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

# Intersects two tracks in the Biopieces Genome Browser.

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


use warnings;
use strict;
use Data::Dumper;
use Maasha::Biopieces;
use Maasha::BGB::Track;
use Maasha::KISS;


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


my ( $user, $options, $in, $out, $record, @contigs, $contig, $track, @tracks, %hash, $fh1, $fh2, $entries, $entry );

$user    = Maasha::Biopieces::biopiecesrc( "BGB_USER" );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'user',     short => 'u', type => 'string', mandatory => 'no',  default => $user, allowed => undef, disallowed => undef },
        { long => 'clade',    short => 'c', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
        { long => 'genome',   short => 'g', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
        { long => 'assembly', short => 'a', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
        { long => 'track1',   short => 't', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
        { long => 'track2',   short => 'T', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
        { long => 'invert',   short => 'i', 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" } );

while ( $record = Maasha::Biopieces::get_record( $in ) )
{
    Maasha::Biopieces::put_record( $record, $out );
}

Maasha::Common::error( qq(Bad user: "$options->{ 'user' }") ) if not grep /^$options->{ 'user' }$/, Maasha::BGB::Track::list_users();

@contigs = Maasha::BGB::Track::list_contigs( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' } );

foreach $contig ( @contigs )
{
    undef %hash;

    @tracks = Maasha::BGB::Track::list_track_dir( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' }, $contig );

    foreach $track ( @tracks )
    {
        if ( index( $track, $options->{ 'track1' } ) >= 0 ) {
            $hash{ '1' } = $track;
        } elsif ( index( $track, $options->{ 'track2' } ) >= 0 ) {
            $hash{ '2' } = $track;
        }
    }

    if ( exists $hash{ '1' } and exists $hash{ '2' } )
    {
        print STDERR "Intersecting:\n$hash{ '1' } and\n$hash{ '2' }\n\n" if $options->{ 'verbose' };

        $fh1 = Maasha::Filesys::file_read_open( "$hash{ '1' }/track_data.kiss" );
        $fh2 = Maasha::Filesys::file_read_open( "$hash{ '2' }/track_data.kiss" );

        $entries = Maasha::KISS::kiss_intersect( $fh1, $fh2, $options->{ 'invert' } );

        foreach $entry ( @{ $entries } )
        {
            if ( $record = Maasha::KISS::kiss2biopiece( $entry ) ) {
                 Maasha::Biopieces::put_record( $record, $out );
            }
        }
    }
}

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


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


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


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


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


__END__