#!/usr/bin/env perl

=head1 NAME

descaffold_assembly

=head1 SYNOPSIS

descaffold_assembly - Given an assembly in FASTA format, output a descaffolded assembly.

=head1 DESCRIPTION

Given an assembly in FASTA format, output a descaffolded assembly.

=head1 CONTACT

path-help@sanger.ac.uk

=head1 METHODS

=cut

package FillGapsWithGapFiller::Main;

use lib "/software/pathogen/internal/prod/lib";
use Moose;
use Getopt::Long;
use Bio::AssemblyImprovement::Scaffold::Descaffold;

my ( $assembly_file, $help );

GetOptions(
    'a|assembly=s'        => \$assembly_file,
    'h|help'              => \$help,
);

( defined($assembly_file) && ( -e $assembly_file ) && !$help ) or die <<USAGE;
Usage: descaffold_assembly [options]
Given an assembly in multi FASTA format, output a descaffolded assembly.

# outputs a file called contigs.scaffolded.fa
descaffold_assembly -a contigs.fa 

# This help message
descaffold_assembly -h

USAGE


my $descaffold_obj = Bio::AssemblyImprovement::Scaffold::Descaffold->new(input_assembly => $assembly_file);
$descaffold_obj->run();
