Made the BAM output of RSEM have all information contained in the input alignments...

[rsem.git] / EM.cpp

diff --git a/EM.cpp b/EM.cpp
index 2ce946fd6e97b3e7deb0b33b7ab42b143efe3046..0d3872836784bcf45c9def4ae8ea09db6c4a7ef7 100644 (file)
--- 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;