From c1720cc8f5cb10e56d715fd9f582bad0ddfb6705 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 16 Sep 2010 18:49:53 +0000
Subject: [PATCH] Now compiles.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4295 348d0f76-0448-11de-a6fe-93d51630548a
---
 scala/qscript/fullCallingPipeline.q | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q
index 1ffb04f81..6864a4c6f 100755
--- a/scala/qscript/fullCallingPipeline.q
+++ b/scala/qscript/fullCallingPipeline.q
@@ -127,10 +127,7 @@ class fullCallingPipeline extends QScript {
     // step through the un-indel-cleaned graph:
     // 1a. call snps and indels
     val snps = new UnifiedGenotyper with CommandLineGATKArgs
-    for ( bam <- bamFiles ) {
-     snps.input_file :+= bam.toNamedFile
-    }
-    //snps.input_file = bamFiles
+    snps.input_file = bamFiles
     snps.group :+= "Standard"
     snps.out = new File(base+".vcf")
     snps.standard_min_confidence_threshold_for_emitting = Some(10)