diff --git a/public/java/src/org/broadinstitute/sting/utils/ContigComparator.java b/public/java/src/org/broadinstitute/sting/utils/ContigComparator.java
new file mode 100644
index 000000000..5e573418d
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/ContigComparator.java
@@ -0,0 +1,57 @@
+package org.broadinstitute.sting.utils;
+
+import java.util.Comparator;
+import java.util.Set;
+import java.util.TreeSet;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: carneiro
+ * Date: 7/23/11
+ * Time: 6:07 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class ContigComparator implements Comparator<String> {
+    private Set<String> specialChrs;
+
+    public ContigComparator() {
+        specialChrs = new TreeSet<String>();
+        specialChrs.add("X");
+        specialChrs.add("Y");
+    }
+
+    public int compare(String chr1, String chr2) {
+        if (chr1.equals(chr2))
+            return 0;
+
+        Integer x = convertStringWithoutException(chr1);
+        Integer y = convertStringWithoutException(chr2);
+        // both contigs are numbered
+        if (x != null && y != null)
+            return (x < y) ? -1:1;
+
+        // both contigs are named
+        if (x == null && y == null) {
+            // both contigs are special contigs or neither contig is a special contigs
+            if (specialChrs.contains(chr1) && specialChrs.contains(chr2) || (!specialChrs.contains(chr1) && !specialChrs.contains(chr2)))
+                return chr1.compareTo(chr2);
+            // one contig is a special and the other is not special
+            if (specialChrs.contains(chr1))
+                return -1;
+            return 1;
+        }
+
+        // one contig is named the other is numbered
+        if (x != null)
+            return -1;
+        return 1;
+    }
+
+    private Integer convertStringWithoutException(String contig) {
+        Integer x = null;
+        try {
+            x = Integer.decode(contig);
+        } catch (NumberFormatException n){}
+        return x;
+    }
+}