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

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

  # target coord_system will have a different ID
  $target_cs_name ||= "clone";
  my $cs_id = $self->get_coord_system_id($target_cs_name);

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

  #
  # We don't want to make clones out of the WGS contigs, only out of
  # the actual BACs with proper embl accessions
  #
  my $select_sth = $dbh->prepare
    ("SELECT cl.clone_id,
             CONCAT(cl.embl_acc, '.', cl.embl_version),
             MAX(ctg.embl_offset+ctg.length-1)
     FROM   $source.clone cl, $source.contig ctg
		 WHERE  cl.clone_id = ctg.clone_id
     AND    cl.embl_acc not like 'C%'
     GROUP BY ctg.clone_id");
 
  $select_sth->execute();

  my ($clone_id, $embl_acc, $length);
  $select_sth->bind_columns(\$clone_id,\$ embl_acc,\$ length);

  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_cln_map (old_id, new_id) VALUES (?, ?)");

  while ($select_sth->fetch()) {
    $insert_sth->execute("$embl_acc", $cs_id, $length);

    #store mapping of old -> new ids in temp table
    $tmp_insert_sth->execute($clone_id, $insert_sth->{'mysql_insertid'});
  }

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

  return;
}


1;

  my $self = shift;

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

  $self->assembly_contig_chromosome();
  $self->assembly_contig_clone();
  $self->assembly_contig_supercontig();
}

#
# Override contig_to_seq_region and clone_to_seq_region to provide 
# mouse specific behaviour
#

# sub contig_to_seq_region {
#   my $self = shift;
#   my $target_cs_name = shift;

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

#   $target_cs_name ||= 'contig';

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

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

#   #There are two types of contigs in mouse:

#   #
#   # Contigs which form BAC clones
#   #
#   my $sth = $dbh->prepare
#     ("INSERT INTO $target.seq_region " .
#      "SELECT contig_id, name, $cs_id, length " .
#      "FROM $source.contig " .
#      "WHERE  name not like 'C%'");

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

#   #
#   # Contigs which were created from whole genome shotgun
#   #
#   $sth = $dbh->prepare
#     ("INSERT INTO $target.seq_region " .
#      "SELECT ctg.contig_id, cln.name, $cs_id, length " .
#      "FROM   $source.contig ctg, $source.clone cln " .
#      "WHERE  ctg.clone_id = cln.clone_id " .
#      "AND    ctg.name like 'C%'");

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

#   return;
# 

  my $self = shift;

  $self->debug("MusMusculus 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", undef   , "default_version"          ,2     ],
     ['clone'      , undef   , 'default_version'          ,3     ],
     ["contig"     , undef   , "default_version,sequence_level",4]);

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

  $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("MusMusculus Specific: creating contig, " .
               "clone, chromosome and supercontig seq_regions");

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