From 683863b75f8d8bef2461039a6911b0e9619cc113 Mon Sep 17 00:00:00 2001
From: Bo Li <bli@cs.wisc.edu>
Date: Sat, 21 Jul 2012 21:11:07 -0500
Subject: [PATCH] Fixed a bug in perl scripts for printing error messages

---
 convert-sam-for-rsem         |  8 ++++----
 rsem-calculate-expression    | 12 ++++++------
 rsem-generate-ngvector       |  8 ++++----
 rsem-plot-transcript-wiggles |  1 +
 rsem-prepare-reference       | 12 ++++++------
 5 files changed, 21 insertions(+), 20 deletions(-)

diff --git a/convert-sam-for-rsem b/convert-sam-for-rsem
index 13b9b13..decf861 100755
--- a/convert-sam-for-rsem
+++ b/convert-sam-for-rsem
@@ -82,16 +82,16 @@ $command = $dir."rsem-sam-validator $out_file";
 
 # command, {err_msg}
 sub runCommand {
-    print STDERR $_[0]."\n";
+    print $_[0]."\n";
     my $status = system($_[0]);
     if ($status != 0) { 
 	my $errmsg;
 	if (scalar(@_) > 1) { $errmsg = $_[1]; }
-	else { $errmsg = "\"$command\" failed! Plase check if you provide correct parameters/options for the script!"; }
-	print STDERR $errmsg."\n";
+	else { $errmsg = "\"$command\" failed! Plase check if you provide correct parameters/options for the pipeline!"; }
+	print $errmsg."\n";
 	exit(-1);
     }
-    print STDERR "\n";
+    print "\n";
 }
 
 __END__
diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index 9e6ef2e..684e33c 100755
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -345,12 +345,12 @@ if ($mTime) {
 sub runCommand {
     print $_[0]."\n";
     my $status = system($_[0]);
-    if ($status != 0) { 
-	my $errmsg;
-	if (scalar(@_) > 1) { $errmsg = $_[1]; }
-	else { $errmsg = "\"$command\" failed! Plase check if you provide correct parameters/options for the pipeline!"; }
-	print $errmsg."\n";
-	exit(-1);
+    if ($status != 0) {
+        my $errmsg = "";
+        if (scalar(@_) > 1) { $errmsg .= $_[1]."\n"; }
+        $errmsg .= "\"$_[0]\" failed! Plase check if you provide correct parameters/options for the pipeline!\n";
+        print $errmsg;
+        exit(-1);
     }
     print "\n";
 }
diff --git a/rsem-generate-ngvector b/rsem-generate-ngvector
index c4d26a8..cd184b6 100755
--- a/rsem-generate-ngvector
+++ b/rsem-generate-ngvector
@@ -28,10 +28,10 @@ sub runCommand {
     print $_[0]."\n";
     my $status = system($_[0]);
     if ($status != 0) {
-        my $errmsg;
-        if (scalar(@_) > 1) { $errmsg = $_[1]; }
-        else { $errmsg = "\"$command\" failed! Plase check if you provide correct parameters/options for the pipeline!"; }
-        print $errmsg."\n";
+        my $errmsg = "";
+        if (scalar(@_) > 1) { $errmsg .= $_[1]."\n"; }
+        $errmsg .= "\"$_[0]\" failed! Plase check if you provide correct parameters/options for the pipeline!\n";
+        print $errmsg;
         exit(-1);
     }
     print "\n";
diff --git a/rsem-plot-transcript-wiggles b/rsem-plot-transcript-wiggles
index 25e8b35..37c7e27 100755
--- a/rsem-plot-transcript-wiggles
+++ b/rsem-plot-transcript-wiggles
@@ -46,6 +46,7 @@ if ($show_unique) {
 $command = $dir."rsem-gen-transcript-plots $ARGV[0] $ARGV[1] $gene_list $show_unique $ARGV[2]";
 &runCommand($command);
 
+
 # command, {err_msg}
 sub runCommand {
     print $_[0]."\n";
diff --git a/rsem-prepare-reference b/rsem-prepare-reference
index 80a9549..56d6972 100755
--- a/rsem-prepare-reference
+++ b/rsem-prepare-reference
@@ -97,12 +97,12 @@ if (!$no_bowtie) {
 sub runCommand {
     print $_[0]."\n";
     my $status = system($_[0]);
-    if ($status != 0) { 
-	my $errmsg;
-	if (scalar(@_) > 1) { $errmsg = $_[1]; }
-	else { $errmsg = "\"$command\" failed! Plase check if you provide correct parameters/options for the pipeline!"; }
-	print $errmsg."\n";
-	exit(-1);
+    if ($status != 0) {
+        my $errmsg = "";
+        if (scalar(@_) > 1) { $errmsg .= $_[1]."\n"; }
+        $errmsg .= "\"$_[0]\" failed! Plase check if you provide correct parameters/options for the pipeline!\n";
+        print $errmsg;
+        exit(-1);
     }
     print "\n";
 }
-- 
2.39.2