FCP only adds the expand intervals QFunction once per script instead of once per QFunction using the ExpandTargets scala trait.

Eval dbSNP's type now based on eval dbSNP instead of genotype dbSNP.
Using an external treemap instead of the JGraphT internal node set to speed up larger graph generation.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5261 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/datasources/pipeline/PipelineProject.java

@@ -85,7 +85,7 @@ public class PipelineProject {
     }
 
     public String getEvalDbsnpType() {
-        return getDbsnpType(genotypeDbsnp);
+        return getDbsnpType(evalDbsnp);
     }
 
     public File getRefseqTable() {

scala/qscript/playground/FullCallingPipeline.q

@@ -160,11 +160,13 @@ class FullCallingPipeline extends QScript {
     val ei : ExpandIntervals = new ExpandIntervals(qscript.pipeline.getProject.getIntervalList, 1, qscript.expandIntervals, new File("Resources", base + ".flanks.interval_list"), qscript.pipeline.getProject.getReferenceFile, "INTERVALS", "INTERVALS")
     ei.jobOutputFile = new File(".queue/logs/Overall/ExpandIntervals.out")
 
+    if (qscript.expandIntervals > 0) {
+      add(ei)
+    }
+
     trait ExpandedIntervals extends CommandLineGATK {
       if (qscript.expandIntervals > 0) {
         this.intervals :+= ei.outList
-
-        add(ei)
       }
     }
 

scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala

@@ -13,6 +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
 
 /**
  * The internal dependency tracker between sets of function input and output files.
@@ -23,7 +24,13 @@ class QGraph extends Logging {
 
   private def dryRun = !settings.run
   private var numMissingValues = 0
+
   private val jobGraph = newGraph
+  // A map of nodes by list of files.
+  private var nodeMap = TreeMap.empty[Iterable[File], QNode](Ordering.Iterable(Ordering.by[File,String](_.getAbsolutePath)))
+  // 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 val nl = "%n".format()
@@ -212,8 +219,12 @@ class QGraph extends Logging {
       }
     }
 
-    if (running)
-      jobGraph.removeAllVertices(jobGraph.vertexSet.filter(isOrphan(_)))
+    if (running) {
+      for (orphan <- jobGraph.vertexSet.filter(isOrphan(_))) {
+        jobGraph.removeVertex(orphan)
+        nodeMap -= orphan.files
+      }
+    }
   }
 
   /**
@@ -606,9 +617,8 @@ class QGraph extends Logging {
   private def newGraph = new SimpleDirectedGraph[QNode, QEdge](new EdgeFactory[QNode, QEdge] {
     def createEdge(input: QNode, output: QNode) = new MappingEdge(input, output)})
 
-  private var nextNodeId = 0
   private def getQNode(files: List[File]) = {
-    jobGraph.vertexSet.find(node => node.files == files) match {
+    nodeMap.get(files) match {
       case Some(node) =>
         node
       case None =>
@@ -617,6 +627,7 @@ class QGraph extends Logging {
         val node = new QNode(nextNodeId, files)
         nextNodeId += 1
         jobGraph.addVertex(node)
+        nodeMap += files -> node
         node
     }
   }