Changing from scala 2.9.2 to 2.10.2.

--modified ivy dependencies
--modified scala classpath in build.xml to include scala-reflect

--changed imports to point to the new scala scala.reflect.internal.util

--set the bootclasspath in QScriptManager as well as the classpath variable.

--removing Set[File] <-> Set[String] conversions
----Set is invariant now and the conversions broke
--removing unit tests for Set[File] <-> Set[String] conversions

build.xml

@@ -526,6 +526,7 @@
             <fileset dir="${lib.dir}">
                 <include name="scala-compiler-*.jar"/>
                 <include name="scala-library-*.jar"/>
+                <include name="scala-reflect-*.jar"/>
             </fileset>
         </path>
         <taskdef resource="scala/tools/ant/antlib.xml">

ivy.xml

@@ -82,8 +82,8 @@
         <dependency org="net.sf.gridscheduler" name="drmaa" rev="latest.integration"/>
 
         <!-- Scala dependancies -->
-        <dependency org="org.scala-lang" name="scala-compiler" rev="2.9.2"/>
+        <dependency org="org.scala-lang" name="scala-compiler" rev="2.10.2"/>
-        <dependency org="org.scala-lang" name="scala-library" rev="2.9.2"/>
+        <dependency org="org.scala-lang" name="scala-library" rev="2.10.2"/>
 
         <!-- testing and evaluation dependencies -->
         <dependency org="org.testng" name="testng" rev="6.8"/>

public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala

@@ -33,10 +33,9 @@ import java.io.File
 import scala.tools.nsc.reporters.AbstractReporter
 import java.lang.String
 import org.apache.log4j.Level
-import scala.tools.nsc.util.{FakePos, NoPosition, Position}
 import org.broadinstitute.sting.queue.util.TextFormatUtils._
 import org.broadinstitute.sting.utils.classloader.JVMUtils
-import tools.util.StringOps
+import scala.reflect.internal.util.{FakePos, NoPosition, Position, StringOps}
 
 /**
  * Plugin manager for QScripts which loads QScripts into the current class loader.
@@ -53,7 +52,10 @@ class QScriptManager() extends Logging {
       settings.outdir.value = tempDir.getPath
 
       // Set the classpath to the current class path.
-      JVMUtils.getClasspathURLs.foreach(url => settings.classpath.append(url.getPath))
+      JVMUtils.getClasspathURLs.foreach(url => {
+          settings.bootclasspath.append(url.getPath)
+          settings.classpath.append(url.getPath)
+      })
 
       val reporter = new QScriptManager.Log4JReporter(settings)
 

public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala

@@ -77,21 +77,6 @@ object StringFileConversions {
     })
   }
 
-  implicit def stringsAsFiles(x: Set[Comparable[_ >: File with String <: Comparable[_ >: File with String <: Comparable[_ >: File with String <: Serializable] with Serializable] with Serializable] with Serializable]): Set[File] = {
-    x.map(_ match {
-      case string: String => stringAsFile(string)
-      case file: File => file
-      case null => null
-    })
-  }
-
-  implicit def filesAsStrings(x: Set[Comparable[_ >: String with File <: Comparable[_ >: String with File <: Comparable[_ >: String with File <: Serializable] with Serializable] with Serializable] with Serializable]): Set[String] = {
-    x.map(_ match {
-      case file: File => fileAsString(file)
-      case string: String => string
-      case null => null
-    })
-  }
 }
 
 /**
@@ -124,11 +109,4 @@ trait StringFileConversions {
     StringFileConversions.filesAsStringsList(x)
   }
 
-  implicit def stringsAsFiles(x: Set[Comparable[_ >: File with String <: Comparable[_ >: File with String <: Comparable[_ >: File with String <: Serializable] with Serializable] with Serializable] with Serializable]): Set[File] = {
-    StringFileConversions.stringsAsFiles(x)
-  }
-
-  implicit def filesAsStrings(x: Set[Comparable[_ >: String with File <: Comparable[_ >: String with File <: Comparable[_ >: String with File <: Serializable] with Serializable] with Serializable] with Serializable]): Set[String] = {
-    StringFileConversions.filesAsStrings(x)
-  }
 }

public/scala/test/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala

@@ -87,44 +87,6 @@ class StringFileConversionsUnitTest {
     Assert.assertEquals(strings, Seq(null, null))
   }
 
-  @Test
-  def testStringToFileSet() {
-    var files = Set(new File("foo"))
-    files += "bar"
-    Assert.assertEquals(files, Set(new File("foo"), new File("bar")))
-
-    files = Set(new File("foo"))
-    files += null.asInstanceOf[String]
-    Assert.assertEquals(files, Set(new File("foo"), null))
-
-    files = Set[File](null)
-    files += "foo"
-    Assert.assertEquals(files, Set(new File("foo"), null))
-
-    files = Set[File](null)
-    files += null.asInstanceOf[String]
-    Assert.assertEquals(files, Set(null))
-  }
-
-  @Test
-  def testFileToStringSet() {
-    var strings = Set("foo")
-    strings += new File("bar")
-    Assert.assertEquals(strings, Set("foo", "bar"))
-
-    strings = Set("foo")
-    strings += null.asInstanceOf[File]
-    Assert.assertEquals(strings, Set("foo", null))
-
-    strings = Set[String](null)
-    strings += new File("foo")
-    Assert.assertEquals(strings, Set("foo", null))
-
-    strings = Set[String](null)
-    strings += null.asInstanceOf[File]
-    Assert.assertEquals(strings, Set(null))
-  }
-
   @Test
   def testStringListToFileList() {
     var files = Seq(new File("foo"))
@@ -163,41 +125,4 @@ class StringFileConversionsUnitTest {
     Assert.assertEquals(strings, Seq(null, null))
   }
 
-  @Test
-  def testStringSetToFileSet() {
-    var files = Set(new File("foo"))
-    files ++= Set("bar")
-    Assert.assertEquals(files, Set(new File("foo"), new File("bar")))
-
-    files = Set(new File("foo"))
-    files ++= Set[String](null)
-    Assert.assertEquals(files, Set(new File("foo"), null))
-
-    files = Set[File](null)
-    files ++= Set("foo")
-    Assert.assertEquals(files, Set(new File("foo"), null))
-
-    files = Set[File](null)
-    files ++= Set[String](null)
-    Assert.assertEquals(files, Set(null))
-  }
-
-  @Test
-  def testFileSetToStringSet() {
-    var strings = Set("foo")
-    strings ++= Set(new File("bar"))
-    Assert.assertEquals(strings, Set("foo", "bar"))
-
-    strings = Set("foo")
-    strings ++= Set[File](null)
-    Assert.assertEquals(strings, Set("foo", null))
-
-    strings = Set[String](null)
-    strings ++= Set(new File("foo"))
-    Assert.assertEquals(strings, Set("foo", null))
-
-    strings = Set[String](null)
-    strings ++= Set[File](null)
-    Assert.assertEquals(strings, Set(null))
-  }
 }