diff --git a/protected/java/test/org/broadinstitute/sting/utils/recalibration/RepeatLengthCovariateUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RepeatLengthCovariateUnitTest.java
index 6880c9d23..d08276147 100644
--- a/protected/java/test/org/broadinstitute/sting/utils/recalibration/RepeatLengthCovariateUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RepeatLengthCovariateUnitTest.java
@@ -49,16 +49,13 @@ import com.google.java.contract.Requires;
 import net.sf.samtools.SAMFileHeader;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.recalibration.EventType;
-import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
-import org.broadinstitute.sting.utils.recalibration.covariates.ReadGroupCovariate;
 import org.broadinstitute.sting.utils.recalibration.covariates.RepeatLengthCovariate;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.variant.utils.BaseUtils;
+import org.broadinstitute.variant.utils.Pair;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -86,38 +83,38 @@ public class RepeatLengthCovariateUnitTest  {
     @Test(enabled = true)
     public void testFindNumberOfRepetitions() {
         // First, test logic to compute number of repetitions of a substring on a given string.
-        int result = GATKVariantContextUtils.findNumberofRepetitions("AC".getBytes(),"ACAC".getBytes(), true);
+        int result = VariantContextUtils.findNumberofRepetitions("AC".getBytes(), "ACAC".getBytes(), true);
         Assert.assertEquals(2,result);
-        result = GATKVariantContextUtils.findNumberofRepetitions("AC".getBytes(),"ACACACAC".getBytes(), true);
+        result = VariantContextUtils.findNumberofRepetitions("AC".getBytes(),"ACACACAC".getBytes(), true);
         Assert.assertEquals(4,result);
-        result = GATKVariantContextUtils.findNumberofRepetitions("AC".getBytes(),"ACACACACGT".getBytes(), true);
+        result = VariantContextUtils.findNumberofRepetitions("AC".getBytes(),"ACACACACGT".getBytes(), true);
         Assert.assertEquals(4,result);
-        result = GATKVariantContextUtils.findNumberofRepetitions("AC".getBytes(),"GTACACACAC".getBytes(), true);
+        result = VariantContextUtils.findNumberofRepetitions("AC".getBytes(),"GTACACACAC".getBytes(), true);
         Assert.assertEquals(0,result);
-        result = GATKVariantContextUtils.findNumberofRepetitions("GCA".getBytes(),"GTAGGGT".getBytes(), true);
+        result = VariantContextUtils.findNumberofRepetitions("GCA".getBytes(),"GTAGGGT".getBytes(), true);
         Assert.assertEquals(0,result);
-        result = GATKVariantContextUtils.findNumberofRepetitions("GCAGCA".getBytes(),"GCAGCAGTAGGGTGTACACACAC".getBytes(), true);
+        result = VariantContextUtils.findNumberofRepetitions("GCAGCA".getBytes(),"GCAGCAGTAGGGTGTACACACAC".getBytes(), true);
         Assert.assertEquals(1,result);
-        result = GATKVariantContextUtils.findNumberofRepetitions("GCAGCA".getBytes(),"GTAGGGTGTACACACACGCAGCAT".getBytes(), true);
+        result = VariantContextUtils.findNumberofRepetitions("GCAGCA".getBytes(),"GTAGGGTGTACACACACGCAGCAT".getBytes(), true);
         Assert.assertEquals(0,result);
-        result = GATKVariantContextUtils.findNumberofRepetitions("GCA".getBytes(),"GTAGGGTGTACACACACGCAGCAGCA".getBytes(), true);
+        result = VariantContextUtils.findNumberofRepetitions("GCA".getBytes(),"GTAGGGTGTACACACACGCAGCAGCA".getBytes(), true);
         Assert.assertEquals(0,result);
         // Same tests but looking backward on string
-        result = GATKVariantContextUtils.findNumberofRepetitions("AC".getBytes(),"ACAC".getBytes(), false);
+        result = VariantContextUtils.findNumberofRepetitions("AC".getBytes(),"ACAC".getBytes(), false);
         Assert.assertEquals(2,result);
-        result = GATKVariantContextUtils.findNumberofRepetitions("AC".getBytes(),"ACACACAC".getBytes(), false);
+        result = VariantContextUtils.findNumberofRepetitions("AC".getBytes(),"ACACACAC".getBytes(), false);
         Assert.assertEquals(4,result);
-        result = GATKVariantContextUtils.findNumberofRepetitions("AC".getBytes(),"ACACACACGT".getBytes(), false);
+        result = VariantContextUtils.findNumberofRepetitions("AC".getBytes(),"ACACACACGT".getBytes(), false);
         Assert.assertEquals(0,result);
-        result = GATKVariantContextUtils.findNumberofRepetitions("AC".getBytes(),"GTACACACAC".getBytes(), false);
+        result = VariantContextUtils.findNumberofRepetitions("AC".getBytes(),"GTACACACAC".getBytes(), false);
         Assert.assertEquals(4,result);
-        result = GATKVariantContextUtils.findNumberofRepetitions("GCA".getBytes(),"GTAGGGT".getBytes(), false);
+        result = VariantContextUtils.findNumberofRepetitions("GCA".getBytes(),"GTAGGGT".getBytes(), false);
         Assert.assertEquals(0,result);
-        result = GATKVariantContextUtils.findNumberofRepetitions("GCAGCA".getBytes(),"GCAGCAGTAGGGTGTACACACAC".getBytes(), false);
+        result = VariantContextUtils.findNumberofRepetitions("GCAGCA".getBytes(),"GCAGCAGTAGGGTGTACACACAC".getBytes(), false);
         Assert.assertEquals(0,result);
-        result = GATKVariantContextUtils.findNumberofRepetitions("GCAGCA".getBytes(),"GTAGGGTGTACACACACGCAGCAT".getBytes(), false);
+        result = VariantContextUtils.findNumberofRepetitions("GCAGCA".getBytes(),"GTAGGGTGTACACACACGCAGCAT".getBytes(), false);
         Assert.assertEquals(0,result);
-        result = GATKVariantContextUtils.findNumberofRepetitions("GCA".getBytes(),"GTAGGGTGTACACACACGCAGCAGCA".getBytes(), false);
+        result = VariantContextUtils.findNumberofRepetitions("GCA".getBytes(),"GTAGGGTGTACACACACGCAGCAGCA".getBytes(), false);
         Assert.assertEquals(3,result);
 
         // test logic to get repeat unit and number of repeats from covariate value