diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java
index dabfbb322..371d5b7e3 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java
@@ -48,7 +48,6 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs;
 
 import com.google.java.contract.Requires;
 
-import java.io.File;
 import java.util.*;
 
 /**
@@ -177,9 +176,9 @@ public class CommonSuffixSplitter {
      */
     @Requires("!middleVertices.isEmpty()")
     protected static SeqVertex commonSuffix(final Collection<SeqVertex> middleVertices) {
-        final List<byte[]> kmers = Utils.getKmers(middleVertices);
-        final int min = Utils.minKmerLength(kmers);
-        final int suffixLen = Utils.compSuffixLen(kmers, min);
+        final List<byte[]> kmers = GraphUtils.getKmers(middleVertices);
+        final int min = GraphUtils.minKmerLength(kmers);
+        final int suffixLen = GraphUtils.compSuffixLen(kmers, min);
         final byte[] kmer = kmers.get(0);
         final byte[] suffix = Arrays.copyOfRange(kmer, kmer.length - suffixLen, kmer.length);
         return new SeqVertex(suffix);
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Utils.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtils.java
similarity index 99%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Utils.java
rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtils.java
index 8cb272925..30c5be190 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Utils.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtils.java
@@ -60,8 +60,8 @@ import java.util.List;
  * Date: 3/25/13
  * Time: 9:42 PM
  */
-final class Utils {
-    private Utils() {}
+final class GraphUtils {
+    private GraphUtils() {}
 
     /**
      * Compute the maximum shared prefix length of list of bytes.
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java
index 4cc7aae2a..97969d098 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java
@@ -70,7 +70,7 @@ public final class SeqGraph extends BaseGraph<SeqVertex> {
      * merging inappropriate head or tail nodes, which introduces large insertion / deletion events
      * as the merge operation creates a link among the non-linked sink / source vertices
      */
-    private final static int MIN_COMMON_SEQUENCE_TO_MERGE_SOURCE_SINK_VERTICES = 10;
+    protected final static int MIN_COMMON_SEQUENCE_TO_MERGE_SOURCE_SINK_VERTICES = 10;
 
     /**
      * Construct an empty SeqGraph
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java
index ca7faa444..f6ee4c3c3 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java
@@ -295,8 +295,8 @@ public class SharedVertexSequenceSplitter {
             min = Math.min(min, v.getSequence().length);
         }
 
-        final int prefixLen = Utils.compPrefixLen(kmers, min);
-        final int suffixLen = Utils.compSuffixLen(kmers, min - prefixLen);
+        final int prefixLen = GraphUtils.compPrefixLen(kmers, min);
+        final int suffixLen = GraphUtils.compSuffixLen(kmers, min - prefixLen);
 
         final byte[] kmer = kmers.get(0);
         final byte[] prefix = Arrays.copyOfRange(kmer, 0, prefixLen);
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java
index ca43ced69..42137e4e4 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java
@@ -47,6 +47,7 @@
 package org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs;
 
 import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.Utils;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -195,8 +196,8 @@ public class SeqGraphUnitTest extends BaseTest {
 
         final SeqGraph graph = new SeqGraph();
 
-        SeqVertex pre1 = new SeqVertex("ACT");
-        SeqVertex pre2 = new SeqVertex("AGT");
+        SeqVertex pre1 = new SeqVertex(Utils.dupString("A", SeqGraph.MIN_COMMON_SEQUENCE_TO_MERGE_SOURCE_SINK_VERTICES) + "CT");
+        SeqVertex pre2 = new SeqVertex(Utils.dupString("A", SeqGraph.MIN_COMMON_SEQUENCE_TO_MERGE_SOURCE_SINK_VERTICES) + "GT");
         SeqVertex top = new SeqVertex("A");
         SeqVertex middle1 = new SeqVertex("GC");
         SeqVertex middle2 = new SeqVertex("TC");
@@ -282,7 +283,7 @@ public class SeqGraphUnitTest extends BaseTest {
             final SeqVertex newMiddle1 = new SeqVertex("G");
             final SeqVertex newMiddle2 = new SeqVertex("T");
             final SeqVertex newBottom = new SeqVertex("C" + bottom.getSequenceString());
-            final SeqVertex newTop = new SeqVertex("A");
+            final SeqVertex newTop = new SeqVertex(Utils.dupString("A", SeqGraph.MIN_COMMON_SEQUENCE_TO_MERGE_SOURCE_SINK_VERTICES));
             final SeqVertex newTopDown1 = new SeqVertex("G");
             final SeqVertex newTopDown2 = new SeqVertex("C");
             final SeqVertex newTopBottomMerged = new SeqVertex("TA");
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java
index 0930d497f..2df783b19 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java
@@ -98,10 +98,10 @@ public class SharedVertexSequenceSplitterUnitTest extends BaseTest {
             min = Math.min(min, s.length());
         }
 
-        final int actualPrefixLen = org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.Utils.compPrefixLen(bytes, min);
+        final int actualPrefixLen = GraphUtils.compPrefixLen(bytes, min);
         Assert.assertEquals(actualPrefixLen, expectedPrefixLen, "Failed prefix test");
 
-        final int actualSuffixLen = org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.Utils.compSuffixLen(bytes, min - actualPrefixLen);
+        final int actualSuffixLen = GraphUtils.compSuffixLen(bytes, min - actualPrefixLen);
         Assert.assertEquals(actualSuffixLen, expectedSuffixLen, "Failed suffix test");
     }