paralellized chimera.uchime for windows for both by group and with a template.

[mothur.git] / parsefastaqcommand.cpp

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 75d6fa01be65bcccf8f176bfd29dcce843efc0e3..9cba70b9d2772edba281cd5f03459d1fdc32a966 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -62,6 +62,7 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
                abort = false; calledHelp = false;   
                
                if(option == "help") {  help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -168,7 +169,7 @@ int ParseFastaQCommand::execute(){
                outFasta.close();
                outQual.close();
                
-               if (m->control_pressed) { outputTypes.clear(); remove(fastaFile.c_str()); remove(qualFile.c_str()); return 0; }
+               if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(fastaFile); m->mothurRemove(qualFile); return 0; }
                
                //set fasta file as new current fastafile
                string current = "";