#!/bin/perl
#use warnings;
use strict;

my $inputfile=$ARGV[0]; ##genesmm9
open (file2,">HafnerIFNTCover2.bed") or die "$!\n";

my %matrix1=0;
my %matrix2=0;

my $temp1=0;
my $temp2=0;

my $var1=0;
my $var2=0;
my $var3=0;

open (INPUT_FILE,$inputfile);
while(my $line1=<INPUT_FILE>)  
 {   
     @{$matrix1{$temp1}}=split(/\s/,$line1);
    # $var1 =${$matrix1{$temp1}}[1];
    # $var2 =${$matrix1{$temp1}}[2];
#$var3=$var2-$var1;
     if (${$matrix1{$temp1}}[3] >= 2 )
      {
        #if ($var3>18)
        #{
 print file2 "${$matrix1{$temp1}}[0]\t${$matrix1{$temp1}}[1]\t${$matrix1{$temp1}}[2]\t${$matrix1{$temp1}}[3]\t${$matrix1{$temp1}}[4]\t${$matrix1{$temp1}}[5]\n";
        #}
       }
    $temp1++;
}
close (file2)