From 8118a439c000c45e16cf404bc28d219d8c37d45d Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 18 Dec 2010 22:24:18 +0000
Subject: [PATCH] Commit for Khalid

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4876 348d0f76-0448-11de-a6fe-93d51630548a
---
 scala/qscript/chartl/expanded_targets.q       | 21 +++++++++++++++++++
 .../ipf/intervals/ExpandIntervals.scala       |  4 ++--
 2 files changed, 23 insertions(+), 2 deletions(-)
 create mode 100755 scala/qscript/chartl/expanded_targets.q

diff --git a/scala/qscript/chartl/expanded_targets.q b/scala/qscript/chartl/expanded_targets.q
new file mode 100755
index 000000000..ca8de6a00
--- /dev/null
+++ b/scala/qscript/chartl/expanded_targets.q
@@ -0,0 +1,21 @@
+import org.broadinstitute.sting.commandline.ArgumentCollection
+import org.broadinstitute.sting.queue.library.ipf.ExpandIntervals
+import org.broadinstitute.sting.queue.pipeline.PipelineArgumentCollection
+import org.broadinstitute.sting.queue.QScript
+
+class expanded_targets extends QScript {
+  @ArgumentCollection var args : PipelineArgumentCollection = new PipelineArgumentCollection
+  @Argument(shortName="bait",doc="The list of baits associated with the target list",required=false) var baitFile : File = _
+
+  def script = {
+
+    val intervalExpands : List[ExpandIntervals] = (new Range(0,40,1)).toList.map( u => {
+      new ExpandIntervals(args.projectIntervals,1+5*u,5,new File(System.getProperty("user.dir")+"/"+args.projectName+"_expanded_%d_%d.interval_list".format(1+5*u,6+5*u)),args.projectRef,"BED")
+    })
+
+    addAll(intervalExpands)
+
+    //  intervalExpands.map(_.outList).foreach(makeCalls(_))
+
+  }
+}
\ No newline at end of file
diff --git a/scala/src/org/broadinstitute/sting/queue/library/ipf/intervals/ExpandIntervals.scala b/scala/src/org/broadinstitute/sting/queue/library/ipf/intervals/ExpandIntervals.scala
index ddc85eb59..7526990b8 100755
--- a/scala/src/org/broadinstitute/sting/queue/library/ipf/intervals/ExpandIntervals.scala
+++ b/scala/src/org/broadinstitute/sting/queue/library/ipf/intervals/ExpandIntervals.scala
@@ -42,11 +42,11 @@ class ExpandIntervals(in : File, start: Int, size: Int, out: File, ref: File, op
       val new1 = parser.createGenomeLoc(current.getContig,current.getStart-startInt-sizeInt,current.getStart-startInt)
       val new2 = parser.createGenomeLoc(current.getContig,current.getStop+startInt,current.getStop+startInt+sizeInt)
       if ( ok(new1) ) {
-        System.out.println("Printing! %s".format(repr(new1)))
+        //System.out.println("Printing! %s".format(repr(new1)))
         output.print("%s%n".format(repr(new1)))
       }
       if ( ok(new2) ) {
-        System.out.println("Printing! %s".format(repr(new2)))
+        //System.out.println("Printing! %s".format(repr(new2)))
         output.print("%s%n".format(repr(new2)))
       }
       previous = current