X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=EM.cpp;h=08fc8c7d2400396a8fef40fc945717be4b166e83;hb=53e8bbb15e0bfed6a0caae7b5ba6777a9a942266;hp=ff257680ead4f4f2087515131623a6e61fb498c1;hpb=58f823f5be6dfbe00896fc44ac3aac5e881e9c5c;p=rsem.git

diff --git a/EM.cpp b/EM.cpp
index ff25768..08fc8c7 100644
--- 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");