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

# Write nucleotide sequences in 2bit format.

# WARNING WARNING There is a bug that prevents 2bit output to be read by Jim Kents tools. WARNING WARNING
#                 Possibly the padding is wrong.

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


use warnings;
use strict;
use Maasha::Fasta;
use Maasha::Biopieces;
use Maasha::Filesys;
use Maasha::TwoBit;


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


my ( $options, $in, $out, $record, $mask, $tmp_dir, $tmp_file, $fh_tmp, $fh_in, $fh_out, $entry );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'data_out',  short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'no_mask',   short => 'N', 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" } );

$mask = 1 if not $options->{ "no_mask" };

$tmp_dir = Maasha::Biopieces::get_tmpdir();

$tmp_file = "$tmp_dir/write_2bit.fna";

$fh_tmp   = Maasha::Filesys::file_write_open( $tmp_file );

$fh_out = Maasha::Biopieces::write_stream( $options->{ "data_out" } );

while ( $record = Maasha::Biopieces::get_record( $in ) ) 
{
    if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) ) {
        Maasha::Fasta::put_entry( $entry, $fh_tmp );
    }

    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
}

close $fh_tmp;

$fh_in = Maasha::Filesys::file_read_open( $tmp_file );

Maasha::TwoBit::fasta2twobit( $fh_in, $fh_out, $mask );

close $fh_in;
close $fh_out;

unlink $tmp_file;

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


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


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


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


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


__END__