diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
index b6fe59f6d..42314c5da 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@@ -7,10 +7,10 @@ import org.broadinstitute.sting.queue.function.ListWriterFunction
 import collection.JavaConversions._
 import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
 import org.broadinstitute.sting.queue.extensions.picard._
-import net.sf.samtools.{SAMFileReader}
+import net.sf.samtools.SAMFileReader
 import net.sf.samtools.SAMFileHeader.SortOrder
 
-import org.broadinstitute.sting.queue.qscripts.utils.Utils
+import org.broadinstitute.sting.queue.util.QScriptUtils
 
 class DataProcessingPipeline extends QScript {
   qscript =>
@@ -123,7 +123,7 @@ class DataProcessingPipeline extends QScript {
 
       // only allow one sample per file. Bam files with multiple samples would require pre-processing of the file
       // with PrintReads to separate the samples. Tell user to do it himself!
-      assert(!Utils.hasMultipleSamples(readGroups), "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam)
+      assert(!QScriptUtils.hasMultipleSamples(readGroups), "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam)
 
       // Fill out the sample table with the readgroups in this file
       for (rg <- readGroups) {
@@ -206,8 +206,8 @@ class DataProcessingPipeline extends QScript {
   def script = {
 
     // keep a record of the number of contigs in the first bam file in the list
-    val bams = Utils.createListFromFile(input)
-    nContigs = Utils.getNumberOfContigs(bams(0))
+    val bams = QScriptUtils.createListFromFile(input)
+    nContigs = QScriptUtils.getNumberOfContigs(bams(0))
 
     val realignedBams = if (useBWApe || useBWAse) {performAlignment(bams)} else {bams}
 
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
index b2960f150..56ca36925 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
@@ -2,9 +2,7 @@ package org.broadinstitute.sting.queue.qscripts
 
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.extensions.gatk._
-import net.sf.samtools.SAMFileReader
-import io.Source._
-import org.broadinstitute.sting.queue.qscripts.utils.Utils
+import org.broadinstitute.sting.queue.util.QScriptUtils
 
 /**
  * Created by IntelliJ IDEA.
@@ -36,8 +34,8 @@ class RecalibrateBaseQualities extends QScript {
 
   def script = {
 
-    val bamList = Utils.createListFromFile(input)
-    nContigs = Utils.getNumberOfContigs(bamList(0))
+    val bamList = QScriptUtils.createListFromFile(input)
+    nContigs = QScriptUtils.getNumberOfContigs(bamList(0))
 
     for (bam <- bamList) {
 
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
similarity index 91%
rename from public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala
rename to public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
index 1189b376c..9fb4fa30d 100644
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/utils/Utils.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.queue.qscripts.utils
+package org.broadinstitute.sting.queue.util
 
 import java.io.File
 import io.Source._
@@ -15,7 +15,7 @@ import collection.JavaConversions._
  * To change this template use File | Settings | File Templates.
  */
 
-object Utils {
+object QScriptUtils {
 
   /**
    * Takes a bam list file and produces a scala list with each file allowing the bam list
@@ -38,7 +38,7 @@ object Utils {
    * Returns the number of contigs in the BAM file header.
    */
   def getNumberOfContigs(bamFile: File): Int = {
-    val samReader = new SAMFileReader(new File(bamFile))
+    val samReader = new SAMFileReader(bamFile)
     samReader.getFileHeader.getSequenceDictionary.getSequences.size()
   }