diff --git a/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBat.java b/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBat.java
index 1beb8fb86..98d8792c6 100644
--- a/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBat.java
+++ b/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBat.java
@@ -6409,7 +6409,28 @@ public class LibBat {
         /**
          * < Detail reservation information for each kind of resource
          */
-        public reserveItem.ByReference items;
+        /*
+          TODO: Go against the JNA recommendations at
+          http://jna.java.net/#structure_use and instead change each structure
+          to use Pointers instead of Structure.ByReference while also providing
+          Structure(Pointer) constructors for use for future API users.
+
+          LSF will often reuse memory for structure arrays but will set the
+          array size / count (reserveCnt above) to zero when the array should
+          not be accessed. When LSF has reused memory and points to a non-null
+          structure pointer (items) the inner structure may contain further
+          garbage pointers (especially items->resName).
+
+          When JNA sees a non-null Structure.ByReference it will autoRead() the
+          member. When autoRead() eventually gets to the items->resName trying
+          to run strlen on the bad memory address causes a SIGSEGV.
+
+          By using a Pointer instead of the Structure.ByReference JNA will not
+          automatically autoRead(), and the API user will have to pass the
+          pointer to the Structure on their own.
+        */
+        //public reserveItem.ByReference items;
+        public Pointer items;
 
         /**
          * < Absolute priority scheduling (APS) string set by administrators to denote ADMIN factor APS value.
diff --git a/scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobRunner.scala b/scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobRunner.scala
index 863da1d4f..553116ce0 100755
--- a/scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobRunner.scala
+++ b/scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobRunner.scala
@@ -15,15 +15,6 @@ trait CommandLineJobRunner extends JobRunner[CommandLineFunction] with Logging {
   /** Which directory to use for the job status files. */
   protected def jobStatusDir = function.jobTempDir
 
-  /** The last time the status returned unknown. */
-  protected var firstUnknownTime: Option[Long] = None
-
-  /** Amount of time the status can return unknown before giving up. */
-  protected val unknownStatusMaxSeconds = 5 * 60
-
-  /** Number of seconds for a non-normal exit status before we give up on expecting LSF to retry the function. */
-  protected val retryExpiredSeconds = 5 * 60
-
   /**
    * Writes the function command line to an exec file.
    */
diff --git a/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala b/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala
index 0a165f10e..53a555aa6 100644
--- a/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala
+++ b/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala
@@ -18,6 +18,11 @@ class FunctionEdge(val function: QFunction, val inputs: QNode, val outputs: QNod
    */
   var retries = 0
 
+  /**
+   * The depth of this edge in the graph.
+   */
+  var depth = -1
+
   /**
    * Initializes with the current status of the function.
    */
diff --git a/scala/src/org/broadinstitute/sting/queue/engine/JobManager.scala b/scala/src/org/broadinstitute/sting/queue/engine/JobManager.scala
index a55e7822b..b8a4dd5a7 100644
--- a/scala/src/org/broadinstitute/sting/queue/engine/JobManager.scala
+++ b/scala/src/org/broadinstitute/sting/queue/engine/JobManager.scala
@@ -17,9 +17,16 @@ trait JobManager[TFunction <: QFunction, TRunner <: JobRunner[TFunction]] {
    */
   def create(function: TFunction): TRunner
 
+  /**
+   * Updates the status on a list of functions.
+   * @param runners Runners to update.
+   */
+  def updateStatus(runners: List[TRunner]) {
+  }
+
   /**
    * Stops a list of functions.
-   * @param runner Runners to stop.
+   * @param runners Runners to stop.
    */
   def tryStop(runners: List[TRunner]) {
   }
diff --git a/scala/src/org/broadinstitute/sting/queue/engine/Lsf706JobManager.scala b/scala/src/org/broadinstitute/sting/queue/engine/Lsf706JobManager.scala
index de85b66b2..b0809ddd2 100644
--- a/scala/src/org/broadinstitute/sting/queue/engine/Lsf706JobManager.scala
+++ b/scala/src/org/broadinstitute/sting/queue/engine/Lsf706JobManager.scala
@@ -9,5 +9,7 @@ class Lsf706JobManager extends JobManager[CommandLineFunction, Lsf706JobRunner]
   def runnerType = classOf[Lsf706JobRunner]
   def functionType = classOf[CommandLineFunction]
   def create(function: CommandLineFunction) = new Lsf706JobRunner(function)
+
+  override def updateStatus(runners: List[Lsf706JobRunner]) { Lsf706JobRunner.updateStatus(runners) }
   override def tryStop(runners: List[Lsf706JobRunner]) { Lsf706JobRunner.tryStop(runners) }
 }
diff --git a/scala/src/org/broadinstitute/sting/queue/engine/Lsf706JobRunner.scala b/scala/src/org/broadinstitute/sting/queue/engine/Lsf706JobRunner.scala
index 08540fbd3..d4bead82d 100644
--- a/scala/src/org/broadinstitute/sting/queue/engine/Lsf706JobRunner.scala
+++ b/scala/src/org/broadinstitute/sting/queue/engine/Lsf706JobRunner.scala
@@ -7,7 +7,6 @@ import org.broadinstitute.sting.queue.QException
 import org.broadinstitute.sting.jna.lsf.v7_0_6.{LibLsf, LibBat}
 import org.broadinstitute.sting.utils.Utils
 import org.broadinstitute.sting.jna.clibrary.LibC
-import java.util.Date
 import org.broadinstitute.sting.jna.lsf.v7_0_6.LibBat.{submitReply, submit}
 import com.sun.jna.ptr.IntByReference
 import com.sun.jna.{StringArray, NativeLong}
@@ -21,10 +20,13 @@ class Lsf706JobRunner(val function: CommandLineFunction) extends CommandLineJobR
   Lsf706JobRunner
 
   /** Job Id of the currently executing job. */
-  var jobId = -1L
+  private var jobId = -1L
 
-  /** Last known run status */
-  private var runStatus: RunnerStatus.Value = _
+  /** Last known status */
+  private var lastStatus: RunnerStatus.Value = _
+
+  /** The last time the status was updated */
+  protected var lastStatusUpdate: Long = _
 
   /**
    * Dispatches the function on the LSF cluster.
@@ -82,7 +84,7 @@ class Lsf706JobRunner(val function: CommandLineFunction) extends CommandLineJobR
       // Allow advanced users to update the request.
       updateJobRun(request)
 
-      runStatus = RunnerStatus.RUNNING
+      updateStatus(RunnerStatus.RUNNING)
       Retry.attempt(() => {
         val reply = new submitReply
         jobId = LibBat.lsb_submit(request, reply)
@@ -93,93 +95,24 @@ class Lsf706JobRunner(val function: CommandLineFunction) extends CommandLineJobR
     }
   }
 
-  /**
-   * Updates and returns the status.
-   */
-  def status = {
-    Lsf706JobRunner.lsfLibLock.synchronized {
-      var jobStatus = LibBat.JOB_STAT_UNKWN
-      var exitStatus = 0
-      var exitInfo = 0
-      var endTime: NativeLong = null
+  def status = this.lastStatus
 
-      var result = 0
-      Retry.attempt(() => {
-        result = LibBat.lsb_openjobinfo(jobId, null, null, null, null, LibBat.ALL_JOB)
-        if (result < 0)
-          throw new QException(LibBat.lsb_sperror("Unable to open LSF job info for job id: " + jobId))
-      }, 0.5, 1, 2)
-      try {
-        if (result > 1)
-          throw new QException(LibBat.lsb_sperror("Recieved " + result + " LSF results for job id: " + jobId))
-        else if (result == 1) {
-          val more = new IntByReference(result)
-          val jobInfo = LibBat.lsb_readjobinfo(more)
-          if (jobInfo == null)
-            throw new QException(LibBat.lsb_sperror("lsb_readjobinfo returned null for job id: " + jobId))
-          jobStatus = jobInfo.status
-          exitStatus = jobInfo.exitStatus
-          exitInfo = jobInfo.exitInfo
-          endTime = jobInfo.endTime
-        }
-      } finally {
-        LibBat.lsb_closejobinfo()
-      }
-
-      logger.debug("Job Id %s status / exitStatus / exitInfo: 0x%02x / 0x%02x / 0x%02x".format(jobId, jobStatus, exitStatus, exitInfo))
-
-      if (Utils.isFlagSet(jobStatus, LibBat.JOB_STAT_UNKWN)) {
-        val now = new Date().getTime
-
-        if (firstUnknownTime.isEmpty) {
-          firstUnknownTime = Some(now)
-          logger.debug("First unknown status for job id: " + jobId)
-        }
-
-        if ((firstUnknownTime.get - now) >= (unknownStatusMaxSeconds * 1000L)) {
-          // Unknown status has been returned for a while now.
-          runStatus = RunnerStatus.FAILED
-          logger.error("Unknown status for %d seconds: job id %d: %s".format(unknownStatusMaxSeconds, jobId, function.description))
-        }
-      } else {
-        // Reset the last time an unknown status was seen.
-        firstUnknownTime = None
-
-        if (Utils.isFlagSet(jobStatus, LibBat.JOB_STAT_EXIT) && !willRetry(exitInfo, endTime)) {
-          // Exited function that (probably) won't be retried.
-          runStatus = RunnerStatus.FAILED
-        } else if (Utils.isFlagSet(jobStatus, LibBat.JOB_STAT_DONE)) {
-          // Done successfully.
-          runStatus = RunnerStatus.DONE
-        }
-      }
-
-      runStatus
-    }
+  private def updateStatus(updatedStatus: RunnerStatus.Value) = {
+    this.lastStatus = updatedStatus
+    this.lastStatusUpdate = System.currentTimeMillis
   }
-
-  /**
-   * Returns true if LSF is expected to retry running the function.
-   * @param exitInfo The reason the job exited.
-   * @param endTime THe time the job exited.
-   * @return true if LSF is expected to retry running the function.
-   */
-  private def willRetry(exitInfo: Int, endTime: NativeLong) = {
-    exitInfo match {
-      case LibBat.EXIT_NORMAL => false
-      case _ => {
-        val seconds = LibC.difftime(LibC.time(null), endTime)
-        (seconds <= retryExpiredSeconds)
-      }
-    }
-  }
-
 }
 
 object Lsf706JobRunner extends Logging {
   private val lsfLibLock = new Object
   private val SIGTERM = 15
 
+  /** Number of seconds for a non-normal exit status before we give up on expecting LSF to retry the function. */
+  private val retryExpiredSeconds = 5 * 60
+
+  /** Amount of time a job can go without status before giving up. */
+  private val unknownStatusMaxSeconds = 5 * 60
+
   init()
 
   /** The name of the default queue. */
@@ -238,6 +171,44 @@ object Lsf706JobRunner extends Logging {
     }
   }
 
+  /**
+   * Updates the status of a list of jobs.
+   */
+  def updateStatus(runners: List[Lsf706JobRunner]) {
+    var updatedRunners = List.empty[Lsf706JobRunner]
+
+    Lsf706JobRunner.lsfLibLock.synchronized {
+      val result = LibBat.lsb_openjobinfo(0L, null, null, null, null, LibBat.ALL_JOB)
+      if (result < 0) {
+        logger.error(LibBat.lsb_sperror("Unable to check LSF job info"))
+      } else {
+        try {
+          val more = new IntByReference(result)
+          while (more.getValue > 0) {
+            val jobInfo = LibBat.lsb_readjobinfo(more)
+            if (jobInfo == null) {
+              logger.error(LibBat.lsb_sperror("Unable to read LSF job info"))
+              more.setValue(0)
+            } else {
+              runners.find(runner => runner.jobId == jobInfo.jobId) match {
+                case Some(runner) =>
+                  updateRunnerStatus(runner, jobInfo)
+                  updatedRunners :+= runner
+                case None => /* not our job */
+              }
+            }
+          }
+        } finally {
+          LibBat.lsb_closejobinfo()
+        }
+      }
+    }
+
+    for (runner <- runners.diff(updatedRunners)) {
+      checkUnknownStatus(runner)
+    }
+  }
+
   /**
    * Tries to stop any running jobs.
    * @param runners Runners to stop.
@@ -246,15 +217,67 @@ object Lsf706JobRunner extends Logging {
     lsfLibLock.synchronized {
       // lsb_killbulkjobs does not seem to forward SIGTERM,
       // only SIGKILL, so send the Ctrl-C (SIGTERM) one by one.
-      for (jobRunner <- runners.filterNot(_.jobId < 0)) {
+      for (runner <- runners.filterNot(_.jobId < 0)) {
         try {
-          if (LibBat.lsb_signaljob(jobRunner.jobId, SIGTERM) < 0)
-            logger.error(LibBat.lsb_sperror("Unable to kill job " + jobRunner.jobId))
+          if (LibBat.lsb_signaljob(runner.jobId, SIGTERM) < 0)
+            logger.error(LibBat.lsb_sperror("Unable to kill job " + runner.jobId))
         } catch {
           case e =>
-            logger.error("Unable to kill job " + jobRunner.jobId, e)
+            logger.error("Unable to kill job " + runner.jobId, e)
         }
       }
     }
   }
+
+  private def updateRunnerStatus(runner: Lsf706JobRunner, jobInfo: LibBat.jobInfoEnt) {
+    val jobStatus = jobInfo.status
+    val exitStatus = jobInfo.exitStatus
+    val exitInfo = jobInfo.exitInfo
+    val endTime = jobInfo.endTime
+
+    logger.debug("Job Id %s status / exitStatus / exitInfo: 0x%02x / 0x%02x / 0x%02x".format(runner.jobId, jobStatus, exitStatus, exitInfo))
+
+    runner.updateStatus(
+      if (Utils.isFlagSet(jobStatus, LibBat.JOB_STAT_DONE)) {
+        // Done successfully.
+        RunnerStatus.DONE
+      } else if (Utils.isFlagSet(jobStatus, LibBat.JOB_STAT_EXIT) && !willRetry(exitInfo, endTime)) {
+        // Exited function that (probably) won't be retried.
+        RunnerStatus.FAILED
+      } else {
+        // Note that we still saw the job in the system.
+        RunnerStatus.RUNNING
+      }
+    )
+  }
+
+  private def checkUnknownStatus(runner: Lsf706JobRunner) {
+    // TODO: Need a second pass through either of the two archive logs using lsb_geteventrecbyline() for disappeared jobs.
+    // Can also tell if we wake up and the last time we saw status was greater than lsb_parameterinfo().cleanPeriod
+    // LSB_SHAREDIR/cluster_name/logdir/lsb.acct (man bacct)
+    // LSB_SHAREDIR/cluster_name/logdir/lsb.events (man bhist)
+    logger.debug("Job Id %s status / exitStatus / exitInfo: ??? / ??? / ???".format(runner.jobId))
+    val unknownStatusSeconds = (System.currentTimeMillis - runner.lastStatusUpdate)
+    if (unknownStatusSeconds > (unknownStatusMaxSeconds * 1000L)) {
+      // Unknown status has been returned for a while now.
+      runner.updateStatus(RunnerStatus.FAILED)
+      logger.error("Unable to read LSF status for %d minutes: job id %d: %s".format(unknownStatusSeconds/60, runner.jobId, runner.function.description))
+    }
+  }
+
+  /**
+   * Returns true if LSF is expected to retry running the function.
+   * @param exitInfo The reason the job exited.
+   * @param endTime THe time the job exited.
+   * @return true if LSF is expected to retry running the function.
+   */
+  private def willRetry(exitInfo: Int, endTime: NativeLong) = {
+    exitInfo match {
+      case LibBat.EXIT_NORMAL => false
+      case _ => {
+        val seconds = LibC.difftime(LibC.time(null), endTime)
+        (seconds <= retryExpiredSeconds)
+      }
+    }
+  }
 }
diff --git a/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala b/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
index ed71b586c..51df7267d 100755
--- a/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
+++ b/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
@@ -13,7 +13,7 @@ import org.broadinstitute.sting.queue.function.{InProcessFunction, CommandLineFu
 import org.broadinstitute.sting.queue.function.scattergather.{CloneFunction, GatherFunction, ScatterGatherableFunction}
 import org.apache.commons.lang.StringUtils
 import org.broadinstitute.sting.queue.util._
-import collection.immutable.TreeMap
+import collection.immutable.{TreeSet, TreeMap}
 
 /**
  * The internal dependency tracker between sets of function input and output files.
@@ -26,18 +26,24 @@ class QGraph extends Logging {
   private var numMissingValues = 0
 
   private val jobGraph = newGraph
+  private val functionOrdering = Ordering.by[FunctionEdge, Iterable[Int]](edge => -graphDepth(edge) +: edge.function.addOrder)
+  private val fileOrdering = Ordering.by[File,String](_.getAbsolutePath)
   // A map of nodes by list of files.
-  private var nodeMap = TreeMap.empty[Iterable[File], QNode](Ordering.Iterable(Ordering.by[File,String](_.getAbsolutePath)))
+  private var nodeMap = TreeMap.empty[Iterable[File], QNode](Ordering.Iterable(fileOrdering))
   // The next unique id for a node if not found in the nodeMap.
   private var nextNodeId = 0
 
   private var running = true
   private val runningLock = new Object
+  private var runningJobs = Set.empty[FunctionEdge]
+
   private val nl = "%n".format()
 
   private val inProcessManager = new InProcessJobManager
   private var commandLineManager: JobManager[CommandLineFunction, _<:JobRunner[CommandLineFunction]] = _
 
+  private def managers = List[Any](inProcessManager, commandLineManager)
+
   /**
    * Adds a QScript created CommandLineFunction to the graph.
    * @param command Function to add to the graph.
@@ -48,8 +54,8 @@ class QGraph extends Logging {
         if (running) {
           command.qSettings = settings.qSettings
           command.freeze
-          val inputs = getQNode(command.inputs.toList.sortWith(_.compareTo(_) < 0))
-          val outputs = getQNode(command.outputs.toList.sortWith(_.compareTo(_) < 0))
+          val inputs = getQNode(command.inputs.toList.sorted(fileOrdering))
+          val outputs = getQNode(command.outputs.toList.sorted(fileOrdering))
           addEdge(new FunctionEdge(command, inputs, outputs))
         }
       }
@@ -143,19 +149,17 @@ class QGraph extends Logging {
   }
 
   /**
-   * Walks up the graph looking for the previous command line edges.
-   * @param function Function to examine for a previous command line job.
-   * @param qGraph The graph that contains the jobs.
-   * @return A list of prior jobs.
+   * Walks up the graph looking for the previous function edges.
+   * @param edge Graph edge to examine for the previous functions.
+   * @return A list of prior function edges.
    */
   private def previousFunctions(edge: QEdge): List[FunctionEdge] = {
     var previous = List.empty[FunctionEdge]
-
     val source = this.jobGraph.getEdgeSource(edge)
     for (incomingEdge <- this.jobGraph.incomingEdgesOf(source)) {
       incomingEdge match {
 
-        // Stop recursing when we find a job along the edge and return its job id
+        // Stop recursing when we find a function edge and return it
         case functionEdge: FunctionEdge => previous :+= functionEdge
 
         // For any other type of edge find the jobs preceding the edge
@@ -190,19 +194,12 @@ class QGraph extends Logging {
     })
   }
 
-  private def getReadyJobs = {
+  private def getReadyJobs(): Set[FunctionEdge] = {
     jobGraph.edgeSet.filter{
       case f: FunctionEdge =>
         this.previousFunctions(f).forall(_.status == RunnerStatus.DONE) && f.status == RunnerStatus.PENDING
       case _ => false
-    }.toList.asInstanceOf[List[FunctionEdge]].sortWith(compare(_,_))
-  }
-
-  private def getRunningJobs = {
-    jobGraph.edgeSet.filter{
-      case f: FunctionEdge => f.status == RunnerStatus.RUNNING
-      case _ => false
-    }.toList.asInstanceOf[List[FunctionEdge]].sortWith(compare(_,_))
+    }.toSet.asInstanceOf[Set[FunctionEdge]]
   }
 
   /**
@@ -260,8 +257,13 @@ class QGraph extends Logging {
    * Dry-runs the jobs by traversing the graph.
    */
   private def dryRunJobs() {
-    updateGraphStatus(false)
-    var readyJobs = getReadyJobs
+    if (settings.startFromScratch) {
+      logger.info("Will remove outputs from previous runs.")
+      foreachFunction(_.resetToPending(false))
+    } else
+      updateGraphStatus(false)
+
+    var readyJobs = getReadyJobs()
     while (running && readyJobs.size > 0) {
       logger.debug("+++++++")
       readyJobs.foreach(edge => {
@@ -270,7 +272,7 @@ class QGraph extends Logging {
           edge.markAsDone
         }
       })
-      readyJobs = getReadyJobs
+      readyJobs = getReadyJobs()
     }
   }
 
@@ -311,39 +313,45 @@ class QGraph extends Logging {
       } else
         updateGraphStatus(true)
 
-      var readyJobs = getReadyJobs
-      var runningJobs = Set.empty[FunctionEdge]
+      var readyJobs = TreeSet.empty[FunctionEdge](functionOrdering)
+      readyJobs ++= getReadyJobs()
+      runningJobs = Set.empty[FunctionEdge]
+      var lastRunningCheck = System.currentTimeMillis
+
       while (running && readyJobs.size + runningJobs.size > 0) {
-        var exitedJobs = List.empty[FunctionEdge]
+
+        while (running && readyJobs.size > 0 && nextRunningCheck(lastRunningCheck) > 0) {
+          val edge = readyJobs.head
+          edge.runner = newRunner(edge.function)
+          edge.start()
+          runningJobs += edge
+          readyJobs -= edge
+        }
+
+        if (readyJobs.size == 0 && runningJobs.size > 0)
+          Thread.sleep(nextRunningCheck(lastRunningCheck))
+
+        lastRunningCheck = System.currentTimeMillis
+        updateStatus()
+
+        var doneJobs = List.empty[FunctionEdge]
         var failedJobs = List.empty[FunctionEdge]
 
-        runningJobs.foreach(runner => runner.status match {
+        runningJobs.foreach(edge => edge.status match {
+          case RunnerStatus.DONE => doneJobs :+= edge
+          case RunnerStatus.FAILED => failedJobs :+= edge
           case RunnerStatus.RUNNING => /* do nothing while still running */
-          case RunnerStatus.FAILED => exitedJobs :+= runner; failedJobs :+= runner
-          case RunnerStatus.DONE => exitedJobs :+= runner
-        })
-        exitedJobs.foreach(runner => runningJobs -= runner)
-
-        readyJobs.foreach(f => {
-          if (running) {
-            f.runner = newRunner(f.function)
-            f.start()
-            f.status match {
-              case RunnerStatus.RUNNING => runningJobs += f
-              case RunnerStatus.FAILED => failedJobs :+= f
-              case RunnerStatus.DONE => /* do nothing and move on */
-            }
-          }
         })
 
-        if (failedJobs.size > 0) {
+        runningJobs --= doneJobs
+        runningJobs --= failedJobs
+
+        if (running && failedJobs.size > 0) {
           emailFailedJobs(failedJobs)
           checkRetryJobs(failedJobs)
         }
 
-        if (readyJobs.size == 0 && runningJobs.size > 0)
-          Thread.sleep(30000L)
-        readyJobs = getReadyJobs
+        readyJobs ++= getReadyJobs()
       }
 
       deleteIntermediateOutputs()
@@ -356,6 +364,8 @@ class QGraph extends Logging {
     }
   }
 
+  private def nextRunningCheck(lastRunningCheck: Long) = 0L max ((30 * 1000L) - (System.currentTimeMillis - lastRunningCheck))
+
   /**
    * Updates the status of edges in the graph.
    * @param cleanOutputs If true will delete outputs when setting edges to pending.
@@ -388,6 +398,22 @@ class QGraph extends Logging {
     }
   }
 
+  /**
+   * Returns the graph depth for the function.
+   * @param edge Function edge to get the edge for.
+   * @return the graph depth for the function.
+   */
+  private def graphDepth(edge: FunctionEdge): Int = {
+    if (edge.depth < 0) {
+      val previous = previousFunctions(edge)
+      if (previous.size == 0)
+        edge.depth = 0
+      else
+        edge.depth = previous.map(f => graphDepth(f)).max + 1
+    }
+    edge.depth
+  }
+
   /**
    * From the previous edges, resets any that are marked as skipped to pending.
    * If those that are reset have skipped edges, those skipped edges are recursively also set
@@ -415,7 +441,7 @@ class QGraph extends Logging {
   }
 
   private def emailFailedJobs(failed: List[FunctionEdge]) {
-    if (running && settings.statusEmailTo.size > 0) {
+    if (settings.statusEmailTo.size > 0) {
       val emailMessage = new EmailMessage
       emailMessage.from = settings.statusEmailFrom
       emailMessage.to = settings.statusEmailTo
@@ -700,32 +726,10 @@ class QGraph extends Logging {
     jobGraph.edgeSet.toList
       .filter(_.isInstanceOf[FunctionEdge])
       .asInstanceOf[List[FunctionEdge]]
-      .sortWith(compare(_,_))
+      .sorted(functionOrdering)
       .foreach(edge => if (running) f(edge))
   }
 
-  private def compare(f1: FunctionEdge, f2: FunctionEdge): Boolean =
-    compare(f1.function, f2.function)
-
-  private def compare(f1: QFunction, f2: QFunction): Boolean = {
-    val len1 = f1.addOrder.size
-    val len2 = f2.addOrder.size
-    val len = len1 min len2
-    
-    for (i <- 0 until len) {
-      val order1 = f1.addOrder(i)
-      val order2 = f2.addOrder(i)
-      if (order1 < order2)
-        return true
-      if (order1 > order2)
-        return false
-    }
-    if (len1 < len2)
-      return true
-    else
-      return false
-  }
-
   /**
    * Utility function for running a method over all functions, but traversing the nodes in order of dependency.
    * @param edgeFunction Function to run for each FunctionEdge.
@@ -800,6 +804,25 @@ class QGraph extends Logging {
     })
   }
 
+
+  private def updateStatus() {
+    val runners = runningJobs.map(_.runner)
+    for (mgr <- managers) {
+      if (mgr != null) {
+        val manager = mgr.asInstanceOf[JobManager[QFunction,JobRunner[QFunction]]]
+        val managerRunners = runners
+          .filter(runner => manager.runnerType.isAssignableFrom(runner.getClass))
+          .asInstanceOf[Set[JobRunner[QFunction]]]
+        if (managerRunners.size > 0)
+          try {
+            manager.updateStatus(managerRunners.toList)
+          } catch {
+            case e => /* ignore */
+          }
+      }
+    }
+  }
+
   /**
    * Returns true if the graph was shutdown instead of exiting on its own.
    */
@@ -813,26 +836,29 @@ class QGraph extends Logging {
     running = false
     // Wait for the thread to finish and exit normally.
     runningLock.synchronized {
-      val runners = getRunningJobs.map(_.runner)
-      val manager = commandLineManager.asInstanceOf[JobManager[QFunction,JobRunner[QFunction]]]
-      if (manager != null) {
-        val managerRunners = runners
-          .filter(runner => manager.runnerType.isAssignableFrom(runner.getClass))
-          .asInstanceOf[List[JobRunner[QFunction]]]
-        if (managerRunners.size > 0)
-          try {
-            manager.tryStop(managerRunners)
-          } catch {
-            case e => /* ignore */
+      val runners = runningJobs.map(_.runner)
+      runningJobs = Set.empty[FunctionEdge]
+      for (mgr <- managers) {
+        if (mgr != null) {
+          val manager = mgr.asInstanceOf[JobManager[QFunction,JobRunner[QFunction]]]
+          val managerRunners = runners
+            .filter(runner => manager.runnerType.isAssignableFrom(runner.getClass))
+            .asInstanceOf[Set[JobRunner[QFunction]]]
+          if (managerRunners.size > 0)
+            try {
+              manager.tryStop(managerRunners.toList)
+            } catch {
+              case e => /* ignore */
+            }
+          for (runner <- managerRunners) {
+            try {
+              runner.removeTemporaryFiles()
+            } catch {
+              case e => /* ignore */
+            }
           }
-      }
-      runners.foreach(runner =>
-        try {
-          runner.removeTemporaryFiles()
-        } catch {
-          case e => /* ignore */
         }
-      )
+      }
     }
   }
 }
diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala
index d880fa524..f1fd4057b 100755
--- a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala
@@ -35,12 +35,8 @@ class ContigScatterFunction extends GATKScatterFunction with InProcessFunction {
   // Include unmapped reads by default.
   this.includeUnmapped = true
 
-  protected override def maxIntervals = {
-    if (this.intervalFilesExist)
-      IntervalUtils.countIntervalArguments(this.referenceSequence, this.intervals, true)
-    else
-      this.scatterCount
-  }
+  protected override def maxIntervals =
+    IntervalUtils.countIntervalArguments(this.referenceSequence, this.intervals, true)
 
   def run() {
     IntervalUtils.scatterIntervalArguments(this.referenceSequence, this.intervals, this.scatterOutputFiles, true)
diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/DistributedScatterFunction.scala b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/DistributedScatterFunction.scala
index 953fe0830..1cef4959d 100644
--- a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/DistributedScatterFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/DistributedScatterFunction.scala
@@ -25,23 +25,24 @@
 package org.broadinstitute.sting.queue.extensions.gatk
 
 import java.io.File
-import org.broadinstitute.sting.queue.function.scattergather.CloneFunction
 import org.broadinstitute.sting.queue.function.InProcessFunction
+import org.broadinstitute.sting.queue.function.scattergather.{ScatterFunction, CloneFunction}
+import org.broadinstitute.sting.commandline.Output
+import util.Random
 
 /**
  * An scatter function that uses the Distributed GATK.
  */
-class DistributedScatterFunction extends GATKScatterFunction with InProcessFunction {
-  private final val processingTracker = "processingTracker"
+class DistributedScatterFunction extends ScatterFunction with InProcessFunction {
+  @Output(doc="processingTracker")
+  var processingTracker: File = _
 
-  this.scatterOutputFiles = List(new File(processingTracker))
-
-  override def initCloneInputs(cloneFunction: CloneFunction, index: Int) {
-    cloneFunction.setFieldValue("processingTracker", new File(this.commandDirectory, this.processingTracker))
+  override def init() {
+    this.processingTracker = new File(this.commandDirectory, "processingTracker.%8d".format(Random.nextInt(100000000)))
   }
 
-  override def bindCloneInputs(cloneFunction: CloneFunction, index: Int) {
-    /* no further work needed after init. */
+  override def initCloneInputs(cloneFunction: CloneFunction, index: Int) {
+    cloneFunction.setFieldValue("processingTracker", this.processingTracker)
   }
 
   def run() {
diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala
index 4abac23d3..f753cd341 100644
--- a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala
@@ -28,64 +28,53 @@ import org.broadinstitute.sting.utils.interval.IntervalUtils
 import java.io.File
 import collection.JavaConversions._
 import org.broadinstitute.sting.queue.util.IOUtils
-import org.broadinstitute.sting.queue.function.scattergather.{CloneFunction, ScatterGatherableFunction, ScatterFunction}
+import org.broadinstitute.sting.queue.function.scattergather.{CloneFunction, ScatterFunction}
 import org.broadinstitute.sting.commandline.Output
 
 trait GATKScatterFunction extends ScatterFunction {
-  /** The total number of clone jobs that will be created. */
-  var scatterCount: Int = _
-
-  /** The reference sequence for the GATK function. */
-  protected var referenceSequence: File = _
-
   /** The runtime field to set for specifying an interval file. */
   private final val intervalsField = "intervals"
 
   /** The runtime field to set for specifying an interval string. */
   private final val intervalsStringField = "intervalsString"
 
+  @Output(doc="Scatter function outputs")
+  var scatterOutputFiles: List[File] = Nil
+
+  /** The original GATK function. */
+  protected var originalGATK: CommandLineGATK = _
+
+  /** The reference sequence for the GATK function. */
+  protected var referenceSequence: File = _
+
   /** The list of interval files ("/path/to/interval.list") or interval strings ("chr1", "chr2") to parse into smaller parts. */
   protected var intervals: List[String] = Nil
 
   /** Whether the last scatter job should also include any unmapped reads. */
   protected var includeUnmapped: Boolean = _
 
-  @Output(doc="Scatter function outputs")
-  var scatterOutputFiles: List[File] = Nil
+  /** The total number of clone jobs that will be created. */
+  override def scatterCount = if (intervalFilesExist) super.scatterCount min this.maxIntervals else super.scatterCount
 
-  /**
-   * Checks if the function is scatter gatherable.
-   * @param originalFunction Function to check.
-   * @return true if the function is a GATK function with the reference sequence set.
-   * @throws IllegalArgumentException if -BTI or -BTIMR are set.  QScripts should not try to scatter gather with those option set.
-   */
-  override def isScatterGatherable(originalFunction: ScatterGatherableFunction): Boolean = {
-    val gatk = originalFunction.asInstanceOf[CommandLineGATK]
-    if (gatk.BTI != null && gatk.BTIMR == null)
-      throw new IllegalArgumentException("BTI requires BTIMR for use with scatter-gather (recommended: INTERSECTION)")
-    gatk.reference_sequence != null
-  }
-
-  /**
-   * Sets the scatter gatherable function.
-   * @param originalFunction Function to bind.
-   */
-  override def setScatterGatherable(originalFunction: ScatterGatherableFunction) = {
-    val gatk = originalFunction.asInstanceOf[CommandLineGATK]
-    this.referenceSequence = gatk.reference_sequence
-    if (gatk.intervals.isEmpty && gatk.intervalsString.isEmpty) {
+  override def init() {
+    this.originalGATK = this.originalFunction.asInstanceOf[CommandLineGATK]
+    this.referenceSequence = this.originalGATK.reference_sequence
+    if (this.originalGATK.intervals.isEmpty && this.originalGATK.intervalsString.isEmpty) {
       this.intervals ++= IntervalUtils.distinctContigs(this.referenceSequence).toList
     } else {
-      this.intervals ++= gatk.intervals.map(_.toString)
-      this.intervals ++= gatk.intervalsString.filterNot(interval => IntervalUtils.isUnmapped(interval))
-      this.includeUnmapped = gatk.intervalsString.exists(interval => IntervalUtils.isUnmapped(interval))
+      this.intervals ++= this.originalGATK.intervals.map(_.toString)
+      this.intervals ++= this.originalGATK.intervalsString.filterNot(interval => IntervalUtils.isUnmapped(interval))
+      this.includeUnmapped = this.originalGATK.intervalsString.exists(interval => IntervalUtils.isUnmapped(interval))
     }
-
-    this.scatterCount = originalFunction.scatterCount
-    this.scatterCount = this.scatterCount min this.maxIntervals
   }
 
-  def initCloneInputs(cloneFunction: CloneFunction, index: Int) = {
+  override def isScatterGatherable = {
+    if (this.originalGATK.BTI != null && this.originalGATK.BTIMR.isEmpty)
+      throw new IllegalArgumentException("BTI requires BTIMR for use with scatter-gather (recommended: INTERSECTION)")
+    this.originalGATK.reference_sequence != null
+  }
+
+  override def initCloneInputs(cloneFunction: CloneFunction, index: Int) {
     cloneFunction.setFieldValue(this.intervalsField, List(new File("scatter.intervals")))
     if (index == this.scatterCount && this.includeUnmapped)
       cloneFunction.setFieldValue(this.intervalsStringField, List("unmapped"))
@@ -93,7 +82,7 @@ trait GATKScatterFunction extends ScatterFunction {
       cloneFunction.setFieldValue(this.intervalsStringField, List.empty[String])
   }
 
-  def bindCloneInputs(cloneFunction: CloneFunction, index: Int) = {
+  override def bindCloneInputs(cloneFunction: CloneFunction, index: Int) {
     val scatterPart = cloneFunction.getFieldValue(this.intervalsField)
             .asInstanceOf[List[File]]
             .map(file => IOUtils.absolute(cloneFunction.commandDirectory, file))
@@ -112,5 +101,5 @@ trait GATKScatterFunction extends ScatterFunction {
    * Returns the maximum number of intervals or this.scatterCount if the maximum can't be determined ahead of time.
    * @return the maximum number of intervals or this.scatterCount if the maximum can't be determined ahead of time.
    */
-  protected def maxIntervals = this.scatterCount
+  protected def maxIntervals: Int
 }
diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
index 94d284877..a651b3c12 100644
--- a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
@@ -32,12 +32,8 @@ import org.broadinstitute.sting.queue.function.InProcessFunction
  * An interval scatter function.
  */
 class IntervalScatterFunction extends GATKScatterFunction with InProcessFunction {
-  protected override def maxIntervals = {
-    if (this.intervalFilesExist)
-      IntervalUtils.countIntervalArguments(this.referenceSequence, this.intervals, false)
-    else
-      this.scatterCount
-  }
+  protected override def maxIntervals =
+    IntervalUtils.countIntervalArguments(this.referenceSequence, this.intervals, false)
 
   def run() {
     IntervalUtils.scatterIntervalArguments(this.referenceSequence, this.intervals, this.scatterOutputFiles, false)
diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala
index 95f311505..9ee7b8087 100644
--- a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala
@@ -1,17 +1,37 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.queue.extensions.gatk
 
-import org.broadinstitute.sting.queue.function.scattergather.{ScatterGatherableFunction, GatherFunction}
+import org.broadinstitute.sting.queue.function.scattergather.GatherFunction
 
 /**
  * Merges a vcf text file.
  */
 class VcfGatherFunction extends CombineVariants with GatherFunction {
 
-  private var originalGATK: CommandLineGATK = _
-
-  override def setScatterGatherable(originalFunction: ScatterGatherableFunction) {
-    this.originalGATK = originalFunction.asInstanceOf[CommandLineGATK]
-  }
+  private lazy val originalGATK = this.originalFunction.asInstanceOf[CommandLineGATK]
 
   override def freezeFieldValues = {
     this.memoryLimit = Some(1)
diff --git a/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala
index bb983e6c0..fa627a7de 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala
@@ -1,8 +1,31 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.queue.function.scattergather
 
 import org.broadinstitute.sting.commandline.ArgumentSource
 import java.io.File
-import org.broadinstitute.sting.queue.QException
 import org.broadinstitute.sting.queue.function.{QFunction, CommandLineFunction}
 
 /**
@@ -10,7 +33,7 @@ import org.broadinstitute.sting.queue.function.{QFunction, CommandLineFunction}
  */
 class CloneFunction extends CommandLineFunction {
   var originalFunction: ScatterGatherableFunction = _
-  var index: Int = _
+  var cloneIndex: Int = _
 
   private var overriddenFields = Map.empty[ArgumentSource, Any]
   private var withScatterPartCount = 0
diff --git a/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala
index cd60cbe02..16d31b777 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala
@@ -10,20 +10,21 @@ import org.broadinstitute.sting.queue.util.IOUtils
  * Base class for Gather command line functions.
  */
 trait GatherFunction extends QFunction {
+  var originalFunction: ScatterGatherableFunction = _
+
+  @Output(doc="The original output of the scattered function")
+  var originalOutput: File = _
+
   @Input(doc="Parts to gather back into the original output")
   var gatherParts: List[File] = Nil
 
   @Input(doc="Other log files that will be gathered before this output", required=false)
   var originalLogFiles: List[File] = Nil
 
-  @Output(doc="The original output of the scattered function")
-  var originalOutput: File = _
-
   /**
-   * Sets the original ScatterGatherableFunction to be gathered.
-   * @param originalFunction The original function to with inputs bind to this scatter function.
+   * Called to initialize the gather function values after all other values have been setup for this function.
    */
-  def setScatterGatherable(originalFunction: ScatterGatherableFunction) {}
+  def init() {}
 
   /**
    * Waits for gather parts to propagate over NFS or throws an exception.
diff --git a/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala
index 2639521d9..632e2d39f 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala
@@ -1,3 +1,27 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.queue.function.scattergather
 
 import java.io.File
@@ -8,26 +32,27 @@ import org.broadinstitute.sting.queue.function.QFunction
  * Base class for Scatter functions.
  */
 trait ScatterFunction extends QFunction {
+  var originalFunction: ScatterGatherableFunction = _
+
   @Input(doc="Original inputs to scatter")
   var originalInputs: Set[File] = _
 
   /**
-   * Returns true if the scatter function can scatter this original function.
-   * @param originalFunction The original function to check.
-   * @return true if the scatter function can scatter this original function.
-   */
-  def isScatterGatherable(originalFunction: ScatterGatherableFunction) = true
-
-  /**
-   * Sets the original ScatterGatherableFunction to be scattered.
+   * Called to initialize scatter function values after all other values have been setup for this function.
    * @param originalFunction The original function to with inputs bind to this scatter function.
    */
-  def setScatterGatherable(originalFunction: ScatterGatherableFunction) {}
+  def init() {}
 
   /**
-   * After a call to setScatterGatherable(), returns the number of clones that should be created.
+   * Returns true if the scatter function can scatter this original function.
+   * @return true if the scatter function can scatter this original function.
    */
-  def scatterCount: Int
+  def isScatterGatherable = true
+
+  /**
+   * Returns the number of clones that should be created.
+   */
+  def scatterCount: Int = originalFunction.scatterCount
 
   /**
    * Initializes the input fields for the clone function.
@@ -36,7 +61,7 @@ trait ScatterFunction extends QFunction {
    * @param cloneFunction CloneFunction to initialize.
    * @param index The one based scatter index.
    */
-  def initCloneInputs(cloneFunction: CloneFunction, index: Int)
+  def initCloneInputs(cloneFunction: CloneFunction, index: Int) {}
 
   /**
    * Binds the input fields for the clone function to this scatter function.
@@ -45,5 +70,5 @@ trait ScatterFunction extends QFunction {
    * @param cloneFunction CloneFunction to bind.
    * @param index The one based scatter index.
    */
-  def bindCloneInputs(cloneFunction: CloneFunction, index: Int)
+  def bindCloneInputs(cloneFunction: CloneFunction, index: Int) {}
 }
diff --git a/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
index 202d7230a..e9f034535 100644
--- a/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
+++ b/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
@@ -1,3 +1,27 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.queue.function.scattergather
 
 import java.io.File
@@ -53,7 +77,40 @@ trait ScatterGatherableFunction extends CommandLineFunction {
    * and that the scatter function can scatter this instance.
    * @return true if the function is ready to be scatter / gathered.
    */
-  def scatterGatherable = this.scatterCount > 1 && scatterFunction.isScatterGatherable(this)
+  def scatterGatherable = this.scatterCount > 1 && scatterFunction.isScatterGatherable
+
+  /**
+   * Sets the scatter gather directory to the command directory if it is not already set.
+   */
+  override def freezeFieldValues = {
+    super.freezeFieldValues
+
+    if (this.scatterGatherDirectory == null) {
+      if (qSettings.jobScatterGatherDirectory != null) {
+        this.scatterGatherDirectory = IOUtils.absolute(qSettings.jobScatterGatherDirectory)
+      } else {
+        this.scatterGatherDirectory = IOUtils.absolute(this.commandDirectory, "queueScatterGather")
+      }
+    }
+  }
+
+  /**
+   * The scatter function.
+   */
+  private lazy val scatterFunction = {
+    val scatterFunction = newScatterFunction()
+    this.copySettingsTo(scatterFunction)
+    scatterFunction.originalFunction = this
+    scatterFunction.originalInputs = this.inputs
+    scatterFunction.commandDirectory = this.scatterGatherTempDir("scatter")
+    scatterFunction.isIntermediate = true
+    scatterFunction.addOrder = this.addOrder :+ 1
+
+    initScatterFunction(scatterFunction)
+    scatterFunction.absoluteCommandDirectory()
+    scatterFunction.init()
+    scatterFunction
+  }
 
   /**
    * Returns a list of scatter / gather and clones of this function
@@ -70,14 +127,6 @@ trait ScatterGatherableFunction extends CommandLineFunction {
     val outputFieldsWithValues = this.outputFields.filter(hasFieldValue(_))
 
     // Create the scatter function based on @Scatter
-    this.copySettingsTo(scatterFunction)
-    scatterFunction.addOrder = this.addOrder :+ 1
-    scatterFunction.commandDirectory = this.scatterGatherTempDir("scatter")
-    scatterFunction.originalInputs = this.inputs
-    scatterFunction.isIntermediate = true
-    scatterFunction.setScatterGatherable(this)
-    initScatterFunction(scatterFunction)
-    scatterFunction.absoluteCommandDirectory()
     functions :+= scatterFunction
 
     // Ask the scatter function how many clones to create.
@@ -93,20 +142,13 @@ trait ScatterGatherableFunction extends CommandLineFunction {
     var gatherOutputs = Map.empty[ArgumentSource, File]
     var gatherAddOrder = numClones + 2
     for (gatherField <- outputFieldsWithValues) {
-      val gatherFunction = this.newGatherFunction(gatherField)
       val gatherOutput = getFieldFile(gatherField)
-      this.copySettingsTo(gatherFunction)
-      gatherFunction.addOrder = this.addOrder :+ gatherAddOrder
-      gatherFunction.commandDirectory = this.scatterGatherTempDir("gather-" + gatherField.field.getName)
-      gatherFunction.originalOutput = gatherOutput
-      gatherFunction.setScatterGatherable(this)
-      initGatherFunction(gatherFunction, gatherField)
-      gatherFunction.absoluteCommandDirectory()
-      functions :+= gatherFunction
-      gatherFunctions += gatherField -> gatherFunction
-      gatherOutputs += gatherField -> gatherOutput
-      gatherAddOrder += 1
 
+      val gatherFunction = this.newGatherFunction(gatherField)
+      this.copySettingsTo(gatherFunction)
+      gatherFunction.originalFunction = this
+      gatherFunction.originalOutput = gatherOutput
+      gatherFunction.commandDirectory = this.scatterGatherTempDir("gather-" + gatherField.field.getName)
       // If this is a gather for a log file, make the gather intermediate just in case the log file name changes
       // Otherwise have the regular output function wait on the log files to gather
       if (isLogFile(gatherOutput)) {
@@ -117,6 +159,17 @@ trait ScatterGatherableFunction extends CommandLineFunction {
       } else {
         gatherFunction.originalLogFiles = logFiles
       }
+      gatherFunction.addOrder = this.addOrder :+ gatherAddOrder
+
+      initGatherFunction(gatherFunction, gatherField)
+      gatherFunction.absoluteCommandDirectory()
+      gatherFunction.init()
+
+      functions :+= gatherFunction
+      gatherFunctions += gatherField -> gatherFunction
+      gatherOutputs += gatherField -> gatherOutput
+
+      gatherAddOrder += 1
     }
 
     // Create the clone functions for running the parallel jobs
@@ -126,12 +179,12 @@ trait ScatterGatherableFunction extends CommandLineFunction {
 
       this.copySettingsTo(cloneFunction)
       cloneFunction.originalFunction = this
-      cloneFunction.index = i
+      cloneFunction.cloneIndex = i
+      cloneFunction.commandDirectory = this.scatterGatherTempDir("temp-"+i)
       cloneFunction.addOrder = this.addOrder :+ (i+1)
       cloneFunction.isIntermediate = true
 
       // Setup the fields on the clone function, outputting each as a relative file in the sg directory.
-      cloneFunction.commandDirectory = this.scatterGatherTempDir("temp-"+i)
       scatterFunction.initCloneInputs(cloneFunction, i)
       for (gatherField <- outputFieldsWithValues) {
         val gatherPart = new File(gatherOutputs(gatherField).getName)
@@ -160,21 +213,6 @@ trait ScatterGatherableFunction extends CommandLineFunction {
     functions
   }
 
-  /**
-   * Sets the scatter gather directory to the command directory if it is not already set.
-   */
-  override def freezeFieldValues = {
-    super.freezeFieldValues
-
-    if (this.scatterGatherDirectory == null) {
-      if (qSettings.jobScatterGatherDirectory != null) {
-        this.scatterGatherDirectory = IOUtils.absolute(qSettings.jobScatterGatherDirectory)
-      } else {
-        this.scatterGatherDirectory = IOUtils.absolute(this.commandDirectory, "queueScatterGather")
-      }
-    }
-  }
-
   /**
    * Creates a new ScatterFunction.
    * @return A ScatterFunction instantiated scatterClass
@@ -242,11 +280,6 @@ trait ScatterGatherableFunction extends CommandLineFunction {
         this.setupCloneFunction(cloneFunction, index)
   }
 
-  /**
-   * The scatter function.
-   */
-  private lazy val scatterFunction = newScatterFunction()
-
   /**
    * Returns a temporary directory under this scatter gather directory.
    * @param Sub directory under the scatter gather directory.