some changes

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");

diff --git a/makefile b/makefile
index 12fc9d61a605ffa5ea7bf76d123388f246141afc..76094590dc81f6396538c4fbee38c335e1596283 100644 (file)
--- a/makefile
+++ b/makefile
@@ -102,7 +102,7 @@ rsem-calculate-credibility-intervals : calcCI.o
        $(CC) -o rsem-calculate-credibility-intervals calcCI.o
 
 #some header files are omitted
-calcCI.o : utils.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h calcCI.cpp
+calcCI.o : utils.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h calcCI.cpp boost/random.hpp
        $(CC) $(COFLAGS) calcCI.cpp
 
 clean: