#!/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 sequences in the stream into subsequences.

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


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


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


my ( $options, $in, $out, $record, $new_record, $i, $step, $subseq, $subqual );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'word_size', short => 'w', type => 'uint', mandatory => 'no', default => 7, allowed => undef, disallowed => 0 },
        { long => 'step_size', short => 's', type => 'uint', mandatory => 'no', default => 1, allowed => undef, disallowed => 0 },
    ]   
);

if ( $options->{ "step_size" } > $options->{ "word_size" } ) {
    Maasha::Common::error( qq(step_size > word_size: $options->{ "step_size" } > $options->{ "word_size" } ) );
}

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

$step = $options->{ "step_size" };

while ( $record = Maasha::Biopieces::get_record( $in ) ) 
{
    if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
    {
        for ( $i = 0; $i < length( $record->{ "SEQ" } ) - $options->{ "word_size" } + 1; $i += $step )
        {
            $subseq  = substr $record->{ "SEQ" }, $i, $options->{ "word_size" };
            $subqual = substr $record->{ "SCORES" }, $i, $options->{ "word_size" } if $record->{ "SCORES" };

            $new_record->{ "SEQ_NAME" } = $record->{ "SEQ_NAME" } . "[" . ( $i + 1 ) . "-" . ( $i + $options->{ "word_size" } ) . "]";
            $new_record->{ "SEQ" }      = $subseq;
            $new_record->{ "SCORES" }   = $subqual if $record->{ "SCORES" };
            $new_record->{ "SEQ_LEN" }  = $options->{ "word_size" };

            Maasha::Biopieces::put_record( $new_record, $out );
        }
    }
    else
    {
        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__