From 5b9a8555cdae42411fa8077cb313360dd7827909 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 21 Apr 2011 12:56:25 +0000
Subject: [PATCH] Queue graph time is currently of O(n^m) where n = num jobs, m
 = num unique base files. This script therefore was running in order 1200^16,
 which I don't think would finish before the heat death of the universe. For
 now, push down the number of files to 1 and gather them outside of Queue,
 once I've fixed up scatter-gather in core, outputs can be uncommented.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5674 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/association/RAWSampleStats.java   | 22 +++++++++++--------
 .../oneoffs/chartl/ScatterGatherAssociation.q |  4 +++-
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RAWSampleStats.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RAWSampleStats.java
index 3d16bd1dd..3a4047c5a 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RAWSampleStats.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RAWSampleStats.java
@@ -51,19 +51,23 @@ public class RAWSampleStats extends LocusWalker<MapHolder,RegionalAssociationHan
         for ( AssociationContext context : handler.getAssociations() ) {
             contextBuf.append("\t");
             contextBuf.append(context.getClass().getSimpleName());
+            StringBuffer caseBuf = new StringBuffer();
+            StringBuffer controlBuf = new StringBuffer();
             boolean first = true;
             for ( Map.Entry<Sample,AlignmentContext> entry : handler.getExtender().getContext().entrySet() ) {
-                if ( ! first ) {
-                    contextBuf.append(";");
-                } else {
-                    contextBuf.append("\t");
-                    first = false;
-                }
-                contextBuf.append(entry.getKey().getId());
-                contextBuf.append("=");
-                contextBuf.append(handleMap(context.map(entry.getValue().getBasePileup())));
+                StringBuffer toAppend = entry.getKey().getProperty("cohort").equals("case") ? caseBuf : controlBuf;
+                toAppend.append(entry.getKey().getId());
+                toAppend.append("=");
+                toAppend.append(handleMap(context.map(entry.getValue().getBasePileup())));
+                toAppend.append(";");
             }
+            caseBuf.deleteCharAt(caseBuf.length()-1);
+            controlBuf.deleteCharAt(controlBuf.length()-1);
             contextBuf.append("\t");
+            contextBuf.append("Case:\t");
+            contextBuf.append(caseBuf);
+            contextBuf.append("\tControl:\t");
+            contextBuf.append(controlBuf);
         }
 
         out.printf("%s%n",contextBuf.toString());
diff --git a/scala/qscript/oneoffs/chartl/ScatterGatherAssociation.q b/scala/qscript/oneoffs/chartl/ScatterGatherAssociation.q
index d015d9b1a..7c896fd4a 100755
--- a/scala/qscript/oneoffs/chartl/ScatterGatherAssociation.q
+++ b/scala/qscript/oneoffs/chartl/ScatterGatherAssociation.q
@@ -41,6 +41,7 @@ class ScatterGatherAssociation extends QScript {
     @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))
@@ -56,7 +57,7 @@ class ScatterGatherAssociation extends QScript {
     @Output(doc="mss")
     @Gather(classOf[SimpleTextGatherFunction])
     var mss : File = new File(String.format("%s.%s.%s",base,"MateSameStrand",ext))
-    @Output(doc="mu")
+    /@Output(doc="mu")
     @Gather(classOf[SimpleTextGatherFunction])
     var mu : File = new File(String.format("%s.%s.%s",base,"MateUnmapped",ext))
     @Output(doc="mmr")
@@ -86,6 +87,7 @@ class ScatterGatherAssociation extends QScript {
     @Output(doc="rwi")
     @Gather(classOf[SimpleTextGatherFunction])
     var rwi : File = new File(String.format("%s.%s.%s",base,"ReadsWithIndels",ext))
+    */
 
     override def commandLine = {
       var bedStr : String = ""