added ':' name check to seq. error and fastq.info. sffinfo now ignores clipQualRight...

[mothur.git] / optionparser.cpp

diff --git a/optionparser.cpp b/optionparser.cpp
index a6d5c0a668be5ebdc259a3108d4ff11341f7cd00..d9d9145f1ffcf73caa4c502fb19acec23476929e 100644 (file)
--- a/optionparser.cpp
+++ b/optionparser.cpp
@@ -116,6 +116,8 @@ map<string, string> OptionParser::getParameters() {
                         it->second = m->getDesignFile();
                     }else if (it->first == "sff") {
                         it->second = m->getSFFFile();
+                    }else if (it->first == "flow") {
+                            it->second = m->getFlowFile();
                     }else if (it->first == "oligos") {
                         it->second = m->getOligosFile();
                     }else if (it->first == "accnos") {