return total;
+    }
+
 
     /**
      * Calculates the log10 cumulative sum of an array with log10 probabilities
@@ -722,6 +733,13 @@ public class MathUtils {
         return average(vals, vals.size());
     }
 
+    public static double average(int[] x) {
+        int sum = 0;
+        for (int v : x)
+            sum += v;
+        return (double) sum / x.length;
+    }
+
     public static byte average(byte[] vals) {
         int sum = 0;
         for (byte v : vals) {
@@ -1079,6 +1097,13 @@ public class MathUtils {
         return getQScoreOrderStatistic(reads, offsets, (int) Math.floor(reads.size() / 2.));
     }
 
+    public static long sum(Collection<Integer> x) {
+        long sum = 0;
+        for (int v : x)
+            sum += v;        
+        return sum;
+    }
+
     /**
      * A utility class that computes on the fly average and standard deviation for a stream of numbers.
      * The number of observations does not have to be known in advance, and can be also very big (so that