diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index 140d860df..a10e631a2 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -146,10 +146,22 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
     public final boolean throughEndOfContigP() { return this.stop == Integer.MAX_VALUE; }
     public final boolean atBeginningOfContigP() { return this.start == 1; }
 
+    /** Sets contig name. UNSAFE since it 1) does NOT update contig index; 2) does not validate the name
+     * 
+     * @param contig
+     */
     public void setContig(String contig) {
         this.contigName = contig;
     }
 
+    /** Sets contig index. UNSAFE since it 1) does NOT update contig name; 2) does not validate the index
+     * 
+     * @param contig
+     */
+    public void setContigIndex(int contig) {
+        this.contigIndex = contig;
+    }
+
     public void setStart(long start) {
         this.start = start;
     }
@@ -296,6 +308,4 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
 
 
 
-
-
 }