removing chime source files from mother project.

[mothur.git] / optionparser.cpp

diff --git a/optionparser.cpp b/optionparser.cpp
index 1e8c4451538683d4725ed60e535a5a86a8a0ea79..0d6ed2d4d0bfa681a7aa30693bcb7ae30a9c77fb 100644 (file)
--- a/optionparser.cpp
+++ b/optionparser.cpp
@@ -91,6 +91,8 @@ map<string, string> OptionParser::getParameters() {
                                        it->second = m->getAccnosFile();
                                }else if (it->first == "taxonomy") {
                                        it->second = m->getTaxonomyFile();
+                }else if (it->first == "biom") {
+                        it->second = m->getBiomFile();
                                }else {
                                        m->mothurOut("[ERROR]: mothur does not save a current file for " + it->first); m->mothurOutEndLine();
                                }
@@ -123,7 +125,7 @@ bool OptionParser::getNameFile(vector<string> files) {
                string namefile = m->getNameFile();
                bool match = false;
                
-               if (namefile != "") {
+               if ((namefile != "")&&(!m->mothurCalling)) {
                        string temp = m->getRootName(m->getSimpleName(namefile));
                        vector<string> rootName;
                        m->splitAtChar(temp, rootName, '.');