#!/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 fixedstep entries from records in the stream.

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


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


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


my ( $options, $in, $out, $record, $tmp_dir, $bed_file, $fh_in, $fh_out,
     $file_hash, $chr, $bed_entry, $fixedstep_file, $fixedstep_entry );

$options = Maasha::Biopieces::parse_options(
    [
        { long => 'check', short => 'C', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
        { long => 'log10', short => 'l', 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" } );

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

$bed_file = "$tmp_dir/calc_fixedstep.bed";
$fh_out   = Maasha::Filesys::file_write_open( $bed_file );

while ( $record = Maasha::Biopieces::get_record( $in ) ) 
{
    if ( $bed_entry = Maasha::UCSC::BED::biopiece2bed( $record ) ) {
        Maasha::UCSC::BED::bed_entry_put( $bed_entry, $fh_out, undef, $options->{ 'check' } );
    }

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

close $fh_out;

$file_hash = Maasha::UCSC::BED::bed_file_split_on_chr( $bed_file, $tmp_dir );

unlink $bed_file;

foreach $chr ( sort keys %{ $file_hash } )
{
    $bed_file       = $file_hash->{ $chr };

    $fixedstep_file = Maasha::UCSC::Wiggle::fixedstep_calc( $bed_file, $chr, $options->{ 'log10' } );        

    #$fixedstep_file = "$bed_file.fixedstep";
    
    # Maasha::Common::run( "bed2fixedstep", "< $bed_file > $fixedstep_file" );

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

    while ( $fixedstep_entry = Maasha::UCSC::Wiggle::fixedstep_entry_get( $fh_in ) )
    {
        if ( $record = Maasha::UCSC::Wiggle::fixedstep2biopiece( $fixedstep_entry ) ) {
            Maasha::Biopieces::put_record( $record, $out );
        }
    }

    close $fh_in;

    unlink $bed_file;
    unlink $fixedstep_file;
}

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


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


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


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


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


__END__