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

my $inputfile=$ARGV[0];
my $inputfile1=$ARGV[1];

open (file2,">$inputfile1.bed") or die "$!\n";

my %matrix1;
my %matrix2;
my %matrix3;

my $temp1=0;
my $temp2=0;
my $temp3=0;


open (INPUT_FILE,$inputfile);
while(my $line1=<INPUT_FILE>)  
 {   
     @{$matrix1{$temp1}}=split(/\s/,$line1);
   #print "${$matrix1{$temp1}}[2]\n";
     $temp1++;
 }


print file2 "${$matrix1{0}}[0]\t${$matrix1{0}}[1]\t${$matrix1{0}}[2]\t${$matrix1{0}}[3]\t${$matrix1{0}}[10]\t${$matrix1{0}}[5]\n";

for ( my $i=0; $i<$temp1; $i++)
 {   
    if  ( ${$matrix1{$i}}[10] ==0 )
   { }
    else
  {print file2 "${$matrix1{$i}}[0]\t${$matrix1{$i}}[1]\t${$matrix1{$i}}[2]\t${$matrix1{$i}}[3]\t${$matrix1{$i}}[10]\t${$matrix1{$i}}[5]\n";
  }

}


 close (file2);