diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index e5a9927e4..78d7d14f0 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -48,19 +48,13 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
 import java.util.*;
 
 public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel {
-    private final int maxReadDeletionLength = 3;
     private final int HAPLOTYPE_SIZE;
 
     private final int minIndelCountForGenotyping;
     private final boolean getAlleleListFromVCF;
-    // todo - the following  need to be exposed for command line argument control
-    private final double indelHeterozygosity = 1.0/8000;
-    boolean useFlatPriors = true;
 
     private boolean DEBUG = false;
 
-    // todo -cleanup
-    private HaplotypeIndelErrorModel model;
     private PairHMMIndelErrorModel pairModel;
 
     private GenomeLoc lastSiteVisited;
@@ -114,7 +108,10 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
 
 
             for ( ExtendedEventPileupElement p : indelPileup.toExtendedIterable() ) {
-                SAMRecord read = p.getRead();
+                //SAMRecord read = p.getRead();
+                 SAMRecord read = ReadUtils.hardClipAdaptorSequence(p.getRead());
+                if (read == null)
+                    continue;     
                 if(ReadUtils.is454Read(read)) {
                     continue;
                 }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index 7ca6f4964..dd81570a1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -583,11 +583,11 @@ public class PairHMMIndelErrorModel {
 
             }
         }
-        for (SAMRecord read : pileup.getReads()) {
-/*            SAMRecord read = ReadUtils.hardClipAdaptorSequence(read);
+        for (SAMRecord pread : pileup.getReads()) {
+           SAMRecord read = ReadUtils.hardClipAdaptorSequence(pread);
             if (read == null)
                 continue;
-  */
+
             if(ReadUtils.is454Read(read)) {
                 continue;
             }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index 9ce58665b..d1f587a20 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -27,7 +27,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot1() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
-                Arrays.asList("a2218244df08dce96d04f8736a6de796"));
+                Arrays.asList("02481347a19d80e09538f2f6aa1be74a"));
         executeTest("test MultiSample Pilot1", spec);
     }
 
@@ -248,7 +248,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -glm INDEL" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("ffeea8550a707871a68f6707159f4ea9"));
+                Arrays.asList("08b63c534a7e129e53cdd1527d51be5c"));
 
         executeTest(String.format("test indel caller in SLX"), spec);
     }
@@ -277,7 +277,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                          " -glm INDEL" +
                          " -L 1:10,000,000-10,500,000",
                  1,
-                 Arrays.asList("897057070aa2e3651d91625a58c5ec4b"));
+                 Arrays.asList("1d1ddad622dbee7e74550b5bb9d0928f"));
 
          executeTest(String.format("test indel calling, multiple technologies"), spec);
      }