added method parameter to get.oturep. options method=abundance or distance. default...

[mothur.git] / optionparser.cpp

diff --git a/optionparser.cpp b/optionparser.cpp
index d9d9145f1ffcf73caa4c502fb19acec23476929e..262ac88286b0639ace8cb3bff4fe10a091ec4748 100644 (file)
--- a/optionparser.cpp
+++ b/optionparser.cpp
@@ -128,6 +128,8 @@ map<string, string> OptionParser::getParameters() {
                         it->second = m->getBiomFile();
                     }else if (it->first == "count") {
                             it->second = m->getCountTableFile();
+                    }else if (it->first == "summary") {
+                            it->second = m->getSummaryFile();
                     }else {
                         m->mothurOut("[ERROR]: mothur does not save a current file for " + it->first); m->mothurOutEndLine();
                     }