indicator command

[mothur.git] / chimeracheckcommand.cpp

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index c28934c5c525bbe4954b00181b512876d6cee29e..5b249d7ff6892a53ce0493c3fa5319468681a8bd 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -81,6 +81,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(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 {
                        vector<string> myArray = setParameters();
@@ -182,6 +183,8 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                                                        //erase from file list
                                                        fastaFileNames.erase(fastaFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setFastaFile(fastaFileNames[i]);
                                                }
                                        }
                                }
@@ -261,6 +264,8 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                                                        //erase from file list
                                                        nameFileNames.erase(nameFileNames.begin()+i);
                                                        i--;
+                                               }else {
+                                                       m->setNameFile(nameFileNames[i]);
                                                }
                                        }
                                }