caveman.c

/**   LICENSE
* Copyright (c) 2014-2018 Genome Research Ltd.
*
* Author: Cancer Genome Project cgpit@sanger.ac.uk
*
* This file is part of CaVEMan.
*
* CaVEMan is free software: you can redistribute it and/or modify it under
* the terms of the GNU Affero General Public License as published by the Free
* Software Foundation; either version 3 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 Affero General Public License for more
* details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*
*    1. The usage of a range of years within a copyright statement contained within
*    this distribution should be interpreted as being equivalent to a list of years
*    including the first and last year specified and all consecutive years between
*    them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007-
*    2009, 2011-2012’ should be interpreted as being identical to a statement that
*    reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright
*    statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being
*    identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008,
*    2009, 2010, 2011, 2012’."
*
*/

#include <setup.h>
#include <split.h>
#include <mstep.h>
#include <merge.h>
#include <estep.h>
#include <dbg.h>
#include <stdio.h>
#include <stdlib.h>
#include <getopt.h>
#include <string.h>

void print_usage (int exit_code){
	printf("Usage: caveman [setup|split|mstep|merge|estep] [-v] [-h] \n\n");
	printf("-v  --version         Print version information\n");
	printf("-h  --help            Display this usage information.\n");
  	exit(exit_code);
}

int setup_options(int argc, char *argv[]){
	const struct option long_opts[] =
	{
             	/*{"setup", no_argument, 0, 's'},
             	{"split", no_argument, 0, 'p'},
             	{"mstep", no_argument, 0, 'm'},
             	{"merge", no_argument, 0, 'e'},
             	{"estep", no_argument, 0, 't'},    */
             	{"help", no_argument, 0, 'h'},
             	{"version", no_argument, 0, 'v'},
             	{ NULL, 0, NULL, 0}
   }; //End of declaring opts

   int index = 0;
   int iarg = 0;

   if(argc < 2){
   	print_usage(0);
   }else if(argc >= 2){
   	char *option = argv[1];
		if(strcmp(option,"setup")==0){
			argv[1]= "";
			return setup_main(argc,argv);
		}else if(strcmp(option,"split")==0){
			argv[1]= "";
			return split_main(argc,argv);
		}else if(strcmp(option,"mstep")==0){
			argv[1]= "";
			return mstep_main(argc,argv);
		}else if(strcmp(option,"merge")==0){
			argv[1]= "";
			return merge_main(argc,argv);
		}else if(strcmp(option,"estep")==0){
			argv[1]= "";
			return estep_main(argc,argv);
		}
   }

   //Iterate through options
   while((iarg = getopt_long(argc, argv, "vh", long_opts, &index)) != -1){
   	switch(iarg){
   		case 'h':
   			print_usage(0);
         	break;

			case 'v':
				printf ("%s\n",CAVEMAN_VERSION);
				return 0;

			case '?':
				print_usage(1);
				break;

      	default:
      		print_usage(1);

   	}; // End of args switch statement

   }//End of iteration through options
   return 0;
}

int main(int argc, char *argv[]){
	return setup_options(argc,argv);
}