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}

sub final_output_filename
{
  my ($self) = @_;
  my ( $filename, $directories, $suffix ) = fileparse( $self->input_assembly, qr/\.[^.]*/ );
  return $self->output_base_directory.'/' . $filename . "." . $self->_output_prefix . $suffix; 
}

sub run {
    my ($self) = @_;
    $self->output_base_directory();
    my $original_cwd = getcwd();
    chdir( $self->_temp_directory );

    copy( $self->input_assembly, $self->_intermediate_filename );

    for my $merge_size ( @{ $self->merge_sizes } ) {
        $self->_single_scaffolding_iteration($merge_size);
    }
    chdir($original_cwd);
    move( $self->_intermediate_filename, $self->final_output_filename );
    return $self;
}

no Moose;
__PACKAGE__->meta->make_immutable;
1;

__END__

=pod

=encoding UTF-8

=head1 NAME

Bio::AssemblyImprovement::Scaffold::SSpace::Iterative - Iteratively run SSpace.

=head1 VERSION

version 1.160490

=head1 SYNOPSIS

Iteratively run SSpace.

   use Bio::AssemblyImprovement::Scaffold::SSpace::Iterative;
   my $iterative_scaffolding = Bio::AssemblyImprovement::Scaffold::SSpace::Iterative->new(
     input_files => ['abc_1.fastq', 'abc_2.fastq'],
     input_assembly => 'contigs.fa'
     insert_size => 250,
     scaffolder_exec => '/path/to/SSPACE.pl',
     merge_sizes => [100,50,30,10]
   )->run;

=head1 METHODS

=head2 run

Run the iterations of SSpace

=head1 SEE ALSO

=for :list * L<Bio::AssemblyImprovement::Scaffold::SSpace::Config>
* L<Bio::AssemblyImprovement::Scaffold::SSpace::Main>

=head1 AUTHOR

Andrew J. Page <ap13@sanger.ac.uk>

=head1 COPYRIGHT AND LICENSE

This software is Copyright (c) 2012 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007

=cut