X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=optionparser.cpp;h=0d6ed2d4d0bfa681a7aa30693bcb7ae30a9c77fb;hb=a6cf29fa4dac0909c7582cb1094151d34093ee76;hp=1e8c4451538683d4725ed60e535a5a86a8a0ea79;hpb=16abd6271c455bd01b34ff89a2e3641bef0fa128;p=mothur.git

diff --git a/optionparser.cpp b/optionparser.cpp
index 1e8c445..0d6ed2d 100644
--- 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, '.');