Fixed a minor bug which only affects paired-end reads for reporting how many alignmen...

[rsem.git] / rsem-generate-ngvector

diff --git a/rsem-generate-ngvector b/rsem-generate-ngvector
index fc97b84e83dfdb058ef2bbe048b56cfc68342507..137fa03db354e8e7078a8dd16b535549034f949e 100755 (executable)
--- a/rsem-generate-ngvector
+++ b/rsem-generate-ngvector
@@ -2,9 +2,12 @@
 
 use Getopt::Long;
 use Pod::Usage;
-use File::Basename;
+use FindBin;
+use lib $FindBin::Bin;
 use strict;
 
+use rsem_perl_utils;
+
 my $k = 25;
 my $help = 0;
 
@@ -14,7 +17,7 @@ GetOptions("k=i" => \$k,
 pod2usage(-verbose => 2) if ($help == 1);
 pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (scalar(@ARGV) != 2);
 
-my ($fn, $dir, $suf) = fileparse($0);
+my $dir = "$FindBin::Bin/";
 my $command = "";
 
 $command = $dir."EBSeq/rsem-for-ebseq-calculate-clustering-info $k $ARGV[0] $ARGV[1].ump";
@@ -23,20 +26,6 @@ $command = $dir."EBSeq/rsem-for-ebseq-calculate-clustering-info $k $ARGV[0] $ARG
 $command = $dir."EBSeq/rsem-for-ebseq-generate-ngvector-from-clustering-info $ARGV[1].ump $ARGV[1].ngvec";
 &runCommand($command);
 
-# command, {err_msg}
-sub runCommand {
-    print $_[0]."\n";
-    my $status = system($_[0]);
-    if ($status != 0) {
-        my $errmsg = "";
-        if (scalar(@_) > 1) { $errmsg .= $_[1]."\n"; }
-        $errmsg .= "\"$_[0]\" failed! Please check if you provide correct parameters/options for the pipeline!\n";
-        print $errmsg;
-        exit(-1);
-    }
-    print "\n";
-}
-
 __END__
 
 =head1 NAME