From 68c382dfb246a5b944ffd630bc3ad9066b559347 Mon Sep 17 00:00:00 2001
From: pascal <pascal@vbsg-bioinf1.vbsg.slu.se>
Date: Wed, 1 Apr 2015 16:53:23 +0200
Subject: [PATCH 1/2] Rio: added option '-p' to give PDF output

---
 tools/Rio | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/tools/Rio b/tools/Rio
index badf4bd5..48295735 100755
--- a/tools/Rio
+++ b/tools/Rio
@@ -1,5 +1,5 @@
 #!/bin/bash
-# Rio: Load CSV from stdin into R as a data.frame, execute given commands, and get the output as CSV or PNG on stdout
+# Rio: Load CSV from stdin into R as a data.frame, execute given commands, and get the output as CSV, PNG or PDF on stdout
 #
 # Example usage:
 # $ < seq 100 | Rio -nf sum (same as Rio -ne 'sum(df)')
@@ -30,6 +30,7 @@ OPTIONS:
    -r      Import dplyr and tidyr
    -s      Import sqldf
    -b      Use same settings as used for book Data Science at the Command Line
+   -p      Export graphic as PDF   
    -v      Verbose
 
 EOF
@@ -57,6 +58,7 @@ REQUIRES=
 DELIMITER=","
 HEADER="T"
 VERBOSE=false
+PDF=false
 
 # OSX `mktemp' requires a temp file template, but Linux `mktemp' has it as optional.
 # This explicitly uses a template, which works for both.  The $TMPDIR is in case
@@ -68,7 +70,7 @@ IN=$(mktemp ${TMPDIR}/Rio-XXXXXXXX)
 OUT=$(mktemp ${TMPDIR}/Rio-XXXXXXXX).png
 ERR=$(mktemp ${TMPDIR}/Rio-XXXXXXXX).err
 
-while getopts "d:hgnprsve:f:b" OPTION
+while getopts "d:hgnprspve:f:b" OPTION
 do
 	case $OPTION in
 		b)
@@ -106,6 +108,9 @@ do
 		v)
 			VERBOSE=true
 			;;
+        p)
+            PDF=true
+            ;;			
 		?)
 			usage
 			exit
@@ -115,6 +120,11 @@ done
 
 cat /dev/stdin > $IN
 
+if $PDF
+then
+    OUT=$(mktemp ${TMPDIR}/Rio-XXXXXXXX).pdf
+fi
+
 if $VERBOSE
 then
 	callR

From 2e583521cefcc2e0a27348dd00dd243a02de2bc0 Mon Sep 17 00:00:00 2001
From: pascal <pascal@vbsg-bioinf1.vbsg.slu.se>
Date: Thu, 2 Apr 2015 08:24:53 +0200
Subject: [PATCH 2/2] Rio pdf: code cleanup and deleting pdf temp file

---
 tools/Rio | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/tools/Rio b/tools/Rio
index 48295735..96dad0fe 100755
--- a/tools/Rio
+++ b/tools/Rio
@@ -37,7 +37,7 @@ EOF
 }
 
 finish() {
-	rm -f $IN $OUT ${OUT%.png} ${ERR%.err}
+	rm -f $IN $OUT ${OUT%.png} ${OUT%.pdf} ${ERR%.err}
 
         ## Removes error file if error file is empty.
     if [[ ! -s $ERR ]]; then
@@ -58,7 +58,6 @@ REQUIRES=
 DELIMITER=","
 HEADER="T"
 VERBOSE=false
-PDF=false
 
 # OSX `mktemp' requires a temp file template, but Linux `mktemp' has it as optional.
 # This explicitly uses a template, which works for both.  The $TMPDIR is in case
@@ -109,7 +108,7 @@ do
 			VERBOSE=true
 			;;
         p)
-            PDF=true
+            OUT=${OUT%.png}.pdf
             ;;			
 		?)
 			usage
@@ -120,11 +119,6 @@ done
 
 cat /dev/stdin > $IN
 
-if $PDF
-then
-    OUT=$(mktemp ${TMPDIR}/Rio-XXXXXXXX).pdf
-fi
-
 if $VERBOSE
 then
 	callR