diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala b/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala
index 03d31a217..3c7cd0a2d 100755
--- a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala
@@ -26,24 +26,24 @@ class VCFExtractIntervals(inVCF: File, outList: File, useFilterSites: Boolean) e
     var cur : String = null
     if ( elems.hasNext ) {
       cur = elems.next
+      while ( elems.hasNext ) {
+        out.printf("%s%n",prev)
+        while ( cur.equals(prev) && elems.hasNext && !cur.equals("") ) {
+          cur = elems.next
+        }
+
+        if ( ! cur.equals(prev) ) {
+          if ( elems.hasNext ) {
+            prev = cur
+            cur = elems.next
+          }
+        }
+      }
+      out.printf("%s%n",prev)
+      out.printf("%s%n",cur)
     } else {
       out.printf("%s%n",prev)
     }
-    while ( elems.hasNext ) {
-      out.printf("%s%n",prev)
-      while ( cur.equals(prev) && elems.hasNext && !cur.equals("") ) {
-        cur = elems.next
-      }
-      
-      if ( ! cur.equals(prev) ) {
-        if ( elems.hasNext ) {
-          prev = cur
-          cur = elems.next
-        }
-      }
-    }
-    out.printf("%s%n",prev)
-    out.printf("%s%n",cur)
 
     out.close
   }