From 91f0ed80597d24eca16b490203d48ff6eb9a2574 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sun, 8 Jul 2012 10:29:13 -0400
Subject: [PATCH] Fixed nasty Rscript typo in VariantRecalibrator when
 compactPDF is available

---
 .../gatk/walkers/variantrecalibration/VariantRecalibrator.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index d1eced5eb..244c5d109 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -463,7 +463,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         stream.println("dev.off()");
 
         stream.println("if (exists(\"compactPDF\")) {");
-        stream.println("compactPDF(ouputPDF)");
+        stream.println("compactPDF(outputPDF)");
         stream.println("}");
 
         stream.close();