#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Find all matches between sequences in the stream.

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


use warnings;
use strict;
use Maasha::Biopieces;
use Maasha::Match;


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


my ( $options, $in, $out, $record, @entries, $results, $tmp_dir );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'word_size', short => 'w', type => 'uint',   mandatory => 'no', default => 20,     allowed => undef,                  disallowed => 0 },
        { long => 'direction', short => 'd', type => 'string', mandatory => 'no', default => 'both', allowed => 'both,forward,reverse', disallowed => undef },
    ]   
);

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

$tmp_dir = Maasha::Biopieces::get_tmpdir();

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

    Maasha::Biopieces::put_record( $record, $out );
}

if ( @entries == 1 )
{
    $results = Maasha::Match::match_mummer( [ $entries[ 0 ] ], [ $entries[ 0 ] ], $options, $tmp_dir );

    map { Maasha::Biopieces::put_record( $_, $out ) } @{ $results };
}
else
{
    $results = Maasha::Match::match_mummer( [ shift @entries ], \@entries, $options, $tmp_dir );

    map { Maasha::Biopieces::put_record( $_, $out ) } @{ $results };
}

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


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


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


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


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


__END__