From aae61767c6574937efcc77a5e2d6e8e0cc76a5ba Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Tue, 10 Jan 2012 17:32:30 -0500
Subject: [PATCH] queueJobReport now compresses PDF when running R 2.13+.
 Updated PostCallingQC.scala's VE and R to include missense to silent ratio
 and plot.

---
 .../broadinstitute/sting/queue/util/queueJobReport.R   | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/public/R/scripts/org/broadinstitute/sting/queue/util/queueJobReport.R b/public/R/scripts/org/broadinstitute/sting/queue/util/queueJobReport.R
index d5ee3626f..ae340e688 100644
--- a/public/R/scripts/org/broadinstitute/sting/queue/util/queueJobReport.R
+++ b/public/R/scripts/org/broadinstitute/sting/queue/util/queueJobReport.R
@@ -1,6 +1,7 @@
 library(gsalib)
-require("ggplot2")
-require("gplots")
+library(ggplot2)
+library(gplots)
+library(tools)
 
 #
 # Standard command line switch.  Can we loaded interactively for development
@@ -201,4 +202,7 @@ for ( group in gatkReportData ) {
   
 if ( ! is.na(outputPDF) ) {
   dev.off()
-} 
+  if (exists("compactPDF")) {
+    compactPDF(outputPDF)
+  }
+}