From 0165dcc248203dce454881b6f1707cdf248497c2 Mon Sep 17 00:00:00 2001
From: Bo Li <bli@cs.wisc.edu>
Date: Thu, 18 Oct 2012 10:32:37 -0500
Subject: [PATCH] Added --version option for rsem-calculate-expression

---
 convert-sam-for-rsem         |  2 +-
 rsem-calculate-expression    | 20 +++++++++++++++++---
 rsem-generate-ngvector       |  2 +-
 rsem-plot-transcript-wiggles |  2 +-
 rsem-prepare-reference       |  2 +-
 5 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/convert-sam-for-rsem b/convert-sam-for-rsem
index decf861..7d60f70 100755
--- a/convert-sam-for-rsem
+++ b/convert-sam-for-rsem
@@ -87,7 +87,7 @@ sub runCommand {
     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!"; }
+	else { $errmsg = "\"$command\" failed! Please check if you provide correct parameters/options for the pipeline!"; }
 	print $errmsg."\n";
 	exit(-1);
     }
diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index f169755..4d1b70a 100755
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -62,6 +62,8 @@ my $keep_intermediate_files = 0;
 
 my $strand_specific = 0;
 
+my $version = 0;
+
 my $mTime = 0;
 my ($time_start, $time_end, $time_alignment, $time_rsem, $time_ci) = (0, 0, 0, 0, 0);
 
@@ -105,11 +107,14 @@ GetOptions("keep-intermediate-files" => \$keep_intermediate_files,
 	   "calc-ci" => \$calcCI,
 	   "ci-memory=i" => \$NMB,
 	   "time" => \$mTime,
+	   "version" => \$version,
 	   "q|quiet" => \$quiet,
 	   "h|help" => \$help) or pod2usage(-exitval => 2, -verbose => 2);
 
-pod2usage(-verbose => 2) if ($help == 1);
+my ($fn, $dir, $suf) = fileparse($0);
 
+pod2usage(-verbose => 2) if ($help == 1);
+&showVersionInfo($dir) if ($version == 1);
 
 #check parameters and options
 
@@ -186,7 +191,6 @@ my ($mate_minL, $mate_maxL) = (1, $maxL);
 
 if ($bowtie_path ne "") { $bowtie_path .= "/"; }
 
-my ($fn, $dir, $suf) = fileparse($0);
 my $command = "";
 
 if (!$is_sam && !$is_bam) {
@@ -350,7 +354,7 @@ sub runCommand {
     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";
+        $errmsg .= "\"$_[0]\" failed! Please check if you provide correct parameters/options for the pipeline!\n";
         print $errmsg;
         exit(-1);
     }
@@ -405,6 +409,16 @@ sub collectResults {
     close(OUTPUT);
 }
 
+# dir
+sub showVersionInfo {
+    open(INPUT, "$_[0]\WHAT_IS_NEW");
+    my $line = <INPUT>;
+    chomp($line);
+    close(INPUT);
+    print "$line\n";
+    exit(0);
+}
+
 __END__
 
 =head1 NAME
diff --git a/rsem-generate-ngvector b/rsem-generate-ngvector
index 99498c0..fc97b84 100755
--- a/rsem-generate-ngvector
+++ b/rsem-generate-ngvector
@@ -30,7 +30,7 @@ sub runCommand {
     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";
+        $errmsg .= "\"$_[0]\" failed! Please check if you provide correct parameters/options for the pipeline!\n";
         print $errmsg;
         exit(-1);
     }
diff --git a/rsem-plot-transcript-wiggles b/rsem-plot-transcript-wiggles
index 37c7e27..46a71aa 100755
--- a/rsem-plot-transcript-wiggles
+++ b/rsem-plot-transcript-wiggles
@@ -54,7 +54,7 @@ sub runCommand {
     if ($status != 0) { 
 	my $errmsg;
 	if (scalar(@_) > 1) { $errmsg = $_[1]; }
-	else { $errmsg = "\"$command\" failed! Plase check if you provide correct parameters/options for the pipeline!"; }
+	else { $errmsg = "\"$command\" failed! Please check if you provide correct parameters/options for the pipeline!"; }
 	print $errmsg."\n";
 	exit(-1);
     }
diff --git a/rsem-prepare-reference b/rsem-prepare-reference
index 56d6972..055bef8 100755
--- a/rsem-prepare-reference
+++ b/rsem-prepare-reference
@@ -100,7 +100,7 @@ sub runCommand {
     if ($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";
+        $errmsg .= "\"$_[0]\" failed! Please check if you provide correct parameters/options for the pipeline!\n";
         print $errmsg;
         exit(-1);
     }
-- 
2.39.2