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#!/usr/bin/perl

=head1 NAME

runDiscovery.pl This program runs literature based discovery with the 
parameters specified in the input file. Please see samples/lbd or 
samples/thresholding for sample input files and descriptions of parameters
and full details on what can be in an LBD input file.

=head1 SYNOPSIS

This utility takes an lbd configuration file and outputs the results
of lbd

=head1 USAGE

Usage: umls-assocation.pl [OPTIONS] LBD_CONFIG_FILE

=head1 INPUT

=head2 LBD_CONFIG_FILE

Configuration file specifying the parameters of LBD. 
See '../config/lbd' for an example

=head1 OPTIONS

Optional command line arguements

=head2 General Options:

=head3 --help

displays help, a quick summary of program options

=head3 --assocConfig

path to a UMLS::Association configuration file. Default location is 
'../config/association'. Replace this file for your computer to avoid having
to specify each time.

=head3 --interfaceConfig

path to a UMLS::Interface configuration file. Default location is 
'../config/interface'. Replace this file for your computer to avoid having
to specify each time.

=head3 --debug

enter debug mode

=head3 --version

display the version number

=head1 OUTPUT

A file containing the results of LBD

=head1 SYSTEM REQUIREMENTS

=over

=item * Perl (version 5.16.5 or better) - http://www.perl.org

=item * UMLS::Interface - http://search.cpan.org/dist/UMLS-Interface

=item * UMLS::Association - http://search.cpan.org/dist/UMLS-Association

=back

=head1 CONTACT US
   
  If you have any trouble installing and using ALBD, 
  You may contact us directly :
    
      Sam Henry: henryst at vcu.edu 

=head1 AUTHOR

 Sam Henry, Virginia Commonwealth University

=head1 COPYRIGHT

Copyright (c) 2017

 Sam Henry, Virginia Commonwealth University 
 henryst at vcu.edu

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.,
 59 Temple Place - Suite 330,
 Boston, MA  02111-1307, USA.

=cut

###############################################################################
#                               THE CODE STARTS HERE
###############################################################################

use strict;
use warnings;

use Getopt::Long;
use ALBD;