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

my $inputfile=$ARGV[0]; ##genesmm9
my $inputfile2=$ARGV[1];#####0hrep

open (file2,">coord0hrep2.bed") or die "$!\n";
#open (file2b,">coord0hrep3b.bed") or die "$!\n";

my %matrix1=0;
my %matrix2=0;
my %matrix3=0;
my %matrix5=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);

     if ( ${$matrix1{$temp1}}[0]=~/(\d{1,6})chr.*/)
     { $var1=$1;}

     @{$matrix3{$var1}}=${$matrix1{$temp1}}[1];
     #print file2b "$var1\t@{$matrix3{$var1}}\n";
     $temp1++;
  }
#die;
open (INPUT_FILE,$inputfile2);
while(my $line2=<INPUT_FILE>)  
 {   
     @{$matrix2{$temp2}}=split(/\s/,$line2);
    #print "${$matrix2{$temp2}}[2]\n";
  #for (my $i=0; $i<$temp1; $i++)
    # {
  $var2=${$matrix2{$temp2}}[2]; 

  #$var3=@{$matrix3{$var2}};

#print "$var2\t${$matrix2{$temp2}}[2]\t@{$matrix3{$var2}}\n";
   #print "$var2\t@{$matrix3{$var2}}\n";
    #if ( ${$matrix1{$i}}[0] =~/\>(.*)/ig)
      #{  my $var1=$0; }
#print "$var1\t${$matrix2{$temp2}}[2]\n";
    # if ( ${$matrix1{$i}}[0] eq ${$matrix2{$temp2}}[2] )
       # {
print file2 "@{$matrix3{$var2}}\t${$matrix2{$temp2}}[0]\t${$matrix2{$temp2}}[1]\t${$matrix2{$temp2}}[2]\t${$matrix2{$temp2}}[3]\t${$matrix2{$temp2}}[4]\t${$matrix2{$temp2}}[5]\t${$matrix2{$temp2}}[6]\t${$matrix2{$temp2}}[7]\t${$matrix2{$temp2}}[8]\n";   
       # }
       # }
 undef %matrix2;
     $temp2++;
  }

close (file2);