ifstream fin;
bool quiet = false;
- if (argc < 5) {
- printf("Usage : rsem-run-em refName read_type sampleName sampleToken [-p #Threads] [-b samInpType samInpF has_fn_list_? [fn_list]] [-q] [--gibbs-out] [--sampling]\n\n");
+ if (argc < 6) {
+ printf("Usage : rsem-run-em refName read_type sampleName imdName statName [-p #Threads] [-b samInpType samInpF has_fn_list_? [fn_list]] [-q] [--gibbs-out] [--sampling]\n\n");
printf(" refName: reference name\n");
printf(" read_type: 0 single read without quality score; 1 single read with quality score; 2 paired-end read without quality score; 3 paired-end read with quality score.\n");
printf(" sampleName: sample's name, including the path\n");
strcpy(refName, argv[1]);
read_type = atoi(argv[2]);
strcpy(outName, argv[3]);
- sprintf(imdName, "%s.temp/%s", argv[3], argv[4]);
- sprintf(statName, "%s.stat/%s", argv[3], argv[4]);
+ strcpy(imdName, argv[4]);
+ strcpy(statName, argv[5]);
nThreads = 1;
genGibbsOut = false;
pt_fn_list = pt_chr_list = NULL;
- for (int i = 5; i < argc; i++) {
+ for (int i = 6; i < argc; i++) {
if (!strcmp(argv[i], "-p")) { nThreads = atoi(argv[i + 1]); }
if (!strcmp(argv[i], "-b")) {
genBamF = true;