X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=EM.cpp;h=0d3872836784bcf45c9def4ae8ea09db6c4a7ef7;hb=c678676b7da64266b4b98258a34d1b32372da6dd;hp=e106335f7b6a17b31e3b479a09849518802907cb;hpb=9eef8b58056b7cdaad1b4bdb2b2904d9fc0ff430;p=rsem.git

diff --git a/EM.cpp b/EM.cpp
index e106335..0d38728 100644
--- a/EM.cpp
+++ b/EM.cpp
@@ -412,7 +412,7 @@ void EM() {
 	double sum;
 
 	double bChange = 0.0, change = 0.0; // bChange : biggest change
-	READ_INT_TYPE totNum = 0;
+	int totNum = 0;
 
 	ModelType model(mparams); //master model
 	ReadReader<ReadType> **readers;
@@ -507,7 +507,7 @@ void EM() {
 				if (bChange < change) bChange = change;
 			}
 
-		if (verbose) { cout<< "ROUND = "<< ROUND<< ", SUM = "<< setprecision(15)<< sum<< ", bChange = " << setprecision(6)<< bChange<< ", totNum = %" << totNum<< endl; }
+		if (verbose) { cout<< "ROUND = "<< ROUND<< ", SUM = "<< setprecision(15)<< sum<< ", bChange = " << setprecision(6)<< bChange<< ", totNum = " << totNum<< endl; }
 	} while (ROUND < MIN_ROUND || (totNum > 0 && ROUND < MAX_ROUND));
 //	} while (ROUND < 1);
 
@@ -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;