my $self = shift;
  my $target_cs_name = shift;

  my $target = $self->target();
  my $source = $self->source();
  my $dbh    = $self->dbh();

  $target_cs_name ||= "chromosome";
  my $cs_id = $self->get_coord_system_id($target_cs_name);

  $self->debug("GallusGallus Specific: Transforming chromosomes into $target_cs_name seq_regions");

  # only take chromosomes which are actually in the assembly table
  my $select_sth = $dbh->prepare
    ("SELECT c.chromosome_id, c.name, c.length " .
     "FROM $source.chromosome c, $source.assembly a " .
     "WHERE c.chromosome_id = a.chromosome_id group by c.chromosome_id");

  my $insert_sth = $dbh->prepare
    ("INSERT INTO $target.seq_region (name, coord_system_id, length) " .
     "VALUES (?,?,?)");

  my $tmp_insert_sth = $dbh->prepare
    ("INSERT INTO $target.tmp_chr_map (old_id, new_id) VALUES (?, ?)");

  $select_sth->execute();

  my ($chrom_id, $name, $length);
  $select_sth->bind_columns(\$chrom_id,\$ name,\$ length);

  while ($select_sth->fetch()) {
    #insert into seq_region table
    $insert_sth->execute($name, $cs_id, $length);
    #copy old/new mapping into temporary table
    $tmp_insert_sth->execute($chrom_id, $insert_sth->{'mysql_insertid'});
  }

  $select_sth->finish();
  $insert_sth->finish();
  $tmp_insert_sth->finish();

  return;

  my $self = shift;
  my $target_cs_name = shift;

  my $target = $self->target();
  my $source = $self->source();
  my $dbh     = $self->dbh();

  $target_cs_name ||= 'contig';

  $self->debug("GallusGallus Specific: Transforming contigs into " .
               "$target_cs_name seq_regions");

  my $cs_id = $self->get_coord_system_id($target_cs_name);

  # this ugly SQL simply takes the first part of the contig name
  # but trims everything after and including the second dot
  my $sth = $dbh->prepare
    ("INSERT INTO $target.seq_region " .
     "SELECT contig_id, SUBSTRING(name,1, LOCATE('.',name) + LOCATE('.',SUBSTRING(name,LOCATE('.',name)+1)) -1), $cs_id, length FROM $source.contig");

  $sth->execute();
  $sth->finish();
}

#
# overridden so that left over garbage in chromosome table is not used
#

  my $self = shift;

  $self->debug("GallusGallus Specific: loading assembly data");
  $self->assembly_contig_chromosome();
  $self->assembly_contig_supercontig();
}




1;

  my $self = shift;

  $self->debug("GallusGallus Specific: loading assembly data");

  my $target = $self->target();
  my $dbh    = $self->dbh();

  my $ass_def = $self->get_default_assembly();

  my @coords =
    (["chromosome" ,  $ass_def, "default_version", 1 ],
     ["supercontig",  $ass_def, "default_version", 2 ],
     ["contig"     ,  undef   , "default_version,sequence_level", 3]);

  my @assembly_mappings =  ("chromosome:$ass_def|contig",
                            "supercontig:$ass_def|contig",
                            "chromosome:$ass_def|contig|supercontig:$ass_def");

  $self->debug("Building coord_system table");

  my $sth = $dbh->prepare("INSERT INTO $target.coord_system " .
                           "(name, version, attrib, rank) VALUES (?,?,?,?)");

  my %coord_system_ids;

  foreach my $cs (@coords) {
    $sth->execute(@$cs);
    $coord_system_ids{$cs->[0]} = $sth->{'mysql_insertid'};
  }
  $sth->finish();

  $self->debug("Adding assembly.mapping entries to meta table");

  $sth = $dbh->prepare("INSERT INTO $target.meta(meta_key, meta_value) " .
                       "VALUES ('assembly.mapping', ?)");

  foreach my $mapping (@assembly_mappings) {
    $sth->execute($mapping);
  }

  $sth->finish();

  return;

  my $self = shift;

  $self->debug("GallusGallus Specific: creating contig, " .
               "clone, chromosome and supercontig seq_regions");

  $self->contig_to_seq_region();
  $self->chromosome_to_seq_region();
  $self->supercontig_to_seq_region();
}

#
# overridden to do trimming of contig names
#