removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / optionparser.cpp

diff --git a/optionparser.cpp b/optionparser.cpp
index 0506da6ff441c5a85e296c1fd6f3033110622335..71714f184e644105041910933a5bf877539deb24 100644 (file)
--- a/optionparser.cpp
+++ b/optionparser.cpp
@@ -21,11 +21,15 @@ OptionParser::OptionParser(string option) {
                        while((option.find_first_of(',') != -1)) {  //while there are parameters
                                m->splitAtComma(value, option);
                                m->splitAtEquals(key, value);
+                               if ((key == "candidate") || (key == "query")) { key = "fasta"; }
+                               if (key == "template") { key = "reference"; }
                                parameters[key] = value;
                        }
                        
                        //in case there is no comma and to get last parameter after comma
                        m->splitAtEquals(key, option);
+                       if ((key == "candidate") || (key == "query")) { key = "fasta"; }
+                       if (key == "template") { key = "reference"; }
                        parameters[key] = option;
                }
        }
@@ -49,7 +53,7 @@ map<string, string> OptionParser::getParameters() {
                        if (it->second == "current") {
                                
                                //look for file types
-                               if ((it->first == "fasta") || (it->first == "candidate")) {
+                               if (it->first == "fasta") {
                                        it->second = m->getFastaFile();
                                }else if (it->first == "qfile") {
                                        it->second = m->getQualFile();