Renamed makefile as Makefile

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

diff --git a/convert-sam-for-rsem b/convert-sam-for-rsem
index 94b7965e88f4061afd5643ea44220aaa98236041..812c8b9ca6ce1e295d62752974588a419182b195 100755 (executable)
--- a/convert-sam-for-rsem
+++ b/convert-sam-for-rsem
@@ -1,13 +1,19 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use Getopt::Long;
 use Pod::Usage;
 use File::Basename;
 use File::Path 'rmtree';
-use strict;
 
+use FindBin;
+use lib $FindBin::RealBin;
 use rsem_perl_utils;
 
+use Env qw(@PATH);
+@PATH = ($FindBin::RealBin, "$FindBin::RealBin/sam", @PATH);
+
+use strict;
+
 my ($in_file, $out_file) = ();
 
 my @tmp_dirs = ();
@@ -31,8 +37,6 @@ $suf = lc(substr($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);
-
 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"; }
 else {
@@ -45,7 +49,7 @@ my $sam_file;
 
 if (!$isSam) {
     $sam_file = "$temp_dir/input.sam";
-    $command = $dir."sam/samtools view -h -o $sam_file $in_file";
+    $command = "samtools view -h -o $sam_file $in_file";
     &runCommand($command); 
 }
 else {
@@ -68,7 +72,7 @@ $command .= " >> $tmp_sam";
 
 # Phase II, parse the temporary SAM file to make paired-end alignments' two mates adjacent to each other
 
-$command = $dir."rsem-scan-for-paired-end-reads $tmp_sam $out_file";
+$command = "rsem-scan-for-paired-end-reads $tmp_sam $out_file";
 &runCommand($command);
 
 # delete temporary directory
@@ -78,7 +82,7 @@ print STDERR "Conversion is completed. $out_file will be checked by 'rsem-sam-va
 
 # Phase III, validate if the resulting bam file is correct
 
-$command = $dir."rsem-sam-validator $out_file";
+$command = "rsem-sam-validator $out_file";
 &runCommand($command);
 
 __END__
@@ -89,11 +93,7 @@ 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