Modified the acknowledgement section of README.md

[rsem.git] / convert-sam-for-rsem

diff --git a/convert-sam-for-rsem b/convert-sam-for-rsem
index 7d60f70974fa7db3dc1b96d615771bd7c23b1206..c0776162e064ef7bec9eeefbdf0412be4a22f8ad 100755 (executable)
--- a/convert-sam-for-rsem
+++ b/convert-sam-for-rsem
@@ -1,11 +1,15 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use Getopt::Long;
 use Pod::Usage;
+use FindBin;
+use lib $FindBin::Bin;
 use File::Basename;
 use File::Path 'rmtree';
 use strict;
 
+use rsem_perl_utils;
+
 my ($in_file, $out_file) = ();
 
 my @tmp_dirs = ();
@@ -29,7 +33,7 @@ $suf = lc(substr($suf, 1));
 pod2usage(-msg => "Input file's suffix is neither sam nor bam!", -exitval => 2, -verbose => 2) if (($suf ne "sam") && ($suf ne "bam"));
 my $isSam = ($suf eq "sam");
 
-($fn, $dir, $suf) = fileparse($0);
+$dir = "$FindBin::Bin/";
 
 my $temp_dir = "$out_file.temp";
 if (-d $temp_dir) { print "Warning: $temp_dir exists, convert-sam-for-rsem will write temporary files into this folder and delete it after it finishes!\n"; }
@@ -79,21 +83,6 @@ 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
@@ -102,11 +91,7 @@ convert-sam-for-rsem
 
 =head1 SYNOPSIS
 
-=over
-
- convert-sam-for-rsem [options] <input.sam/input.bam> output_file_name
-
-=back
+convert-sam-for-rsem [options] <input.sam/input.bam> output_file_name
 
 =head1 ARGUMENTS