X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=optionparser.cpp;h=0d6ed2d4d0bfa681a7aa30693bcb7ae30a9c77fb;hb=d205e70ae86dbee2efc2df02f2717975854de6ba;hp=06a900d8137a031236d52261882c744bb169b440;hpb=57b3c96832667c1b70d4d526331f52e3d49e8237;p=mothur.git

diff --git a/optionparser.cpp b/optionparser.cpp
index 06a900d..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();
 				}