--- a/bowtie2bed.pl	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-#!/usr/bin/perl
-
-# write bowtie output to bed file
-
-# perl bowtie2bed.pl s_5_trimmed.map outputfile 200
-# input
-# 	inputfile
-#	extension
-
-$inputfile = $ARGV[0];
-$extension = $ARGV[2];
-$outputfile = $ARGV[1];#$inputfile.".extended_$extension"."bp.bed";
-
-print "input file: $inputfile\n";
-print "output file: $outputfile\n";
-print "track name: $outputfile\n";
-
-open (IN,$inputfile) or die $!;
-open (OUT,">$outputfile") or die $!;
-
-print OUT "track name=$outputfile itemRgb=On\n";
-
-while(<IN>)
-{
-    @flds = split/\t/;
-    $flds[0] =~ s/ /-/g;#substitute space to dash
-
-    if ($flds[1] eq "+")
-    {
-     print OUT join("\t",$flds[2],$flds[3],$flds[3]+$extension+length($flds[4]),$flds[0],1,$flds[1],$flds[3],$flds[3]+length($flds[4]),"255,0,0","\n");
-    }
-    else
-    {
-     
-     print OUT join("\t",$flds[2],max(0,$flds[3]-$extension),$flds[3]+length($flds[4]),$flds[0],1,$flds[1],$flds[3],$flds[3]+length($flds[4]),"0,255,0","\n");
-    }
-}
-close(IN);
-close(OUT);
-
-sub max()
-{
- ($a,$b) = @_;
- return $a>$b?$a:$b;
-}