X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=optionparser.cpp;h=d9d9145f1ffcf73caa4c502fb19acec23476929e;hb=79ca496859f48f1c38803c0f7c603faac348fe4c;hp=e3850e52c56f629a6e5395203f31cc1299a6193b;hpb=d70a1c2d70c5a516e74880709e3b48cfc1ce0321;p=mothur.git

diff --git a/optionparser.cpp b/optionparser.cpp
index e3850e5..d9d9145 100644
--- 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") {
@@ -124,7 +126,7 @@ map<string, string> OptionParser::getParameters() {
                         it->second = m->getTaxonomyFile();
                     }else if (it->first == "biom") {
                         it->second = m->getBiomFile();
-                    }else if (it->first == "counttable") {
+                    }else if (it->first == "count") {
                             it->second = m->getCountTableFile();
                     }else {
                         m->mothurOut("[ERROR]: mothur does not save a current file for " + it->first); m->mothurOutEndLine();