# -*- perl -*-
########################################################################
# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
#
# This file is part of the SEED Toolkit.
# 
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License. 
#
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.
########################################################################


use FIG;
use FIGV;
my $fig = new FIG;

$usage = "usage: predict_starts [-orgdir=OrgDir] Objects ClearCalls ProposedCorrections";

$orgdir_flag = "";
if ($ARGV[0] =~ /-orgdir=(\S+)/) {
    $fig = new FIGV($1);
    $orgdir_flag = $ARGV[0];
    shift @ARGV;
}

(
 ($objects       = shift @ARGV) &&
 ($clear_calls   = shift @ARGV) &&
 ($proposed      = shift @ARGV)
)
    || die $usage;

&FIG::run("make_calls_for_start_predictions < $objects > $FIG_Config::temp/with.calls.$$"); 
&FIG::run("order_corrections_for_start_predictions < $FIG_Config::temp/with.calls.$$ 2> $FIG_Config::temp/clear$$ > $FIG_Config::temp/proposed$$");
system "cat $FIG_Config::temp/clear$$ >> $clear_calls";
system "cat $FIG_Config::temp/proposed$$ >> $proposed";
system "cat $FIG_Config::temp/with.calls.$$";
unlink("$FIG_Config::temp/with.calls.$$","$FIG_Config::temp/clear$$","$FIG_Config::temp/proposed$$");