use strict;
use warnings ;
use Getopt::Long;
use Database::Conn #Its a private module 

my $conn;
my $snp_list = {};
my $ind_list = {};
eval {

 $conn = Sanger::CGP::Database::Conn->new('live');
 $conn->addConnection(DBI->connect('dbi:Oracle:SNP.world','snp','snp', {RaiseError =>1 , AutoCommit=>0}),'snp');
 
 my $snparray = $conn->executeArrRef('snp::Sequenom::getSnpsforPlex');


#get the list of snps and ids id for the plexes 
 foreach my $snp (@ {$snparray} ) {

  $snp_list->{$snp->[0]} = $snp->[1];

 }
#fetch all the sample fer the study 6637 CGPP that has gone through sequenom.
 my $indsent = $conn->executeArrRef('snp::Sequenom::getIndForPlateSent');
 foreach my $ind ( @ { $indsent } ) {
  
	$ind_list->{$ind->[1]} = $ind->[0];

 }

 foreach my $id_ind ( sort keys % { $ind_list } ) {

	foreach my $snpname ( sort keys % { $snp_list } ) {
		print "$snpname|$id_ind|$ind_list->{$id_ind}\n"; #I get 3072 samples(as expected) if  I don't have the next ine to get the genotype from DB
		#my $genotype = $conn->executeHashRef('snp::Sequenom::getGenotypeCalls', $id_ind , $snp_list->{$snpname});
		#print "$snpname|$id_ind|$ind_list->{$id_ind}|" , join "|", values %$genotype, "\n" if (defined $genotype) ; #I get only 288 samples with or without genotyp calls.
		#print "$snpname|$id_ind|$ind_list->{$id_ind}\n" if (!$genotype);

	}# end of foreach %$snp_list




 }# end of foreach %$ind_list

}; #end of eval block