/*-------------------------------------------------------------------*/
/* mcluster.c        Mohammad Rezaei                                 */
/*                                                                   */
/* grid-based clustering of markers                                  */
/*                                                                   */
/* Version: 0.00                                                     */
/* Last updated : 16.6.2014                                          */
/*-------------------------------------------------------------------*/
#define ProgName        "mcluster"

#define pi 3.14159265358979323846

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <unistd.h>
#include "math.h"

typedef struct { 
  char   outputFilename[300];
  char   inputFilename[300];
} PARAMS;

PARAMS parseInputArgs(int argc, char** argv)
{
  int c;
  PARAMS params;
  
  opterr = 0;
  
  while ((c = getopt (argc, argv, "f:i:")) != -1) {
    switch (c) {
	  case 'f':
        strcpy(params.outputFilename, optarg);
        break;
	  case 'i':
	    strcpy(params.inputFilename, optarg);
        break;
      default:
        break;
    }
  }
 
  return params;
}

int main(int argc, char* argv[])
{
  PARAMS params;
  char t[100];
  FILE *fp1, *fp2, *fp3;
  int i;
 
  params = parseInputArgs(argc, argv);
  
  fp3 = fopen("kk.txt", "w");
  fclose(fp3);
  
  fp1 = fopen(params.inputFilename, "r");
  fp2 = fopen(params.outputFilename, "w");
  
  printf("this is a test!\n");
  for ( i = 0 ; i < 5 ; i++ ) {
    fscanf(fp1, "%s\n", &t);
	fprintf(fp2, "%s\n", t);
  }
  fclose(fp1);
  fclose(fp2);
 
  return 0;
}  /* main() */