#!/usr/bin/perl -w 



if(scalar(@ARGV)==2){
$file = $ARGV[0];
$cutoff = $ARGV[1];
$cutoff = int($cutoff);
$check = $file;
$check =~ s/\.//s;
#has one only dot
if($check =~ /\W/){print "file nonword ? $file\n";exit;}
open(IF,"$file");
open(OF,">co$cutoff.$file");
while($a=<IF>){
@b = split(/\t/,$a);
#chrom start end name score strand thicks thicke rgb blcnt sizes starts 
if($b[9] == 1){print OF $a;}
else{
$ok=1;
@sizes = split(/,/,$b[10]);
@starts = split(/,/,$b[11]);
for($i=1;$i<$b[9];$i++){
$istart = $b[1] + $starts[$i-1] + $sizes[$i-1];
$iend = $b[1] + $starts[$i];
if(($iend -$istart ) > 200){$ok++;}
}
if($ok == 1){ print OF $a;}
}
}
}
else{
print "./script ./filename cutoff_intron_size\n";
print "./script file.bed 200 \n";
print "removes entries with intron > x\n";
exit;

}