added pcr.seqs command. fixed bug in rarefacftion.single that caused parsing error...

[mothur.git] / optionparser.cpp

diff --git a/optionparser.cpp b/optionparser.cpp
index 1e8c4451538683d4725ed60e535a5a86a8a0ea79..06a900d8137a031236d52261882c744bb169b440 100644 (file)
--- a/optionparser.cpp
+++ b/optionparser.cpp
@@ -123,7 +123,7 @@ 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, '.');