--- a/flexbar.pl	Mon Dec 31 00:50:58 2012 +0100
+++ b/flexbar.pl	Mon Dec 31 18:40:01 2012 +0100
@@ -5,38 +5,29 @@
 use warnings;
 use strict;
 
-my $flexbarDir = "";
-
-my $pwd = $ENV{PWD};
+my $format  = pop @ARGV;
+my $folder  = pop @ARGV;
+my $id      = pop @ARGV;
+my $outFile = pop @ARGV;
 
-my $lastIdx = $#ARGV;
-my $format  = $ARGV[$lastIdx];
-my $folder  = $ARGV[$lastIdx - 1];
-my $id      = $ARGV[$lastIdx - 2];
-my $outFile = $ARGV[$lastIdx - 3];
+my $call = join " ", @ARGV;
 
-my $call = join " ", @ARGV[0..($lastIdx - 4)];
+system $call .' --target reads > '. $outFile and exit 1;
 
-system $flexbarDir . $call .' --target reads > '. $outFile;
 
-foreach(<$pwd ."/reads"*>){
+foreach(<reads*>){
 	
-	if(/^\.\//){
-		my $file = $pwd ."/". $_;
-		
-		s/^\.\///;
-		my $fileType;
-		
-		$fileType = $1         if /\.(\w+)$/;
-		$fileType = $format    if /\.\w+fast\w$/;
-		$fileType = 'tabular'  if $fileType eq 'lengthdist';
-		
-		s/_//g;
-		
-		my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;
-		
-		rename $file, $name;
-		rename $name, $folder;
-	}
+	my $fileType;
+	
+	$fileType = $1         if /\.(\w+)$/;
+	$fileType = $format    if /\.\w+fast\w$/;
+	$fileType = 'tabular'  if $fileType eq 'lengthdist';
+	
+	s/_//g;
+	
+	my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;
+	
+	rename $_, $name;
+	rename $name, $folder;
 }