minor mods to seq.error

[mothur.git] / chimerabellerophoncommand.cpp

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 1fcb4fc2956023801d72b9242429b544715bc247..0031acb15b750823bb8cb3afed79d79f9a07d399 100644 (file)
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -77,6 +77,7 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        
@@ -170,6 +171,8 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setFastaFile(fastaFileNames[i]);
                                                }
                                        }
                                }