use Getopt::Long;
use Pod::Usage;
+use FindBin;
+use lib $FindBin::Bin;
use File::Basename;
use File::Path 'rmtree';
use strict;
pod2usage(-msg => "Input file's suffix is neither sam nor bam!", -exitval => 2, -verbose => 2) if (($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"; }
=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