Bio::EnsEMBL::Analysis::Tools::FragmentTranscriptFilter

  my $filter = new Bio::EnsEMBL::Analysis::Tools::FragmentTranscriptFilter->
  new->(
        -coverage => 80,
        -percent_id => 90,
       );

  my @filtered_results = @{$filter->filter_results(\@results)};

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

  my %trans_by_hid;

  foreach my $tran (@$transcripts) {
    # transcript will only have one supporting feature for use cases of this filter
    my ($sf) = @{$tran->get_all_supporting_features};

    next if defined($self->min_score) and $sf->score < $self->min_score;
    next if defined($self->min_percent) and $sf->percent_id < $self->min_percent;

    push @{$trans_by_hid{$sf->hseqname}}, { 
      tran => $tran,
      score => $sf->score,
    };
  }

  my @good_transcripts;

  foreach my $hid (keys %trans_by_hid) {
    # sort transcripts by score
    my @trans = map { $_->{tran} } sort { $b->{score} <=> $a->{score} } @{$trans_by_hid{$hid}};
    
    my (@all_t_sfs);

    TRANSCRIPT:
    foreach my $tran (@trans) {
      my @t_sfs;

      foreach my $exon (@{$tran->get_all_Exons}) {
        my ($sf) = @{$exon->get_all_supporting_features};

        # check that this does not overlap with any of the previous overlap features
        foreach my $f (@all_t_sfs) {
          if ($sf->hstart <= $f->hend and $sf->hend >= $f->hstart) {            
            next TRANSCRIPT;
          }
        }
       
        push @t_sfs, $sf;
      }

      # if we get here, the transcript has passed;
      push @all_t_sfs, @t_sfs;
      push @good_transcripts, $tran;
    }
  }

  return\@ good_transcripts;
}

# containers

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

  return exists($self->{'_min_percent'}) ? $self->{'_min_percent'} : undef;

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

  return exists($self->{'_min_score'}) ? $self->{'_min_score'} : undef;
}



1;

  my ($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  &verbose('WARNING');
  my (
      $min_percent,
      $min_score,
      ) = 
        rearrange([
                   'PERCENT_ID',
                   'SCORE',
                   ], @args); 

  ######################
  #SETTING THE DEFAULTS#
  ######################

  $self->min_percent($min_percent) if defined $min_percent;
  $self->min_score($min_score) if defined $min_score;

  return $self;
}


#filter methods