diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 1457a5ae8..3c12f7930 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -168,7 +168,7 @@ public class GenomeAnalysisEngine {
     /** commands that get executed for each engine, regardless of the type */
     private void genericEngineSetup() {
         Reads sourceInfo = extractSourceInfoFromArguments(argCollection);
-        engine.setMaxReads(argCollection.maximumEngineIterations);
+        engine.setMaximumIterations(argCollection.maximumEngineIterations);
         engine.initialize();
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
index bedd7fcc4..610dd3169 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
@@ -17,7 +17,7 @@ public abstract class TraversalEngine {
     private final long N_RECORDS_TO_PRINT = 1000000;
 
     // Maximum number of reads to process before finishing
-    protected long maxReads = -1;
+    protected long maximumIterations = -1;
 
     // the stored header
     private SAMFileHeader myHeader = null;
@@ -25,20 +25,14 @@ public abstract class TraversalEngine {
     /** our log, which we want to capture anything from this class */
     protected static Logger logger = Logger.getLogger(TraversalEngine.class);
 
-    // --------------------------------------------------------------------------------------------------------------
-    //
-    // Manipulating the underlying engine parameters
-    //
-    // --------------------------------------------------------------------------------------------------------------
-    public void setMaxReads(final int maxReads) {
-        this.maxReads = maxReads;
+    /**
+     * set the max number of iterations
+     * @param maximumIterations the number of iterations
+     */
+    public void setMaximumIterations(final int maximumIterations) {
+        this.maximumIterations = maximumIterations;
     }
 
-    // --------------------------------------------------------------------------------------------------------------
-    //
-    // functions for dealing locations (areas of the genome we're traversing over)
-    //
-    // --------------------------------------------------------------------------------------------------------------
     /**
      * get the associated SAM header for our run
      *
@@ -58,11 +52,6 @@ public abstract class TraversalEngine {
     public void setSAMHeader(SAMFileHeader myHeader) {
         this.myHeader = myHeader;
     }
-    // --------------------------------------------------------------------------------------------------------------
-    //
-    // printing
-    //
-    // --------------------------------------------------------------------------------------------------------------
 
     /**
      * @param curTime (current runtime, in millisecs)
@@ -140,16 +129,9 @@ public abstract class TraversalEngine {
         logger.info(String.format("  -> %d reads with indels", TraversalStatistics.nSkippedIndels));
     }
 
-    // --------------------------------------------------------------------------------------------------------------
-    //
-    // Initialization
-    //
-    // --------------------------------------------------------------------------------------------------------------
-
     /** Initialize the traversal engine.  After this point traversals can be run over the data */
     public void initialize() {
         lastProgressPrintTime = startTime = System.currentTimeMillis();
-        // Initial the reference ordered data iterators
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
index 03711ba92..6b3893ea9 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
@@ -200,7 +200,7 @@ public class TraverseDuplicates extends TraversalEngine {
 
             printProgress("dups", site);
 
-            if (this.maxReads > 0 && TraversalStatistics.nRecords > this.maxReads) {
+            if (this.maximumIterations > 0 && TraversalStatistics.nRecords > this.maximumIterations) {
                 logger.warn(String.format(("Maximum number of duplicate sets encountered, terminating traversal " + TraversalStatistics.nRecords)));
                 break;
             }
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
index 70f8d2cae..5db9c23eb 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
@@ -64,7 +64,7 @@ public class TraverseLoci extends TraversalEngine {
                 sum = locusWalker.reduce(x, sum);
             }
 
-            if (this.maxReads > 0 && TraversalStatistics.nRecords > this.maxReads) {
+            if (this.maximumIterations > 0 && TraversalStatistics.nRecords > this.maximumIterations) {
                 logger.warn(String.format("Maximum number of reads encountered, terminating traversal " + TraversalStatistics.nRecords));
                 break;
             }
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLocusWindows.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLocusWindows.java
index 20dda7636..037868dc8 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLocusWindows.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLocusWindows.java
@@ -80,7 +80,7 @@ public class TraverseLocusWindows extends TraversalEngine {
                 leftmostIndex = read.getAlignmentStart();
             if ( read.getAlignmentEnd() > rightmostIndex )
                 rightmostIndex = read.getAlignmentEnd();
-            if ( this.maxReads > 0 && TraversalStatistics.nRecords > this.maxReads ) {
+            if ( this.maximumIterations > 0 && TraversalStatistics.nRecords > this.maximumIterations) {
                 logger.warn(String.format("Maximum number of reads encountered, terminating traversal " + TraversalStatistics.nRecords));
                 done = true;
             }