diff --git a/java/src/org/broadinstitute/sting/utils/PrimitivePair.java b/java/src/org/broadinstitute/sting/utils/PrimitivePair.java
index 7363ba3c3..8abb41414 100644
--- a/java/src/org/broadinstitute/sting/utils/PrimitivePair.java
+++ b/java/src/org/broadinstitute/sting/utils/PrimitivePair.java
@@ -29,5 +29,147 @@ public class PrimitivePair {
         the member field.
     */
     public int getSecond() { return second; }
+
+       /** Increments the elements of this pair by the
+        * corresponding elements of the pair <code>p</code> and returns this
+        * pair (modified). This method does not allocate a new pair, but changes
+        * in place the values stored in the object the method is invoked from. The
+        * method is unsafe: if p is null, a runtime exception will be thrown.
+        * @param p
+        * @return
+        */
+    public PrimitivePair.Int add(PrimitivePair.Int p) {
+        first += p.first;
+        second += p.second;
+        return this;
+    }
+
+       /** Decrements the elements of this pair by the
+        * corresponding elements of the pair <code>p</code> and returns this
+        * pair (modified). This method does not allocate a new pair, but changes
+        * in place the values stored in the object the method is invoked from. The
+        * method is unsafe: if p is null, a runtime exception will be thrown.
+        * @param p
+        * @return
+        */
+    public PrimitivePair.Int subtract(PrimitivePair.Int p) {
+        first -= p.first;
+        second -= p.second;
+        return this;
+    }
+
+       /** Copies values from the argument <code>p</code> into the corresponding
+        * elements of this pair and returns this pair (modified).
+        * @param p
+        * @return
+        */
+    public PrimitivePair.Int assignFrom(PrimitivePair.Int p ) {
+        first = p.first;
+        second = p.second;
+        return this;
+    }
+
+
   }
+
+    public static class Long {
+      // declare public, STL-style for easier and more efficient access:
+      public long first;
+      public long second;
+
+      public Long(long x, long y) { first = x; second = y; }
+      public Long() { first = second = 0; }
+
+      public void set(long x, long y) { first = x; second = y; }
+
+      /** Java-style getter; note that we currently allow direct access to
+          the member field.
+      */
+      public long getFirst() { return first; }
+
+      /** Java-style getter; note that we currently allow direct access to
+          the member field.
+      */
+      public long getSecond() { return second; }
+
+        /** Increments the elements of this pair by the
+         * corresponding elements of the pair <code>p</code> and returns this
+         * pair (modified). This method does not allocate a new pair, but changes
+         * in place the values stored in the object the method is invoked from. The
+         * method is unsafe: if p is null, a runtime exception will be thrown.
+         * @param p
+         * @return
+         */
+     public PrimitivePair.Long add(PrimitivePair.Int p) {
+         first += p.first;
+         second += p.second;
+         return this;
+     }
+
+        /** Increments the elements of this pair by the
+         * corresponding elements of the pair <code>p</code> and returns this
+         * pair (modified). This method does not allocate a new pair, but changes
+         * in place the values stored in the object the method is invoked from. The
+         * method is unsafe: if p is null, a runtime exception will be thrown.
+         * @param p
+         * @return
+         */
+     public PrimitivePair.Long add(PrimitivePair.Long p) {
+         first += p.first;
+         second += p.second;
+         return this;
+     }
+
+        /** Decrements the elements of this pair by the
+         * corresponding elements of the pair <code>p</code> and returns this
+         * pair (modified). This method does not allocate a new pair, but changes
+         * in place the values stored in the object the method is invoked from. The
+         * method is unsafe: if p is null, a runtime exception will be thrown.
+         * @param p
+         * @return
+         */
+     public PrimitivePair.Long subtract(PrimitivePair.Int p) {
+         first -= p.first;
+         second -= p.second;
+         return this;
+     }
+
+        /** Decrements the elements of this pair by the
+         * corresponding elements of the pair <code>p</code> and returns this
+         * pair (modified). This method does not allocate a new pair, but changes
+         * in place the values stored in the object the method is invoked from. The
+         * method is unsafe: if p is null, a runtime exception will be thrown.
+         * @param p
+         * @return
+         */
+     public PrimitivePair.Long subtract(PrimitivePair.Long p) {
+         first -= p.first;
+         second -= p.second;
+         return this;
+     }
+
+     /** Copies values from the argument <code>p</code> into the corresponding
+       * elements of this pair and returns this pair (modified).
+       * @param p
+       * @return
+     */
+     public PrimitivePair.Long assignFrom(PrimitivePair.Long p ) {
+         first = p.first;
+         second = p.second;
+         return this;
+     }
+
+     /** Copies values from the argument <code>p</code> into the corresponding
+       * elements of this pair and returns this pair (modified).
+       * @param p
+       * @return
+     */
+     public PrimitivePair.Long assignFrom(PrimitivePair.Int p ) {
+            first = p.first;
+            second = p.second;
+            return this;
+     }
+
+    }
+
 }