#!/usr/local/bin/perl  -w


use strict;
use Getopt::Long;
use Tie::IxHash;

my ($bpfile , $intfile, $out);

my $usage = " USAGE: perl beadpool_int.pl  -bpfile <file with snp,chr,beadpoolid> -int <intensities file from b2i>\n";

GetOptions("bp=s" =>\$bpfile,
	   "int=s" =>\$intfile,
	   "out=s" =>\$out) || warn "Error $!\n";
	   
if(!$bpfile) {die "\n$usage\n"};

my %beads;

tie my %ints,"Tie::IxHash";
open BP, "<$bpfile" or die $!;
open INT, "<$intfile" or die $!;
open OUT, ">$out"or die $!;

while (my $line= <BP>) {

  chomp $line;
  my @bp = split(/,/,$line);
  $beads{$bp[0]} = $bp[2];

}

close BP;

#my ($snp, @array)
my @intensities;
while (my $line = <INT>){

  chomp $line;
  my $LABELS_REGEX =qr(^SNP\s+Coor);
  if ($line !~ $LABELS_REGEX) {
   
   my ($snp, $coor, $allele,@array) = split(/\t/,$line);
   $ints{$snp} = \@array;
   @intensities = @array;
   
   }
   
}

close INT;

foreach my $snp(keys %ints) {

    foreach my $snpbs(keys %beads){
    
      if($snp eq $snpbs){
      
         my @ints;
         for(my $i = 0;$i<scalar(@intensities);$i++) {
	 
	  push @ints, $ints{$snp}[$i] ;
	 
	 } 
         
	print OUT "$beads{$snpbs}\t$snp\t", join("\t",@ints), "\n";
	
      }
      #print OUT "\n";
    }
    
    
}