diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CountIntervals.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CountIntervals.java
new file mode 100755
index 000000000..4d74261cd
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/CountIntervals.java
@@ -0,0 +1,47 @@
+package org.broadinstitute.sting.oneoffprojects.walkers;
+
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.RefWalker;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.collections.Pair;
+
+import java.util.List;
+
+/**
+ * Counts the number of contiguous regions the walker traverses over. Slower than it needs to be, but
+ * very useful since overlapping intervals get merged, so you can count the number of intervals the GATK merges down to.
+ * This was its very first use.
+ */
+public class CountIntervals extends RefWalker<GenomeLoc, Pair<GenomeLoc,Long>> {
+
+    public Pair<GenomeLoc,Long> reduceInit() {
+        return new Pair<GenomeLoc,Long>(null,0l);
+    }
+
+    public GenomeLoc map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if ( tracker == null ) {
+            return null;
+        }
+
+        return ref.getLocus();
+    }
+
+    public Pair<GenomeLoc,Long> reduce(GenomeLoc loc, Pair<GenomeLoc,Long> prev) {
+        if ( prev.first == null || prev.first.distance(loc) > 1 ) {
+            prev.second ++;
+        }
+
+        prev.first = loc;
+
+        return prev;
+    }
+
+    public void onTraversalDone(Pair<GenomeLoc,Long> finalReduce ) {
+        out.printf("Number of contiguous intervals: %d",finalReduce.second);
+    }
+}