diff --git a/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
index 036477758..c624b09b8 100755
--- a/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -1,8 +1,10 @@
 package org.broadinstitute.sting.utils.sam;
 
+import java.lang.reflect.Method;
 import java.util.*;
 
 import net.sf.samtools.*;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 /**
@@ -16,6 +18,11 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
  *   if they are ever modified externally then one must also invoke the
  *   setReadGroup() method here to ensure that the cache is kept up-to-date.
  *
+ * 13 Oct 2010 - mhanna - this class is fundamentally flawed: it uses a decorator
+ *                        pattern to wrap a heavyweight object, which can lead
+ *                        to heinous side effects if the wrapping is not carefully
+ *                        done.  Hopefully SAMRecord will become an interface and
+ *                        this will eventually be fixed.
  */
 public class GATKSAMRecord extends SAMRecord {
 
@@ -327,6 +334,76 @@ public class GATKSAMRecord extends SAMRecord {
 
     public void setValidationStringency(net.sf.samtools.SAMFileReader.ValidationStringency validationStringency) { mRecord.setValidationStringency(validationStringency); }
 
+    public Object getAttribute(final String tag) { return mRecord.getAttribute(tag); }
+
+    public Integer getIntegerAttribute(final String tag) { return mRecord.getIntegerAttribute(tag); }
+
+    public Short getShortAttribute(final String tag) { return mRecord.getShortAttribute(tag); }
+
+    public Byte getByteAttribute(final String tag) { return mRecord.getByteAttribute(tag); }
+
+    public String getStringAttribute(final String tag) { return mRecord.getStringAttribute(tag); }
+
+    public Character getCharacterAttribute(final String tag) { return mRecord.getCharacterAttribute(tag); }
+
+    public Float getFloatAttribute(final String tag) { return mRecord.getFloatAttribute(tag); }
+
+    public byte[] getByteArrayAttribute(final String tag) { return mRecord.getByteArrayAttribute(tag); }
+
+    protected Object getAttribute(final short tag) {
+        Object attribute;
+        try {
+            Method method = mRecord.getClass().getDeclaredMethod("getAttribute",Short.TYPE);
+            method.setAccessible(true);
+            attribute = method.invoke(mRecord,tag);
+        }
+        catch(Exception ex) {
+            throw new ReviewedStingException("Unable to invoke getAttribute method",ex);    
+        }
+        return attribute;
+    }
+
+    public void setAttribute(final String tag, final Object value) { mRecord.setAttribute(tag,value); }
+
+    protected void setAttribute(final short tag, final Object value) {
+        try {
+            Method method = mRecord.getClass().getDeclaredMethod("setAttribute",Short.TYPE,Object.class);
+            method.setAccessible(true);
+            method.invoke(mRecord,tag,value);
+        }
+        catch(Exception ex) {
+            throw new ReviewedStingException("Unable to invoke setAttribute method",ex);
+        }
+    }
+
+    public void clearAttributes() { mRecord.clearAttributes(); }
+
+    protected void setAttributes(final SAMBinaryTagAndValue attributes) {
+        try {
+            Method method = mRecord.getClass().getDeclaredMethod("setAttributes",SAMBinaryTagAndValue.class);
+            method.setAccessible(true);
+            method.invoke(mRecord,attributes);
+        }
+        catch(Exception ex) {
+            throw new ReviewedStingException("Unable to invoke setAttributes method",ex);
+        }
+    }
+
+    protected SAMBinaryTagAndValue getBinaryAttributes() {
+        SAMBinaryTagAndValue binaryAttributes;
+        try {
+            Method method = mRecord.getClass().getDeclaredMethod("getBinaryAttributes");
+            method.setAccessible(true);
+            binaryAttributes = (SAMBinaryTagAndValue)method.invoke(mRecord);
+        }
+        catch(Exception ex) {
+            throw new ReviewedStingException("Unable to invoke getBinaryAttributes method",ex);
+        }
+        return binaryAttributes;
+    }
+
+    public List<SAMTagAndValue> getAttributes() { return mRecord.getAttributes(); }
+
     public SAMFileHeader getHeader() { return mRecord.getHeader(); }
 
     public void setHeader(SAMFileHeader samFileHeader) { mRecord.setHeader(samFileHeader); }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
index fba9b4fd3..712953e55 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
@@ -9,7 +9,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
 
     @Test
     public void testRealignerLod5() {
-        String[] md5s = {"2265e03ed1a2290e60208559925c30ef", "c4ef635f2597b12b93a73199f07e509b"};
+        String[] md5s = {"a377de4e2eb4df8ef79590e4131afe35", "c4ef635f2597b12b93a73199f07e509b"};
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
                  2,
@@ -19,7 +19,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
 
     @Test
     public void testRealignerLod50() {
-        String[] md5s = {"2265e03ed1a2290e60208559925c30ef", "3735a510513b6fa4161d92155e026283"};
+        String[] md5s = {"a377de4e2eb4df8ef79590e4131afe35", "3735a510513b6fa4161d92155e026283"};
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T IndelRealigner -noPG -LOD 50 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
                  2,
@@ -29,7 +29,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
 
     @Test
     public void testRealignerKnownsOnly() {
-        String[] md5s = {"dc2fe2856840b12a34bb57de2ca71cd0", "74652bd8240291293ec921f8ecfa1622"};
+        String[] md5s = {"654cb0c845c3f25af6a3f8911ac06a73", "74652bd8240291293ec921f8ecfa1622"};
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T IndelRealigner -noPG -LOD 1.0 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B:knownIndels,VCF " + validationDataLocation + "NA12878.indels.vcf4 -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly",
                  2,