#!/usr/bin/env perl
package Bio::AssemblyImprovement::Bin::DescaffoldAssembly;

# ABSTRACT: Given an assembly in FASTA format, output a descaffolded assembly.
# PODNAME: descaffold_assembly


BEGIN { unshift( @INC, '../lib' ) }
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();

__END__

=pod

=head1 NAME

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

=head1 VERSION

version 1.132610

=head1 SYNOPSIS

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

   descaffold_assembly -a contigs.fa

=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
