The number of loci can easily overflow an int. Change reduce type to a Long.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1233 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java

@@ -13,14 +13,14 @@ import java.util.List;
  * Time: 3:22:14 PM
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-public class CountLociWalker extends LocusWalker<Integer, Integer> implements TreeReducible<Integer> {
+public class CountLociWalker extends LocusWalker<Integer, Long> implements TreeReducible<Long> {
     public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
         return 1;
     }
 
-    public Integer reduceInit() { return 0; }
+    public Long reduceInit() { return 0l; }
 
-    public Integer reduce(Integer value, Integer sum) {
+    public Long reduce(Integer value, Long sum) {
         return value + sum;
     }
 
@@ -28,7 +28,7 @@ public class CountLociWalker extends LocusWalker<Integer, Integer> implements Tr
      * Reduces two subtrees together.  In this case, the implementation of the tree reduce
      * is exactly the same as the implementation of the single reduce.
      */
-    public Integer treeReduce(Integer lhs, Integer rhs) {
+    public Long treeReduce(Long lhs, Long rhs) {
         return lhs + rhs;
     }
 }