#!/usr/bin/env perl

# Copyright (C) 2007-2010 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Calculate the mean or local mean of quality SCORES in the stream.

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


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


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


my ( $options, $in, $out, $record );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'local',       short => 'l', type => 'flag',  mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'window_size', short => 'w', type => 'uint',  mandatory => 'no', default => 5,     allowed => undef, disallowed => 0 },
        { long => 'min',         short => 'm', type => 'float', mandatory => 'no', default => 15,    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 ) ) 
{
    if ( $record->{ 'SCORES' } )
    {
        if ( $options->{ "local" } )
        {
            $record->{ 'SCORES_LOCAL_MEAN' } = sprintf( "%.2f", Maasha::Fastq::solexa_str_mean_window(
                                                                    $record->{ 'SCORES' }, 
                                                                    $options->{ 'window_size' }, 
                                                                    $options->{ 'min' }
                                                                ) );
        }
        else
        {
            $record->{ 'SCORES_MEAN' } = sprintf( "%.2f", Maasha::Fastq::solexa_str_mean( $record->{ 'SCORES' } ) );
        }  
    }

    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__