diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index fcfbead92..3b81dbb68 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -406,8 +406,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
 
     private void emitReadLists() {
         // pre-merge lists with priority queue for constrained SAMFileWriter
+        logger.warn("EMIT currentInterval " + currentInterval);
         readsNotToClean.addAll(readsToClean.getReads());
-        emit(readsNotToClean);
+        emit(ReadUtils.coordinateSortReads(readsNotToClean));
         readsToClean.clear();
         readsNotToClean.clear();
     }
diff --git a/java/src/org/broadinstitute/sting/utils/sam/ConstrainedMateFixingSAMFileWriter.java b/java/src/org/broadinstitute/sting/utils/sam/ConstrainedMateFixingSAMFileWriter.java
index 131229fa4..1069752ff 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/ConstrainedMateFixingSAMFileWriter.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/ConstrainedMateFixingSAMFileWriter.java
@@ -156,7 +156,7 @@ public class ConstrainedMateFixingSAMFileWriter implements SAMFileWriter {
      * @{inheritDoc}
      */
     public void addAlignment( SAMRecord newRead ) {
-        if ( DEBUG ) logger.info("New read pos " + newRead.getAlignmentStart());
+        if ( DEBUG ) logger.info("New read pos " + newRead.getAlignmentStart() + " OP = " + newRead.getAttribute("OP"));
 
         //final long curTime = timer.currentTime();
         //if ( curTime - lastProgressPrintTime > PROGRESS_PRINT_FREQUENCY ) {
@@ -217,8 +217,9 @@ public class ConstrainedMateFixingSAMFileWriter implements SAMFileWriter {
                     forMateMatching.remove(read.getReadName());
 
                     if ( DEBUG )
-                        logger.warn(String.format("EMIT!  At %d: read %s at %d with isize %d, mate start %d",
-                                newRead.getAlignmentStart(), read.getReadName(), read.getAlignmentStart(), read.getInferredInsertSize(), read.getMateAlignmentStart()));
+                        logger.warn(String.format("EMIT!  At %d: read %s at %d with isize %d, mate start %d, op = %s",
+                                newRead.getAlignmentStart(), read.getReadName(), read.getAlignmentStart(),
+                                read.getInferredInsertSize(), read.getMateAlignmentStart(), read.getAttribute("OP")));
                     // emit to disk
                     finalDestination.addAlignment(waitingReads.remove());
                 } else {
diff --git a/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index d689af645..50da4890d 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -27,8 +27,7 @@ package org.broadinstitute.sting.utils.sam;
 
 import net.sf.samtools.*;
 
-import java.util.Map;
-import java.util.HashMap;
+import java.util.*;
 import java.io.File;
 
 /**
@@ -208,5 +207,25 @@ public class ReadUtils {
             }
         }
         return flags;
-    }    
+    }
+
+    /**
+     * Returns the collections of reads sorted in coordinate order, according to the order defined
+     * in the reads themselves
+     *
+     * @param reads
+     * @return
+     */
+    public final static List<SAMRecord> coordinateSortReads(Collection<SAMRecord> reads) {
+        final int n = reads.size();
+
+        if ( n > 0 ) {
+            final SAMRecordComparator comparer = new SAMRecordCoordinateComparator();
+            final Queue<SAMRecord> sorted = new PriorityQueue<SAMRecord>(reads.size(), comparer);
+            sorted.addAll(reads);
+            return new ArrayList<SAMRecord>(sorted);
+        } else {
+            return Collections.emptyList();
+        }
+    }
 }