diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java
index 69e130cfa..a9df8cd11 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java
@@ -60,6 +60,8 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
     private TreeSet<ComparableSAMRecord> readsToWrite = null;
     private TreeSet<ComparableSAMRecord> nextSetOfReadsToWrite = null;
 
+    private boolean debugOn = false;
+
     public void initialize() {
 
         if ( LOD_THRESHOLD < 0.0 )
@@ -224,12 +226,19 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
         ArrayList<AlignedRead> altReads = new ArrayList<AlignedRead>();               // reads that don't perfectly match
         LinkedList<AlignedRead> altAlignmentsToTest = new LinkedList<AlignedRead>();  // should we try to make an alt consensus from the read?
         ArrayList<AlignedRead> leftMovedIndels = new ArrayList<AlignedRead>();
-        HashSet<Consensus> altConsenses = new HashSet<Consensus>();                   // list of alt consenses
+        Set<Consensus> altConsenses = new LinkedHashSet<Consensus>();                   // list of alt consenses
         int totalMismatchSum = 0;
 
+
         // decide which reads potentially need to be cleaned
         for ( SAMRecord read : reads ) {
 
+            //            if ( debugOn ) {
+            //                System.out.println(read.getReadName()+" "+read.getCigarString()+" "+read.getAlignmentStart()+"-"+read.getAlignmentEnd());
+            //                System.out.println(reference.substring((int)(read.getAlignmentStart()-leftmostIndex),(int)(read.getAlignmentEnd()-leftmostIndex)));
+            //                System.out.println(read.getReadString());
+            //            } 
+
             // we currently can not deal with clipped reads correctly (or screwy record)
             if ( read.getCigar().numCigarElements() == 0 || readIsClipped(read) ) {
                 refReads.add(read);
@@ -247,6 +256,7 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
             }
 
             int mismatchScore = mismatchQualitySumIgnoreCigar(aRead, reference, read.getAlignmentStart()-(int)leftmostIndex);
+            //            if ( debugOn ) System.out.println("mismatchScore="+mismatchScore);
 
             // if this doesn't match perfectly to the reference, let's try to clean it
             if ( mismatchScore > 0 ) {
@@ -256,11 +266,14 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
                 // if it has an indel, let's see if that's the best consensus
                 if ( numBlocks == 2 )
                     altConsenses.add(createAlternateConsensus(aRead.getAlignmentStart() - (int)leftmostIndex, aRead.getCigar(), reference, aRead.getReadString()));
-                else
+                else {
+                    //                    if ( debugOn ) System.out.println("Going to test...");
                     altAlignmentsToTest.add(aRead);
+                }
             }
             // otherwise, we can emit it as is
             else {
+                // if ( debugOn ) System.out.println("Emitting as is...");
                 refReads.add(read);
             }
         }
@@ -271,8 +284,12 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
                 // do a pairwise alignment against the reference
                 SWPairwiseAlignment swConsensus = new SWPairwiseAlignment(reference, aRead.getReadString(), SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND);
                 Consensus c = createAlternateConsensus(swConsensus.getAlignmentStart2wrt1(), swConsensus.getCigar(), reference, aRead.getReadString());
-                if ( c != null)
+                if ( c != null) {
+                    //                    if ( debugOn ) System.out.println("NEW consensus generated by SW: "+c.str ) ; 
                     altConsenses.add(c);
+                } else {
+                    //   if ( debugOn ) System.out.println("FAILED to create Alt consensus from SW");
+                }
             }
         } else {
             // choose alternate consenses randomly
@@ -290,9 +307,14 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
 
         Consensus bestConsensus = null;
         Iterator<Consensus> iter = altConsenses.iterator();
+
+        // if ( debugOn ) System.out.println("------\nChecking consenses...\n--------\n");
+
         while ( iter.hasNext() ) {
             Consensus consensus = iter.next();
 
+            // if ( debugOn ) System.out.println("Consensus: "+consensus.str);
+
             for ( int j = 0; j < altReads.size(); j++ ) {
                 AlignedRead toTest = altReads.get(j);
                 Pair<Integer, Integer> altAlignment = findBestOffset(consensus.str, toTest);
@@ -458,6 +480,8 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
         sb.append(reference.substring(refIdx));
         String altConsensus =  sb.toString(); // alternative consensus sequence we just built from the cuurent read
 
+        // if ( debugOn ) System.out.println("Alt consensus generated: "+altConsensus);
+
         return new Consensus(altConsensus, c, indexOnRef);
     }