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

# Split the values of a key into new key/value pairs.

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


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


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


my ( $options, $in, $out, $record, $beg, $end, $len );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'beg', short => 'b', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'end', short => 'e', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'len', short => 'l', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 },
    ]   
);

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

if ( not defined $options->{ "beg" } or $options->{ "beg" } < 0 ) {
    $beg = 0;
} else {
    $beg = $options->{ "beg" } - 1;   # correcting for start offset
}

if ( defined $options->{ "end" } and $options->{ "end" } - 1 < $beg ) {
    $end = $beg - 1;
} elsif ( defined $options->{ "end" } ) {
    $end = $options->{ "end" } - 1;   # correcting for start offset
}

$len = $options->{ "len" };

#    print "beg->$beg,  end->$end,  len->$len\n";

while ( $record = Maasha::Biopieces::get_record( $in ) ) 
{
    if ( $record->{ "SEQ" } )
    {
        if ( defined $beg and defined $end )
        {
            if ( $end - $beg + 1 > length $record->{ "SEQ" } )
            {
                $record->{ "SEQ" }    = substr $record->{ "SEQ" }, $beg;
                $record->{ "SCORES" } = substr $record->{ "SEQ" }, $beg if $record->{ "SCORES" };
            }
            else
            {
                $record->{ "SEQ" }    = substr $record->{ "SEQ" }, $beg, $end - $beg + 1;
                $record->{ "SCORES" } = substr $record->{ "SCORES" }, $beg, $end - $beg + 1 if $record->{ "SCORES" };
            }
        }
        elsif ( defined $beg and defined $len )
        {
            if ( $len > length $record->{ "SEQ" } )
            {
                $record->{ "SEQ" }    = substr $record->{ "SEQ" }, $beg;
                $record->{ "SCORES" } = substr $record->{ "SCORES" }, $beg if $record->{ "SCORES" };
            }
            else
            {
                $record->{ "SEQ" }    = substr $record->{ "SEQ" }, $beg, $len;
                $record->{ "SCORES" } = substr $record->{ "SCORES" }, $beg, $len if $record->{ "SCORES" };
            }
        }
        elsif ( defined $beg )
        {
            $record->{ "SEQ" }    = substr $record->{ "SEQ" }, $beg;
            $record->{ "SCORES" } = substr $record->{ "SCORES" }, $beg if $record->{ "SCORES" };
        }

        $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
    }

    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__