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            ### $contig_seq

            # add contig seq to database
            $ali->add_seq(
                Seq->new( seq_id => $contig_id, seq => $contig_seq )
            );
        }
    }

    # store contig database for org
    (my $outfile = $org) =~ tr/ /_/;
        $outfile .= '_new_cap3.fasta';
    $ali->store( file($outdir, $outfile) );
}

__END__

=pod

=head1 NAME

compress-db.pl - Post-process assembler for transcript enrichment using 42

=head1 VERSION

version 0.213470

=head1 USAGE

    compress.pl --config=<file> --indir=<dir> [optional arguments]

=head1 REQUIRED ARGUMENTS

=over

=item --config=<file>

Path to YAML C<config> file for 42.

=for Euclid: file.type: string

=item --indir=<dir>

Path to input tax-report files.

=for Euclid: dir.type: str

=back

=head1 OPTIONAL ARGUMENTS

=item --cap3-o=<n>

Overlap length cutoff for CAP3 (should be > 15) [default: 40].

=for Euclid: n.type:    n > 15
    n.default: 40

=item --cap3-p=<n>

Overlap percent identity cutoff for CAP3 (should be > 65) [default: 90].

=for Euclid: n.type:    n > 65
    n.default: 90

=item --verbosity=<level>

Verbosity level for logging to STDERR [default: 0]. Available levels range from
0 to 6. Level 6 corresponds to debugging mode.

=for Euclid: level.type: int, level >= 0 && level <= 6
    level.default: 1

=item --version

=item --usage

=item --help

=item --man

=over

Print the usual program information

=back

=head1 AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

=head1 COPYRIGHT AND LICENSE

This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.

=cut