From 825682f58c26b44b9b0493f1bebae5aa7bdaece5 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 4 May 2011 20:17:05 +0000
Subject: [PATCH] oops, putting the script back into a sensible state

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5765 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../qscript/oneoffs/rpoplin/Phase1ProjectConsensus.scala  | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/scala/qscript/oneoffs/rpoplin/Phase1ProjectConsensus.scala b/scala/qscript/oneoffs/rpoplin/Phase1ProjectConsensus.scala
index cc9dd1ad7..5fbc0a9cd 100755
--- a/scala/qscript/oneoffs/rpoplin/Phase1ProjectConsensus.scala
+++ b/scala/qscript/oneoffs/rpoplin/Phase1ProjectConsensus.scala
@@ -65,7 +65,7 @@ class Phase1ProjectConsensus extends QScript {
 
   def script = {
 
-    for(chr <- List(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23)) {
+    for(chr <- List(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23)) {
       val chrObject = new Chromosome(chr)
       val basesPerJob: Int = 3000000
       val lastBase: Int = qscript.chromosomeLength(chr - 1)
@@ -142,12 +142,6 @@ class Phase1ProjectConsensus extends QScript {
       clean.targetIntervals = targetIntervals
       clean.out = cleanedBam
       clean.doNotUseSW = true
-      clean.maxInMemory = 8000
-      clean.maxReads = 100
-      clean.greedy = 80
-      clean.LOD = 7.0
-      clean.knownsOnly = true
-      clean.maxConsensuses = 10
       clean.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF
       clean.simplifyBAM = true
       clean.rodBind :+= RodBind("indels1", "VCF", qscript.dindelCalls)