some changes

[rsem.git] / EM.cpp

diff --git a/EM.cpp b/EM.cpp
index ff257680ead4f4f2087515131623a6e61fb498c1..08fc8c7d2400396a8fef40fc945717be4b166e83 100644 (file)
--- a/EM.cpp
+++ b/EM.cpp
@@ -633,8 +633,8 @@ int main(int argc, char* argv[]) {
                printf("Usage : rsem-run-em refName read_type sampleName sampleToken [-p #Threads] [-b samInpType samInpF has_fn_list_? [fn_list]] [-q] [--gibbs-out]\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("  samplePath: sample path.\n");
-               printf("  sampleName: sample name.\n");
+               printf("  sampleName: sample's name, including the path\n");
+               printf("  sampleToken: sampleName excludes the path\n");
                printf("  -p: number of threads which user wants to use. (default: 1)\n");
                printf("  -b: produce bam format output file. (default: off)\n");
                printf("  -q: set it quiet\n");