X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=EM.cpp;h=0d3872836784bcf45c9def4ae8ea09db6c4a7ef7;hp=2ce946fd6e97b3e7deb0b33b7ab42b143efe3046;hb=509ffe2d71cf6a6f5cca8c39909f8ee10b8db899;hpb=4496388fd52d4354c746f36b1998477f31c2b0dd

diff --git a/EM.cpp b/EM.cpp
index 2ce946f..0d38728 100644
--- a/EM.cpp
+++ b/EM.cpp
@@ -652,8 +652,8 @@ int main(int argc, char* argv[]) {
 	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");
@@ -672,8 +672,8 @@ int main(int argc, char* argv[]) {
 	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;
 
@@ -682,7 +682,7 @@ int main(int argc, char* argv[]) {
 	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;