diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
index 73301c511..e3a1b61bd 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
@@ -282,7 +282,7 @@ public class GATKBAMIndex {
             final int nBins = readInteger();
             // System.out.println("# nBins: " + nBins);
             for (int j = 0; j < nBins; j++) {
-                final int bin = readInteger();
+                skipInteger();
                 final int nChunks = readInteger();
                 // System.out.println("# bin[" + j + "] = " + bin + ", nChunks = " + nChunks);
                 skipBytes(16 * nChunks);
@@ -334,6 +334,10 @@ public class GATKBAMIndex {
         return buffer.getInt();
     }
 
+    private void skipInteger() {
+        skipBytes(INT_SIZE_IN_BYTES);
+     }
+
     /**
      * Reads an array of <count> longs from the file channel, returning the results as an array.
      * @param count Number of longs to read.