my $self = shift;

    my $pop_MOPTI; #population_id for the mopti strain
    my $pop_PEST;  #population_id for the pest strain
    #first of all, add to the population table the 2 strains: PEST and MOPTI
    foreach my $population_name (keys %STRAINS){
      $self->{'dbVariation'}->do(qq{INSERT INTO sample (name,description)
				    VALUES ('$population_name', '$STRAINS{$population_name}')});
      #store in the same hash the id for the population
      $STRAINS{$population_name} = $self->{'dbVariation'}->{'mysql_insertid'};
    }
    #and copy the data from the sample to the Population table
    debug("Loading population table with data from sample");
    $self->{'dbVariation'}->do(qq{INSERT INTO population (sample_id,is_strain) 
				  SELECT sample_id, 1
				  FROM sample
				 });
    

    #then, get from dbSNP the relation between ssId and mopti/pest strain
    debug("Dumping strain information from dbSNP");

    dumpSQL($self->{'dbSNP'}, qq{SELECT subsnp_id, loc_snp_id
				 FROM SubSNP
				});
    
    create_and_load($self->{'dbVariation'},'tmp_strain', "subsnp_id i*", "strain");

    debug("Updating allele table with strain alleles");
    #first, update the MOPTI alleles
    $self->{'dbVariation'}->do(qq{UPDATE allele , variation_synonym, tmp_strain
				      SET allele.sample_id = $STRAINS{'MOPTI'}, allele.frequency = 1
				      WHERE allele.variation_id = variation_synonym.variation_id
				      AND SUBSTRING(variation_synonym.name,3) = tmp_strain.subsnp_id
				      AND tmp_strain.strain like '%mopti%'
				  });

    #and do the same for the PEST alleles
    $self->{'dbVariation'}->do(qq{UPDATE allele , variation_synonym, tmp_strain
				      SET allele.sample_id = $STRAINS{'PEST'}, allele.frequency = 1
				      WHERE allele.variation_id = variation_synonym.variation_id
				      AND SUBSTRING(variation_synonym.name,3) = tmp_strain.subsnp_id
				      AND tmp_strain.strain like '%pest%'
				  });
    
    #and finally, drop the temporary table
    $self->{'dbVariation'}->do(qq{DROP TABLE tmp_strain});

    my $self = shift;
    #first, dump all dbSNP data as usual
    $self->SUPER::dump_dbSNP();
    #then, get strain information
    $self->add_strains();

    my $self = shift;

    my %scaff; #contains relation AAAB -> NW
    open(IN,"gzip -dc dbSNP/scaff_NW_chr_CRA_AAAB.gz |") || die "Could not get file with scaff mapping data: $!\n";
    my @line;
    while (<IN>){
	chomp;
	@line = split /\t/;
	$scaff{$line[3]} = $line[0];
    }
    ### TBD not sure if variations with map_weight > 1 or 2 should be
    ### imported.
    debug("Dumping seq_region data");
    my $sth = $self->{'dbCore'}->dbc()->prepare(qq{SELECT sr.seq_region_id, sr.name
						 FROM   seq_region sr, coord_system cs
						 WHERE sr.coord_system_id = cs.coord_system_id
						 AND cs.name = "scaffold"});
    $sth->execute();
    open(FH,">" . $self->{'tmpdir'} . '/' . $self->{'tmpfile'}); #open the file with the data dump from the core database

    my ($tablename1,$tablename2,$row);

    while($row = $sth->fetchrow_arrayref()) {
	my @row = @$row;
	$row[1] = $scaff{$row[1]} if (defined $scaff{$row[1]});
	@row = map {(defined($_)) ? $_ : '\N'} @row;  # convert undefined to NULL;
	print FH join("\t", @row), "\n";
    }

    $sth->finish();
    close(FH);

    debug("Loading seq_region data");
    create_and_load($self->{'dbVariation'}, "tmp_seq_region", "seq_region_id", "name *");

    debug("Dumping SNPLoc data");

    
    my ($assembly_version) =  $self->{'assembly_version'} =~ /^[a-zA-Z]+(\d+)\.*.*$/; $assembly_version=2;
    print "assembly_version again is $assembly_version\n";

    my $sth1 = $self->{'dbSNP'}->prepare(qq{SHOW TABLES LIKE 
					 '$self->{'dbSNP_version'}\_SNPContigLoc\_$assembly_version\__'});
    $sth1->execute();

    while($row = $sth1->fetchrow_arrayref()) {
      $tablename1 = $row->[0];
    }

    my $sth2 = $self->{'dbSNP'}->prepare(qq{SHOW TABLES LIKE 
					   '$self->{'dbSNP_version'}\_ContigInfo\_$assembly_version\__'});
    $sth2->execute();

    while($row = $sth2->fetchrow_arrayref()) {
      $tablename2 = $row->[0];
    }
    print "table_name1 is $tablename1 table_name2 is $tablename2\n";

    dumpSQL($self->{'dbSNP'}, qq{SELECT t1.snp_id, t2.contig_acc,
				 t1.lc_ngbr+2,t1.rc_ngbr,
				 IF(orientation, -1, 1)
				 FROM   $tablename1 t1, $tablename2 t2
				 WHERE t1.ctg_id=t2.ctg_id
				 $self->{'limit'}});
    
    debug("Loading SNPLoc data");
    
    create_and_load($self->{'dbVariation'}, "tmp_contig_loc", "snp_id i*", "contig *", "start i", 
		    "end i", "strand i");
    
    #creating the temporary table with the genotyped variations

     $self->{'dbVariation'}->do(qq{CREATE TABLE tmp_genotyped_var SELECT DISTINCT variation_id FROM tmp_individual_genotype_single_bp});
     $self->{'dbVariation'}->do(qq{CREATE UNIQUE INDEX variation_idx ON tmp_genotyped_var (variation_id)});
     $self->{'dbVariation'}->do(qq{INSERT IGNORE INTO  tmp_genotyped_var SELECT DISTINCT variation_id FROM individual_genotype_multiple_bp});



    debug("Creating variation_feature data");
    
    $self->{'dbVariation'}->do(qq{INSERT INTO variation_feature 
				      (variation_id, seq_region_id,
				       seq_region_start, seq_region_end, seq_region_strand,
				       variation_name, flags, source_id, validation_status)
				      SELECT v.variation_id, ts.seq_region_id, tcl.start, tcl.end,
				      tcl.strand, v.name, IF(tgv.variation_id,'genotyped',NULL), v.source_id, v.validation_status
				      FROM   variation v LEFT JOIN tmp_genotyped_var tgv ON v.variation_id = tgv.variation_id, tmp_contig_loc tcl, tmp_seq_region ts
				      WHERE  v.snp_id = tcl.snp_id
				      AND    tcl.contig = ts.name});
    
    $self->{'dbVariation'}->do("DROP TABLE tmp_contig_loc");
    $self->{'dbVariation'}->do("DROP TABLE tmp_seq_region");
    $self->{'dbVariation'}->do("DROP TABLE tmp_genotyped_var");
}

1;