From 2ffa98aea5446178223858f5a31dd4b43247a4ef Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 29 Aug 2010 02:34:41 +0000
Subject: [PATCH] Ugh! varout --> out

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4157 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 e7e5703b5..870cc060b 100755
--- a/scala/qscript/fullCallingPipeline.q
+++ b/scala/qscript/fullCallingPipeline.q
@@ -181,7 +181,7 @@ class fullCallingPipeline extends QScript {
     annotated.rodBind :+= RodBind("variant", "VCF", snps.out)
     annotated.rodBind :+= RodBind("refseq", "AnnotatorInputTable", qscript.refseqTable)
     annotated.rodBind :+= RodBind("dbsnp", "AnnotatorInputTable", qscript.dbsnpTable)
-    annotated.vcfOutput = swapExt(new File(snps.variants_out),".vcf",".annotated.vcf").getAbsolutePath
+    annotated.vcfOutput = swapExt(snps.out,".vcf",".annotated.vcf").getAbsolutePath
     annotated.select :+= "dbsnp.name,dbsnp.refUCSC,dbsnp.strand,dbsnp.observed,dbsnp.avHet"
     annotated.rodToIntervalTrackName = "variant"