--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flexbar.pl	Sun Dec 30 14:01:39 2012 -0500
@@ -0,0 +1,42 @@
+#!/usr/bin/env perl
+
+# Author: Johannes T. Roehr
+
+use warnings;
+use strict;
+
+my $flexbarDir = "";
+
+my $pwd = $ENV{PWD};
+
+my $lastIdx = $#ARGV;
+my $format  = $ARGV[$lastIdx];
+my $folder  = $ARGV[$lastIdx - 1];
+my $id      = $ARGV[$lastIdx - 2];
+my $outFile = $ARGV[$lastIdx - 3];
+
+my $call = join " ", @ARGV[0..($lastIdx - 4)];
+
+system $flexbarDir . $call .' --target reads > '. $outFile;
+
+foreach(<$pwd ."/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;
+	}
+}
+