X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=optionparser.cpp;h=a6d5c0a668be5ebdc259a3108d4ff11341f7cd00;hb=69c8f63401e9bab2a640cf606686b1c47fc1a6e0;hp=2d13cd0cc5d2e1706d424c92440cd97c426b8fa8;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/optionparser.cpp b/optionparser.cpp
index 2d13cd0..a6d5c0a 100644
--- a/optionparser.cpp
+++ b/optionparser.cpp
@@ -124,6 +124,8 @@ map<string, string> OptionParser::getParameters() {
                         it->second = m->getTaxonomyFile();
                     }else if (it->first == "biom") {
                         it->second = m->getBiomFile();
+                    }else if (it->first == "count") {
+                            it->second = m->getCountTableFile();
                     }else {
                         m->mothurOut("[ERROR]: mothur does not save a current file for " + it->first); m->mothurOutEndLine();
                     }