-while ((u = getopt(argc, argv, ":r:c:g:b:t:f:o:")) != -1) {
- switch(u) {
- case 'r':
- numbers = atoi(optarg);
- printf("The number of features/rows is %d.\n", numbers);
- row = numbers;
- rflag = 1;
- break;
- case 'c':
- numbers = atoi(optarg);
- printf("The number of samples/columns is %d.\n", numbers);
- col = numbers;
- cflag = 1;
- break;
- case 'g':
- numbers = atoi(optarg);
- printf("Your g-value is %d.\n", numbers);
- g = numbers;
- break;
- case 'b':
- numbers = atoi(optarg);
- printf("The number of permutations is %d\n", numbers);
- B = numbers;
- break;
- case 't':
- numb = atof(optarg);
- printf("Threshold is is %lf\n", numb);
- thresh = numb;
- break;
- case 'f':
- filename = optarg;
- printf("filename input is %s\n", filename);
- strcpy(location,filename);
- break;
- case 'o':
- filename = optarg;
- printf("filename output %s\n", filename);
- strcpy(output,filename);
- break;
- case ':':
- printf("-%c without filename\n", optopt);
- break;
- case '?':
- printf("unknown arg %c\n", optopt);
- break;
- }
-}
-
- FILE *jobj, *out;
- jobj=fopen(location,"r");
+int metastat_main (char* outputFileName, int numRows, int numCols, double threshold, int numPermutations, double** data, int secondGroupingStart){