From c2f8536e028c0ec5ab57e5a10a8b0a0f977894a2 Mon Sep 17 00:00:00 2001
From: carneiro <carneiro@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 3 May 2011 21:40:39 +0000
Subject: [PATCH] removing old GATK options

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5745 348d0f76-0448-11de-a6fe-93d51630548a
---
 scala/qscript/oneoffs/carneiro/dataProcessingV2.scala | 1 -
 1 file changed, 1 deletion(-)

diff --git a/scala/qscript/oneoffs/carneiro/dataProcessingV2.scala b/scala/qscript/oneoffs/carneiro/dataProcessingV2.scala
index e4a9dfc00..6462df8c4 100755
--- a/scala/qscript/oneoffs/carneiro/dataProcessingV2.scala
+++ b/scala/qscript/oneoffs/carneiro/dataProcessingV2.scala
@@ -310,7 +310,6 @@ class dataProcessingV2 extends QScript {
     if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
     else if (qscript.intervals != null) this.intervals :+= qscript.intervals
 //    this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION  // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
-//    this.index_output_bam_on_the_fly = true
     this.scatterCount = nContigs
     this.isIntermediate = false
     this.analysisName = queueLogDir + outBam + ".recalibration"