Added a simple utility method Utils.optimumHashSize() to calculate the optimum

initial size for a Java hash table (HashMap, HashSet, etc.) given an expected
maximum number of elements. The optimum size is the smallest size that's
guaranteed not to result in any rehash / table-resize operations.

Example Usage:
Map<String, Object> hash = new HashMap<String, Object>(Utils.optimumHashSize(expectedMaxElements));

I think we're paying way too heavy a price in unnecessary rehash operations across
the GATK. If you don't specify an initial size, you get a table of size 16 that gets
completely rehashed and doubles in size every time it becomes 75% full. This means you
do at least twice as much work as you need to in order to populate your table:

(n + n/2 + n/4 + ... 16 ~= (1 + 1/2 + 1/4...) * n ~= 2 * n

public/java/src/org/broadinstitute/sting/utils/Utils.java

@@ -42,6 +42,21 @@ public class Utils {
     /** our log, which we want to capture anything from this class */
     private static Logger logger = Logger.getLogger(Utils.class);
 
+    public static final float JAVA_DEFAULT_HASH_LOAD_FACTOR = 0.75f;
+
+    /**
+     * Calculates the optimum initial size for a hash table given the maximum number
+     * of elements it will need to hold. The optimum size is the smallest size that
+     * is guaranteed not to result in any rehash/table-resize operations.
+     *
+     * @param maxElements  The maximum number of elements you expect the hash table
+     *                     will need to hold
+     * @return             The optimum initial size for the table, given maxElements
+     */
+    public static int optimumHashSize ( int maxElements ) {
+        return (int)(maxElements / JAVA_DEFAULT_HASH_LOAD_FACTOR) + 2;
+    }
+
     public static String getClassName(Class c) {
         String FQClassName = c.getName();
         int firstChar;