my $runnable = Bio::EnsEMBL::Analysis::Runnable::CPG->new
  (
   -query => $slice,
   -program => 'cpg',
  );
  $runnable->run;
  my @simple_features = @{$runnable->output};

  my $self = shift;
  $self->{'min_gc_content'} = shift if(@_);
  return $self->{'min_gc_content'};

  my $self = shift;
  $self->{'min_length'} = shift if(@_);
  return $self->{'min_length'};

  my $self = shift;
  $self->{'min_oe'} = shift if(@_);
  return $self->{'min_oe'};

  my ($class,@args) = @_;
  my $self = $class->SUPER::new(@args);

  my ($min_length, $min_gc, $min_oe) = rearrange(['MIN_LENGTH',
                                                  'MIN_GC_CONTENT',
                                                  'MIN_OE',
                                                 ], @args);
  ##################
  #SETTING DEFAULTS#
  ##################
  $self->program('cpg') if(!$self->program);
  $self->min_length(400);
  $self->min_gc_content(50);
  $self->min_oe(0.6);
  #################

  $self->min_length($min_length) if($min_length);
  $self->min_gc_content($min_gc) if($min_gc);
  $self->min_oe($min_oe) if($min_oe);
  return $self;

  my ($self, $results) = @_;

  if(!$results){
    $results = $self->resultsfile;
  }
  my $ff = $self->feature_factory;
  if(!-e $results){
    throw("Can't parse an no existance results file ".$results.
          " CPG:parse_results");
  }
  my @output;
  open(CPG, $results) or throw("FAILED to open ".$results.
                               " CPG:parse_results");
  LINE:while(<CPG>){
    if (/\d+/){ #ignore introductory lines
      chomp;
      my @elements = split;
      my ($name, $start, $end, $score, $gc_content, $oe) 
        = @elements[0, 1, 2, 3, 6, 7];
      if($oe eq "-"){ 
        $oe = 0; 
      }
      my $length = $end - $start + 1;
      next LINE unless($length >= $self->min_length && 
                       $gc_content >= $self->min_gc_content &&
                       $oe >= $self->min_oe);
      my $sf = $ff->create_simple_feature($start, $end, 0, $score,
                                          "oe = $oe", $name, 
                                          $self->query); 
      push(@output, $sf);
    }
  }
  $self->output(\@output);
  close(CPG) or throw("FAILED to close ".$results.
                      " CPG:parse_results");
}


1;

  Arg [1]   : Bio::EnsEMBL::Analysis::Runnable::CPG
  Arg [2]   : int, minimun value
  Function  : container for specified variable. This pod refers to the
  three methods below min_length, min_gc_content, min_oe. These are simple 
  containers which dont do more than hold and return an given value
  nothing is defined
  Returntype: int
  Exceptions: 
  Example   :