major change to the tree class to use the count table class instead of tree map....

[mothur.git] / optionparser.cpp

diff --git a/optionparser.cpp b/optionparser.cpp
index 2d13cd0cc5d2e1706d424c92440cd97c426b8fa8..a6d5c0a668be5ebdc259a3108d4ff11341f7cd00 100644 (file)
--- a/optionparser.cpp
+++ b/optionparser.cpp
@@ -124,6 +124,8 @@ map<string, string> OptionParser::getParameters() {
                         it->second = m->getTaxonomyFile();
                     }else if (it->first == "biom") {
                         it->second = m->getBiomFile();
+                    }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();
                     }