#!/usr/bin/env perl

# Copyright (C) 2007-2009 Martin A. Hansen.

# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.

# http://www.gnu.org/copyleft/gpl.html


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Using the first sequence in the stream as reference, tile all subsequent sequences based on pairwise alignments.

# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


use warnings;
use strict;
use Maasha::Biopieces;
use Maasha::Align;

use constant {
    SEQ_NAME => 0,
    SEQ      => 1,
};


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


my ( $options, $in, $out, $record, $first, $ref_entry, @entries );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'identity',       short => 'i', type => 'uint', mandatory => 'no', default => 70,    allowed => undef, disallowed => 0 },
        { long => 'supress_indels', short => 's', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
    ]   
);

$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );

$first = 1;

while ( $record = Maasha::Biopieces::get_record( $in ) ) 
{
    if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
    {
        if ( $first )
        {
            $ref_entry = [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];

            $first = 0;
        }
        else
        {
            push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
        }
    }
    else
    {
        Maasha::Biopieces::put_record( $record, $out );
    }
}

@entries = Maasha::Align::align_tile( $ref_entry, \@entries, $options );

map { Maasha::Biopieces::put_record( { SEQ_NAME => $_->[ SEQ_NAME ], SEQ => $_->[ SEQ ] }, $out ) } @entries;

Maasha::Biopieces::close_stream( $in );
Maasha::Biopieces::close_stream( $out );


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


BEGIN
{
    Maasha::Biopieces::status_set();
}


END
{
    Maasha::Biopieces::status_log();
}


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


__END__