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

# Intersect records in the stream based on overlapping intervals contained in values to specific keys.

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


use warnings;
use strict;
use Maasha::Biopieces;
use Data::Dumper;


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


my ( $options, $in, $out, $record, $opt_key, $opt_strand, $found, $pos, $lookup_hash );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'key',     short => 'k', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
        { long => 'strand',  short => 's', type => 'flag',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
        { long => 'inverse', 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" } );

$opt_key    = $options->{ 'key' };
$opt_strand = $options->{ 'strand' };

while ( $record = Maasha::Biopieces::get_record( $in ) ) 
{
    if ( exists $record->{ 'S_ID' } and exists $record->{ 'S_BEG' } and exists $record->{ 'S_END' } )
    {
        $record->{ 'STRAND' } ||= '.';

        if ( exists $record->{ $opt_key } )
        {
            map { $lookup_hash->{ $record->{ 'S_ID' } }->{ $record->{ 'STRAND' } }->{ $_ } = 1 } ( $record->{ 'S_BEG' } .. $record->{ 'S_END' } );
        }
        else
        {
            $found = 0;

            foreach $pos ( $record->{ 'S_BEG' } .. $record->{ 'S_END' } )
            {
                if ( $opt_strand )
                {
                    if ( exists $lookup_hash->{ $record->{ 'S_ID' } }->{ $record->{ 'STRAND' } }->{ $pos } )
                    {
                        $found = 1;

                        last;
                    }
                }
                else
                {
                    if ( exists $lookup_hash->{ $record->{ 'S_ID' } }->{ '+' }->{ $pos } or
                         exists $lookup_hash->{ $record->{ 'S_ID' } }->{ '-' }->{ $pos }
                    )
                    {
                        $found = 1;

                        last;
                    }
                }
            }

            if ( (     $found and not $options->{ 'inverse' } ) or
                 ( not $found and     $options->{ 'inverse' } )
            )
            {
                Maasha::Biopieces::put_record( $record, $out );
            }
        }
    }
}

# print Dumper( $lookup_hash );

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


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


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


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


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


__END__