From cd90fdeca15b0169c1f5f006744ad23a3b117647 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 23 Mar 2011 20:08:53 +0000
Subject: [PATCH] Right. The issue was not setting the scatter/gather classes
 appropriately.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5501 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../oneoffs/chartl/ScatterGatherAssociation.q | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/scala/qscript/oneoffs/chartl/ScatterGatherAssociation.q b/scala/qscript/oneoffs/chartl/ScatterGatherAssociation.q
index ec16611c1..8d883abee 100755
--- a/scala/qscript/oneoffs/chartl/ScatterGatherAssociation.q
+++ b/scala/qscript/oneoffs/chartl/ScatterGatherAssociation.q
@@ -1,5 +1,5 @@
 import org.broadinstitute.sting.commandline.{Argument, Output, Input}
-import org.broadinstitute.sting.queue.extensions.gatk.CommandLineGATK
+import org.broadinstitute.sting.queue.extensions.gatk.{IntervalScatterFunction, CommandLineGATK}
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.utils.text.XReadLines
 import collection.JavaConversions._
@@ -36,35 +36,49 @@ class ScatterGatherAssociation extends QScript {
     // the rest are output files implicitly constructed by the multiplexer
 
     @Output(doc="bqs")
+    @Gather(classOf[SimpleTextGatherFunction])
     var bqs : File = new File(String.format("%s.%s.%s", base, "BaseQualityScore", ext))
     @Output(doc="isd")
+    @Gather(classOf[SimpleTextGatherFunction])
     var isd : File = new File(String.format("%s.%s.%s",base,"InsertSizeDistribution",ext))
     @Output(doc="mq0")
+    @Gather(classOf[SimpleTextGatherFunction])
     var mq0 : File = new File(String.format("%s.%s.%s",base,"MappingQuality0",ext))
     @Output(doc="mmq")
+    @Gather(classOf[SimpleTextGatherFunction])
     var mmq : File = new File(String.format("%s.%s.%s",base,"MateMappingQuality",ext))
     @Output(doc="moc")
+    @Gather(classOf[SimpleTextGatherFunction])
     var moc : File = new File(String.format("%s.%s.%s",base,"MateOtherContig",ext))
     @Output(doc="mss")
+    @Gather(classOf[SimpleTextGatherFunction])
     var mss : File = new File(String.format("%s.%s.%s",base,"MateSameStrand",ext))
     @Output(doc="mu")
+    @Gather(classOf[SimpleTextGatherFunction])
     var mu : File = new File(String.format("%s.%s.%s",base,"MateUnmapped",ext))
     @Output(doc="mmr")
+    @Gather(classOf[SimpleTextGatherFunction])
     var mmr : File = new File(String.format("%s.%s.%s",base,"MismatchRate",ext))
     @Output(doc="pp")
+    @Gather(classOf[SimpleTextGatherFunction])
     var pp : File = new File(String.format("%s.%s.%s",base,"ProperPairs",ext))
     @Output(doc="rc")
+    @Gather(classOf[SimpleTextGatherFunction])
     var rc : File = new File(String.format("%s.%s.%s",base,"ReadClipping",ext))
     @Output(doc="ri")
+    @Gather(classOf[SimpleTextGatherFunction])
     var ri : File = new File(String.format("%s.%s.%s",base,"ReadIndels",ext))
     @Output(doc="rmq")
+    @Gather(classOf[SimpleTextGatherFunction])
     var rmq : File = new File(String.format("%s.%s.%s",base,"ReadMappingQuality",ext))
     @Output(doc="rm")
+    @Gather(classOf[SimpleTextGatherFunction])
     var rm : File = new File(String.format("%s.%s.%s",base,"ReferenceMismatches",ext))
     @Output(doc="sd")
+    @Gather(classOf[SimpleTextGatherFunction])
     var sd : File = new File(String.format("%s.%s.%s",base,"SampleDepth",ext))
 
-    override def commandLine = super.commandLine + " -o %s".format(base)
+    override def commandLine = super.commandLine + " -AT ALL -o %s".format(base)
   }
 
   def script = {
@@ -83,6 +97,7 @@ class ScatterGatherAssociation extends QScript {
     association.input_file ++= asScalaIterable((new XReadLines(bamList)).readLines).map(u => new File(u)).toList
     association.scatterCount = scatterJobs
     association.memoryLimit = Some(memLimit)
+    association.scatterClass = classOf[IntervalScatterFunction]
 
     add(association)
   }