my $self = shift;

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


  $self->debug("CaenorhabditisBriggsae Specific: loading contig/clone " .
               "assembly relationship");

  my $asm_sth = $dbh->prepare
    ("INSERT INTO $target.assembly " .
     "set asm_seq_region_id = ?, ".
     "    asm_start = ?, " .
     "    asm_end   = ?, " .
     "    cmp_seq_region_id = ?, ".
     "    cmp_start = ?, " .
     "    cmp_end   = ?, " .
     "    ori       = ?");

  # get a list of the contigs that have clones, their ids, and the
  # corresponding clone ids
  my $ctg_sth = $dbh->prepare
    ("SELECT ctg.name, ctg.contig_id, ctg.length, cln.new_id " .
     "FROM   $source.contig ctg, $target.tmp_cln_map cln " .
     "WHERE  ctg.name not like 'c%' " .  # only contigs w/ proper accessions
     "AND    ctg.clone_id = cln.old_id");

  $ctg_sth->execute();

  my ($ctg_name, $ctg_id, $ctg_len, $cln_id);

  $ctg_sth->bind_columns(\$ctg_name,\$ ctg_id,\$ ctg_len,\$ cln_id);

  while($ctg_sth->fetch()) {
    my (undef,$cln_start, $cln_end) = split(/\./, $ctg_name);
    my $cln_len = $cln_end - $cln_start + 1;
    if($cln_len != $ctg_len) {
      die("Contig len $ctg_len != Clone len $cln_len");
    }

    $asm_sth->execute($cln_id, $cln_start, $cln_end,
                      $ctg_id, 1, $ctg_len, 1);
  }

  $ctg_sth->finish();
  $asm_sth->finish();

  return;
}



#
# Override contig_to_seq_region and clone_to_seq_region to provide 
# briggsae 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';

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

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

#   #There are two types of contigs in briggsae:

#   #
#   # cosmids/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();

#   #
#   # WGS contigs
#   #
#   $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;
  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("CaenorhabditisBriggsae Specific: Transforming " .
               "chromosomes into $target_cs_name seq_regions");


  ## For consistancy with mart and v19 we need to keep chr name the same for
  ## now, so the following section is commented out and replaced:
  ##strip off the leading 'cb25.' from the chromosome name
  #my $select_sth = $dbh->prepare
  #  ("SELECT chromosome_id,substring(name,6),length FROM $source.chromosome");

  my $select_sth = $dbh->prepare
    ("SELECT chromosome_id,name,length FROM $source.chromosome");


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

  $self->debug("CaenorhabditisBriggsae 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 clones with proper embl accessions.  Also for some reason the embl_offset
  # is not set in the briggsae 17/18/19 databases, which means we have to deduce the
  # length from the name of the contigs!
  #
  my $select_sth = $dbh->prepare
    ("SELECT cl.clone_id,
             CONCAT(cl.embl_acc, '.', cl.embl_version),
             ctg.name
     FROM   $source.clone cl, $source.contig ctg
		 WHERE  cl.clone_id = ctg.clone_id
     AND    cl.embl_acc not like 'c%'
     ORDER BY cl.clone_id");

  $select_sth->execute();

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

  my $highest_end = undef;
  my $current_clone = undef;
  my $current_clone_id = undef;
  my $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()) {
    #extract the end position of the contig
    my $ctg_end;
    (undef,undef,$ctg_end) = split(/\./, $ctg_name);

    if(!defined($current_clone)) {
      $current_clone = $embl_acc;
      $current_clone_id = $clone_id;
      $highest_end   = $ctg_end;
    }

    if($current_clone ne $embl_acc) {
      #started new clone, store last one

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

      $current_clone = $embl_acc;
      $current_clone_id = $clone_id;
      $highest_end = $ctg_end;
    } elsif($ctg_end > $highest_end) {
      #same clone, adjust end if end of contig is highest yet seen
      $highest_end = $ctg_end;
    }
  }

  #insert the last clone
  $insert_sth->execute($current_clone, $cs_id, $highest_end);
  $tmp_insert_sth->execute($current_clone_id, $insert_sth->{'mysql_insertid'});


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

  return;
}


1;

  my $self = shift;

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

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




#
# Override the assembly contig clone method because the briggsae database
# does not have any embl_offsets
#

  my $self = shift;

  $self->debug("CaenorhabditisBriggsae Specific: creating clone, scaffold," .
              " and contig coordinate systems");

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

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

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

  my @assembly_mappings =  ("scaffold:$ass_def|contig",
                            "clone|contig",
                            "scaffold:$ass_def|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("CaenorhabditisBriggsae Specific: creating contig, " .
               "clone, contig and scaffold seq_regions");

  $self->contig_to_seq_region();
  $self->clone_to_seq_region();
  $self->chromosome_to_seq_region('scaffold');