Fixed a minor bug which only affects paired-end reads for reporting how many alignmen...

[rsem.git] / synthesisRef.cpp

diff --git a/synthesisRef.cpp b/synthesisRef.cpp
index 3bb28086b3fee8755d81b88ad8f053b1ffd5a0af..8ce268c197dfff87b7c6d989077fe863cc0d1a4c 100644 (file)
--- a/synthesisRef.cpp
+++ b/synthesisRef.cpp
@@ -17,7 +17,7 @@ int M;
 map<string, string> name2seq;
 map<string, string>::iterator iter;
 
-Transcripts transcripts;
+Transcripts transcripts(1); // no genome, just transcript set
 char groupF[STRLEN], tiF[STRLEN], refFastaF[STRLEN], chromListF[STRLEN];
 
 bool hasMappingFile;
@@ -104,7 +104,7 @@ void writeResults(char* refName) {
 }
 
 int main(int argc, char* argv[]) {
-       if (argc < 5 || (hasMappingFile = atoi(argv[3])) && argc < 6) {
+  if (argc < 5 || ((hasMappingFile = atoi(argv[3])) && argc < 6)) {
                printf("Usage: synthesisRef refName quiet hasMappingFile [mappingFile] reference_file_1 [reference_file_2 ...]\n");
                exit(-1);
        }