There's actually a subtle but important difference between foo++ and ++foo

public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java

@@ -78,7 +78,7 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
     public Long reduce(final GenomeLoc value, Long reduce) {
         if (value != null) {
             out.println(value.toString());
-            return reduce++;
+            return ++reduce;
         } else
             return reduce;
     }