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 e00b394b2..c69eb4c77 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -206,7 +206,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             emit(readsNotToClean);
         }
 
-        writer.close();
+        if ( writer != null )
+            writer.close();
 
         if ( OUT_INDELS != null ) {
             try {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java
new file mode 100644
index 000000000..07c23ff13
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java
@@ -0,0 +1,56 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2009 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+package org.broadinstitute.sting.gatk.walkers.indels;
+
+import net.sf.samtools.*;
+
+/**
+ * Extends Picard's Comparator for sorting SAMRecords by coordinate.  This one actually deals with unmapped reads
+ * (among other things) sitting at the same position as their mates (so that they both can be put into the same set).
+ */
+public class SAMRecordCoordinateComparatorWithUnmappedReads extends SAMRecordCoordinateComparator {
+    public int compare(final SAMRecord samRecord1, final SAMRecord samRecord2) {
+        int cmp = fileOrderCompare(samRecord1, samRecord2);
+        if ( cmp != 0 )
+            return cmp;
+
+        // deal with unmapped reads
+        if ( samRecord1.getReadUnmappedFlag() != samRecord2.getReadUnmappedFlag() )
+            return (samRecord1.getReadUnmappedFlag()? 1: -1);        
+
+        if ( samRecord1.getReadNegativeStrandFlag() != samRecord2.getReadNegativeStrandFlag() )
+            return (samRecord1.getReadNegativeStrandFlag()? 1: -1);
+
+        // even the names can be the same
+        cmp = samRecord1.getReadName().compareTo(samRecord2.getReadName());
+        if ( cmp != 0 )
+            return cmp;
+
+        if ( samRecord1.getDuplicateReadFlag() != samRecord2.getDuplicateReadFlag() )
+            return (samRecord1.getDuplicateReadFlag()? -1: 1);
+
+        // such a case was actually observed
+        return samRecord1.getMappingQuality() - samRecord2.getMappingQuality();
+    }
+}
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/SortingSAMFileWriter.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/SortingSAMFileWriter.java
index 72bd87afe..748aeea00 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/SortingSAMFileWriter.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/SortingSAMFileWriter.java
@@ -23,7 +23,7 @@ public class SortingSAMFileWriter implements SAMFileWriter {
     private int window;
 
     // the reads we are accumulating
-    private TreeSet<SAMRecord> cachedReads = new TreeSet<SAMRecord>(new SAMRecordCoordinateComparator());
+    private TreeSet<SAMRecord> cachedReads = new TreeSet<SAMRecord>(new SAMRecordCoordinateComparatorWithUnmappedReads());
 
 
     /**