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

# Read FASTQ entries from one or more files.

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


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


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


my ( $options, $in, $out, $record, $data_in, $num, $entry );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'num',     short => 'n', type => 'uint',   mandatory => 'no', default => undef, allowed => undef, disallowed => 0     },
        { long => 'quality', short => 'q', type => 'uint',   mandatory => 'no', default => 20,    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 );
}

if ( $options->{ 'data_in' } )
{
    $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );

    $num = 1;

    while ( $entry = Maasha::Fastq::get_entry( $data_in ) ) 
    {
        if ( $record = Maasha::Fastq::fastq2biopiece( $entry ) )
        {
            lowercase_low_scores( $record, $options->{ 'quality' } );

            Maasha::Biopieces::put_record( $record, $out );
        }

        last if $options->{ "num" } and $num == $options->{ "num" };

        $num++;
    }

    close $data_in;
}

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


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


sub lowercase_low_scores
{
    # Martin A. Hansen, July 2009.

    # Lowercase residues in sequence that are below a given score threshold.

    # This one would be lovely to have written in C.

    my ( $record,    # Biopiece record
         $quality,   # quality threshold
       ) = @_;

    # Returns nothing.

    my ( @seqs, @scores, $i );

    @seqs   = split //, $record->{ 'SEQ' };
    @scores = split /;/, $record->{ 'SCORES' };

    for ( $i = 0; $i < @scores; $i++ ) {
        $seqs[ $i ] = lc $seqs[ $i ] if $scores[ $i ] < $quality;
    }

    $record->{ 'SEQ' }    = join "",  @seqs;
    $record->{ 'SCORES' } = join ";", @scores;
}


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


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


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


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


__END__