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

# Create a fixedstep index from fixedstep entries in the stream for use with [get_fixedstep].

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


use warnings;
use strict;
use Maasha::Common;
use Maasha::Biopieces;
use Maasha::UCSC::Wiggle;
use Maasha::Filesys;


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


my ( $default, $formats, $options, $in, $out, $record, $tmp_dir, $file_out, $fh_out, $entry );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'no_stream',  short => 'x', type => 'flag',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
        { long => 'directory',  short => 'd', type => 'dir',    mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
        { long => 'index_name', short => 'i', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
    ]   
);

Maasha::Common::error( qq(Directory already exists: "$options->{ 'directory' }") ) if -d $options->{ 'directory' };

Maasha::Filesys::dir_create_if_not_exists( $options->{ 'directory' } );

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

$file_out = "$options->{ 'directory' }/$options->{ 'index_name' }.wig";
$fh_out   = Maasha::Filesys::file_write_open( $file_out );

while ( $record = Maasha::Biopieces::get_record( $in ) ) 
{
    if ( $entry = Maasha::UCSC::Wiggle::biopiece2fixedstep( $record ) ) {
        Maasha::UCSC::Wiggle::fixedstep_entry_put( $entry, $fh_out );
    }

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

close $fh_out;

Maasha::UCSC::Wiggle::fixedstep_index( $file_out, $options->{ 'directory' }, $options->{ 'index_name' } . ".index" );

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


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


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


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


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


__END__