--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/carpet-src-1/tools/CARPET/gff2bed_v2.pl	Tue Jun 07 16:50:41 2011 -0400
@@ -0,0 +1,44 @@
+#! /usr/bin/perl 
+  
+# Copyright 2009 Matteo Cesaroni, Lucilla Luzi
+#
+# This program is free software; ; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or (at your
+# option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+
+$fname=$ARGV[0];  #legge il nome del file che gli passi dopo il comando
+$col3=$ARGV[1];
+ 
+qx {sort -k 1,1 -k 4,4n $fname >$fname.sortato};   
+ 
+open(FILE, "< $fname.sortato") or die "Cannot find file $fname\n";
+
+@array=<FILE>; 
+
+print "track type=wiggle_0 name=\"$col3\" description=\"raw_data ratio\" visibility=full autoscale=off maxHeightPixels=100:50:20 color=200,100,0 altColor=0,100,200 \n";
+
+for ($i=0;$i<$#array;$i++){
+	@array_new= split("\t",$array[$i]);
+	@array_new2=split("\t",$array[$i+1]);
+	$dist=$array_new[4]-$array_new2[3];
+	if (($array_new[4]>=$array_new2[3])&&("$array_new[0]"eq"$array_new2[0]")){
+		$fine=$array_new2[3]-1;
+	}	  
+	else {
+		$fine=$array_new[4];
+		
+		}
+	print "$array_new[0]\t$array_new[3]\t$fine\t$array_new[5]\n";
+	
+	}
+	@array_fine=split("\t",	$array[$#array]);
+	print "$array_fine[0]\t$array_fine[3]\t$array_fine[4]\t$array_fine[5]\n";
+
+ close FILE;