#!/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}}[9]\t${$matrix1{0}}[5]\n";

for ( my $i=1; $i<$temp1; $i++)
 {   
    if  ((( ${$matrix1{$i-1}}[0] eq ${$matrix1{$i}}[0] )&&( ${$matrix1{$i-1}}[1] eq ${$matrix1{$i}}[1] )&&( ${$matrix1{$i-1}}[2] eq ${$matrix1{$i}}[2] ) &&( ${$matrix1{$i-1}}[3] eq ${$matrix1{$i}}[3] )&&( ${$matrix1{$i-1}}[4] eq ${$matrix1{$i}}[4] ) &&( ${$matrix1{$i-1}}[5] eq ${$matrix1{$i}}[5] )&&( ${$matrix1{$i-1}}[6] eq ${$matrix1{$i}}[6] ) &&( ${$matrix1{$i-1}}[7] eq ${$matrix1{$i}}[7] )&&( ${$matrix1{$i-1}}[8] eq ${$matrix1{$i}}[8] ) &&( ${$matrix1{$i-1}}[9] eq ${$matrix1{$i}}[9] )&& ( ${$matrix1{$i-1}}[10] eq ${$matrix1{$i}}[10] ) &&( ${$matrix1{$i-1}}[11] eq ${$matrix1{$i}}[11] ) ))
   { }
    else
  {print file2 "${$matrix1{$i}}[0]\t${$matrix1{$i}}[1]\t${$matrix1{$i}}[2]\t${$matrix1{$i}}[3]\t${$matrix1{$i}}[9]\t${$matrix1{$i}}[5]\n";
  }

}


 close (file2);