X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=convert-sam-for-rsem;h=94b7965e88f4061afd5643ea44220aaa98236041;hb=52f1bd6f44f9b2630b839f192fb9ece18581983b;hp=7d60f70974fa7db3dc1b96d615771bd7c23b1206;hpb=da3cf29fde8e879f83cde41831ddbc0456ba35dd;p=rsem.git

diff --git a/convert-sam-for-rsem b/convert-sam-for-rsem
index 7d60f70..94b7965 100755
--- a/convert-sam-for-rsem
+++ b/convert-sam-for-rsem
@@ -6,6 +6,8 @@ use File::Basename;
 use File::Path 'rmtree';
 use strict;
 
+use rsem_perl_utils;
+
 my ($in_file, $out_file) = ();
 
 my @tmp_dirs = ();
@@ -79,21 +81,6 @@ print STDERR "Conversion is completed. $out_file will be checked by 'rsem-sam-va
 $command = $dir."rsem-sam-validator $out_file";
 &runCommand($command);
 
-
-# command, {err_msg}
-sub runCommand {
-    print $_[0]."\n";
-    my $status = system($_[0]);
-    if ($status != 0) { 
-	my $errmsg;
-	if (scalar(@_) > 1) { $errmsg = $_[1]; }
-	else { $errmsg = "\"$command\" failed! Please check if you provide correct parameters/options for the pipeline!"; }
-	print $errmsg."\n";
-	exit(-1);
-    }
-    print "\n";
-}
-
 __END__
 
 =head1 NAME