From 8d7ef1bb519d2525ff82812f02ba5f3f18e3066f Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Thu, 21 Jul 2011 21:39:00 -0400
Subject: [PATCH] Complete refactor of the ReplicationValidation framework,
 plus the following new functionality:  * merges all pools in a lane.  *
 merges all lanes in a site.

---
 .../src/org/broadinstitute/sting/utils/MathUtils.java | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
index 36ed506aa..f823e6d42 100755
--- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
@@ -727,6 +727,17 @@ public class MathUtils {
         return count;
     }
 
+    public static <T> int countOccurrences(byte element, byte [] array) {
+        int count = 0;
+        for (byte y : array) {
+            if (element == y)
+                count++;
+        }
+
+        return count;
+    }
+
+
     /**
      * Returns n random indices drawn with replacement from the range 0..(k-1)
      *