diff --git a/public/java/src/org/broadinstitute/sting/utils/collections/LoggingNestedIntegerArray.java b/public/java/src/org/broadinstitute/sting/utils/collections/LoggingNestedIntegerArray.java
index 617391714..6fda0245b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/collections/LoggingNestedIntegerArray.java
+++ b/public/java/src/org/broadinstitute/sting/utils/collections/LoggingNestedIntegerArray.java
@@ -34,7 +34,12 @@ import java.io.PrintStream;
  * to the provided output stream. For testing/debugging purposes.
  *
  * Log entries are of the following form (fields are tab-separated):
- * LABEL    VALUE   KEY1    KEY2    ...     KEY_N
+ * LABEL    OPERATION    VALUE   KEY1    KEY2    ...     KEY_N
+ *
+ * A header line is written before the log entries giving the dimensions of this NestedIntegerArray.
+ * It has the form:
+ *
+ * # LABEL    SIZE_OF_FIRST_DIMENSION    SIZE_OF_SECOND_DIMENSION    ...    SIZE_OF_NTH_DIMENSION
  *
  * @author David Roazen
  */
@@ -43,6 +48,9 @@ public class LoggingNestedIntegerArray<T> extends NestedIntegerArray<T> {
     private PrintStream log;
     private String logEntryLabel;
 
+    public static final String HEADER_LINE_PREFIX = "# ";
+    public enum NestedIntegerArrayOperation { GET, PUT };
+
     /**
      *
      * @param log output stream to which to log update operations
@@ -57,6 +65,37 @@ public class LoggingNestedIntegerArray<T> extends NestedIntegerArray<T> {
         }
         this.log = log;
         this.logEntryLabel = logEntryLabel != null ? logEntryLabel : "";
+
+        // Write the header line recording the dimensions of this NestedIntegerArray:
+        StringBuilder logHeaderLine = new StringBuilder();
+
+        logHeaderLine.append(HEADER_LINE_PREFIX);
+        logHeaderLine.append(this.logEntryLabel);
+        for ( int dimension : dimensions ) {
+            logHeaderLine.append("\t");
+            logHeaderLine.append(dimension);
+        }
+
+        this.log.println(logHeaderLine.toString());
+    }
+
+    @Override
+    public T get( final int... keys ) {
+        StringBuilder logEntry = new StringBuilder();
+
+        logEntry.append(logEntryLabel);
+        logEntry.append("\t");
+        logEntry.append(NestedIntegerArrayOperation.GET);
+        logEntry.append("\t");  // empty field for the datum value
+
+        for ( int key : keys ) {
+            logEntry.append("\t");
+            logEntry.append(key);
+        }
+
+        log.println(logEntry.toString());
+
+        return super.get(keys);
     }
 
     @Override
@@ -67,6 +106,8 @@ public class LoggingNestedIntegerArray<T> extends NestedIntegerArray<T> {
 
         logEntry.append(logEntryLabel);
         logEntry.append("\t");
+        logEntry.append(NestedIntegerArrayOperation.PUT);
+        logEntry.append("\t");
         logEntry.append(value);
         for ( int key : keys ) {
             logEntry.append("\t");