diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
index c98fe4d3c..4d50ef951 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
@@ -130,7 +130,7 @@ public class ConstrainedMateFixingManager {
     private static final boolean DEBUG = false;
 
     /** How often do we check whether we want to emit reads? */
-    private final static int EMIT_FREQUENCY = 1000;
+    protected final static int EMIT_FREQUENCY = 1000;
 
     /**
      * How much could a single read move in position from its original position?
@@ -324,7 +324,8 @@ public class ConstrainedMateFixingManager {
                            || noReadCanMoveBefore(read.getMateAlignmentStart(), newRead ) ) ) { // we're already past where the mate started
 
                     // remove reads from the map that we have emitted -- useful for case where the mate never showed up
-                    forMateMatching.remove(read.getReadName());
+                    if ( !read.getNotPrimaryAlignmentFlag() )
+                        forMateMatching.remove(read.getReadName());
 
                     if ( DEBUG )
                         logger.warn(String.format("EMIT!  At %d: read %s at %d with isize %d, mate start %d, op = %s",
@@ -346,7 +347,8 @@ public class ConstrainedMateFixingManager {
 
     private void writeRead(SAMRecord read) {
         try {
-            writer.addAlignment(read);
+            if ( writer != null )
+                writer.addAlignment(read);
         } catch (IllegalArgumentException e) {
             throw new UserException("If the maximum allowable reads in memory is too small, it may cause reads to be written out of order when trying to write the BAM; please see the --maxReadsInMemory argument for details.  " + e.getMessage(), e);
         }
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManagerUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManagerUnitTest.java
index 9bcd7a3a3..0f910507e 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManagerUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManagerUnitTest.java
@@ -66,9 +66,10 @@ public class ConstrainedMateFixingManagerUnitTest extends BaseTest {
 
     @BeforeClass
     public void beforeClass() {
-        header = ArtificialSAMUtils.createArtificialSamHeader(3, 1, 100);
+        header = ArtificialSAMUtils.createArtificialSamHeader(3, 1, 10000);
         genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
     }
+
     @Test
     public void testSecondaryAlignmentsDoNotInterfere() {
         final List<GATKSAMRecord> properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 10, 30, true, false);
@@ -105,4 +106,29 @@ public class ConstrainedMateFixingManagerUnitTest extends BaseTest {
         }
     }
 
+    @Test
+    public void testSecondaryAlignmentsDoNotCauseAccidentalRemovalOfMate() {
+        final List<GATKSAMRecord> properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 530, 1594, true, false);
+        final GATKSAMRecord read1 = properReads.get(0);
+        read1.setFlags(99);   // first in proper pair, mate negative strand
+
+        final GATKSAMRecord read2Primary = properReads.get(1);
+        read2Primary.setFlags(147);   // second in pair, mate unmapped, not primary alignment
+        read2Primary.setAlignmentStart(1596); // move the read
+
+        final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary);
+        read2NonPrimary.setReadName("foo");
+        read2NonPrimary.setFlags(393);   // second in proper pair, on reverse strand
+        read2NonPrimary.setAlignmentStart(451);
+        read2NonPrimary.setMateAlignmentStart(451);
+
+        final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 10000, 200, 10000);
+        manager.addRead(read2NonPrimary, false, false);
+        manager.addRead(read1, false, false);
+
+        for ( int i = 0; i < ConstrainedMateFixingManager.EMIT_FREQUENCY; i++ )
+            manager.addRead(ArtificialSAMUtils.createArtificialRead(header, "foo" + i, 0, 1500, 10), false, false);
+
+        Assert.assertTrue(manager.forMateMatching.containsKey("foo"));
+    }
 }
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