diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java
index 697186463..d8c3a3ebd 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java
@@ -47,7 +47,8 @@
 package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
 
 import com.google.caliper.Param;
-import org.apache.commons.codec.digest.DigestUtils;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.haplotype.Haplotype;
 import org.broadinstitute.sting.utils.pairhmm.ActiveRegionTestDataSet;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@@ -64,7 +65,7 @@ import java.util.*;
  * Time: 2:48 PM
  * To change this template use File | Settings | File Templates.
  */
-public class ActiveRegionTestDataSetUnitTest  {
+public class ActiveRegionTestDataSetUnitTest extends BaseTest {
 
 
 
@@ -419,6 +420,6 @@ public class ActiveRegionTestDataSetUnitTest  {
                     "CTGGGAGCCTAAGGCATCACTCAAGATACAGGCTCGGTAACGTACGCTCTAGCCATCTAA" +
                     "CTATCCCCTATGTCTTATAGGGACCTACGTTATCTGCCTG";
 
-    protected final static String REF_MD5 = new String(DigestUtils.md5(REF));
+    protected final static String REF_MD5 = Utils.calcMD5(REF);
 
 }
\ No newline at end of file
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java
index fc40edc42..c1d822eec 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java
@@ -46,7 +46,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs;
 
-import org.apache.commons.lang.ArrayUtils;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.Utils;
diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java
index cee8d358e..84b995749 100644
--- a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java
+++ b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java
@@ -49,14 +49,13 @@ package org.broadinstitute.sting.utils.pairhmm;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
-import org.apache.commons.math.MathException;
 import org.apache.commons.math.distribution.ExponentialDistribution;
-import org.apache.commons.math.distribution.ExponentialDistributionImpl;
 import org.broadinstitute.sting.gatk.walkers.haplotypecaller.AssemblyResult;
 import org.broadinstitute.sting.gatk.walkers.haplotypecaller.AssemblyResultSet;
 import org.broadinstitute.sting.gatk.walkers.haplotypecaller.Civar;
 import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.ReadThreadingGraph;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.haplotype.Haplotype;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
@@ -325,7 +324,7 @@ public class ActiveRegionTestDataSet {
                 this.setReadName(r.getReadName());
             }
 
-        ExponentialDistribution indelLengthDist = new ExponentialDistributionImpl(1.0/0.9);
+        ExponentialDistribution indelLengthDist = MathUtils.exponentialDistribution(1.0 / 0.9);
 
         public MyGATKSAMRecord(final GATKSAMRecord r, final Random rnd) {
             super(r.getHeader(), r.getReferenceIndex(), r.getAlignmentStart(), (short) r.getReadNameLength(),
@@ -390,7 +389,7 @@ public class ActiveRegionTestDataSet {
             final int length;
             try {
                 length = (int) Math.round(indelLengthDist.inverseCumulativeProbability(rnd.nextDouble()) + 1);
-            } catch (MathException e) {
+            } catch (Exception e) {
                 throw new RuntimeException(e);
             }
             return length;
diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
index 0b6cd4b1d..82c9fe751 100644
--- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
@@ -27,6 +27,8 @@ package org.broadinstitute.sting.utils;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
+import org.apache.commons.math.distribution.ExponentialDistribution;
+import org.apache.commons.math.distribution.ExponentialDistributionImpl;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
@@ -1510,4 +1512,7 @@ public class MathUtils {
         return dirichletMultinomial(params,sum(params),counts,(int) sum(counts));
     }
 
+    public static ExponentialDistribution exponentialDistribution( final double mean ) {
+        return new ExponentialDistributionImpl(mean);
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/Utils.java b/public/java/src/org/broadinstitute/sting/utils/Utils.java
index 41a36c235..9657bc403 100644
--- a/public/java/src/org/broadinstitute/sting/utils/Utils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/Utils.java
@@ -744,7 +744,7 @@ public class Utils {
     /**
      * @see #calcMD5(byte[])
      */
-    public static String calcMD5(final String s) throws NoSuchAlgorithmException {
+    public static String calcMD5(final String s) {
         return calcMD5(s.getBytes());
     }
 
@@ -753,17 +753,21 @@ public class Utils {
      *
      * @param bytes the bytes to calculate the md5 of
      * @return the md5 of bytes, as a 32-character long string
-     * @throws NoSuchAlgorithmException
      */
     @Ensures({"result != null", "result.length() == 32"})
-    public static String calcMD5(final byte[] bytes) throws NoSuchAlgorithmException {
+    public static String calcMD5(final byte[] bytes) {
         if ( bytes == null ) throw new IllegalArgumentException("bytes cannot be null");
-        final byte[] thedigest = MessageDigest.getInstance("MD5").digest(bytes);
-        final BigInteger bigInt = new BigInteger(1, thedigest);
+        try {
+            final byte[] thedigest = MessageDigest.getInstance("MD5").digest(bytes);
+            final BigInteger bigInt = new BigInteger(1, thedigest);
 
-        String md5String = bigInt.toString(16);
-        while (md5String.length() < 32) md5String = "0" + md5String; // pad to length 32
-        return md5String;
+            String md5String = bigInt.toString(16);
+            while (md5String.length() < 32) md5String = "0" + md5String; // pad to length 32
+            return md5String;
+        }
+        catch ( NoSuchAlgorithmException e ) {
+            throw new IllegalStateException("MD5 digest algorithm not present");
+        }
     }
 
     /**