return 1;

  my $self = shift;

  return unless(defined($self->{'genome_db'}));
  
  print("calc_inter_genic_distance for '", $self->{'genome_db'}->name(), "'\n");

  my $memberDBA = $self->{'comparaDBA'}->get_MemberAdaptor();
  $memberDBA->_final_clause("ORDER BY m.chr_name, m.chr_start");
  my $sortedMembers = $memberDBA->fetch_by_source_taxon('ENSEMBLGENE', $self->{'genome_db'}->taxon_id);
  print(scalar(@{$sortedMembers}) . " members to process\n");

  my $intergenic_stats = Statistics::Descriptive::Full->new();
  my $genesize_stats = Statistics::Descriptive::Full->new();
  my $overlapCount=0;
  
  my $lastMember = shift @{$sortedMembers};
  #$lastMember->print_member;
  foreach my $member (@{$sortedMembers}) {
    #$member->print_member;
    $genesize_stats->add_data($member->chr_end - $member->chr_start);

    if($lastMember->chr_name ne $member->chr_name) {
      print("broken syntenty from\n ");
      $lastMember->print_member;
      $member->print_member;
    }
    else {
      my $dist = ($member->chr_start - $lastMember->chr_end);
      if($dist < 0) { $dist=0; $overlapCount++; }
      $intergenic_stats->add_data($dist);
    }
    $lastMember = $member;
  }

  $intergenic_stats->{'overlapCount'} = $overlapCount;
  
  print("intergenic overlap = ",$overlapCount,"\n");
  print("intergenic overlap = ",$intergenic_stats->{'overlapCount'},"\n");

  $self->insert_statistics($intergenic_stats, 'intergenic');
  $self->insert_statistics($genesize_stats, 'gene_size');

 return 20;

  my( $self) = @_;

  $self->throw("No input_id") unless defined($self->input_id);
  print("input_id = ".$self->input_id."\n");
  $self->throw("Improper formated input_id") unless ($self->input_id =~ /{/);

  my $input_hash = eval($self->input_id);
  my $genome_db_id = $input_hash->{'gdb'};
  $self->throw("No genome_db_id in input_id") unless defined($genome_db_id);
  
  #create a Compara::DBAdaptor which shares the same DBI handle
  #with the pipeline DBAdaptor that is based into this runnable
  $self->{'comparaDBA'} = Bio::EnsEMBL::Compara::DBSQL::DBAdaptor->new(-DBCONN => $self->db->dbc);

  #get the Compara::GenomeDB object for the genome_db_id
  $self->{'genome_db'} = $self->{'comparaDBA'}->get_GenomeDBAdaptor->fetch_by_dbID($genome_db_id);
  
  
  return 1;

  my $self = shift;
  my $stats = shift;
  my $dataType = shift; 
  
  my $sql = "INSERT ignore INTO genome_db_stats SET data_type='$dataType'"
            ." ,genome_db_id=".$self->{'genome_db'}->dbID
            ." ,count='".$stats->count()."'"
            ." ,mean='".$stats->mean()."'"
            ." ,median='".$stats->median()."'"
            ." ,mode='".$stats->mode()."'"
            ." ,stddev='".$stats->standard_deviation()."'"
            ." ,variance='".$stats->variance()."'"
            ." ,min='".$stats->min()."'"
            ." ,max='".$stats->max()."'";

  $sql .=  " ,overlap_count='".$stats->{'overlapCount'}."'" if($stats->{'overlapCount'});

  print("$sql\n");            
  my $sth = $self->db->dbc->prepare($sql);
  $sth->execute;
  $sth->finish;
}


1;

  my $self = shift;

  $self->{'comparaDBA'}->dbc->disconnect_when_inactive(0);
  
  $self->calc_intergenic_stats();
  
  $self->{'comparaDBA'}->dbc->disconnect_when_inactive(1);
                                          
  return 1;

  
  my $self = shift;
  #need to subclass otherwise it defaults to a version that fails
  #just return 1 so success

  return 1;
}


######################################
#
# subroutines
#
#####################################

  Contact Jessica Severin on module implemetation/design detail: jessica@ebi.ac.uk
  Contact Abel Ureta-Vidal on EnsEMBL/Compara: abel@ebi.ac.uk
  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk