X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=optionparser.cpp;h=262ac88286b0639ace8cb3bff4fe10a091ec4748;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hp=a6d5c0a668be5ebdc259a3108d4ff11341f7cd00;hpb=5a4ac4f954c4b4445bcee272f1f8220ddcc9c1e4;p=mothur.git

diff --git a/optionparser.cpp b/optionparser.cpp
index a6d5c0a..262ac88 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") {
@@ -126,6 +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();
                     }