From 5e710050d64439adb998fefcb87d93ab6462b964 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 31 Aug 2010 16:03:35 +0000
Subject: [PATCH] minor change, bamFiles comes from the input list, not the
 script

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4170 348d0f76-0448-11de-a6fe-93d51630548a
---
 scala/qscript/fullCallingPipeline.q | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q
index 631ec1576..a75c1f107 100755
--- a/scala/qscript/fullCallingPipeline.q
+++ b/scala/qscript/fullCallingPipeline.q
@@ -156,7 +156,7 @@ class fullCallingPipeline extends QScript {
     var indelGenotypers = List.empty[IndelGenotyperV2 with CommandLineGATKArgs]
     var loopNo = 0
     var priority = ""
-    for ( bam <- qscript.bamFiles ) {
+    for ( bam <- bamFiles ) {
       val indel = new IndelGenotyperV2 with CommandLineGATKArgs
       indel.input_file :+= bam.toNamedFile
       indel.out = swapExt(bam,".bam",".indels.vcf")