Merge remote-tracking branch 'origin/master'

[mothur.git] / pipelinepdscommand.cpp

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index d1309edde7631d2c8edb0f54c67be9cf02e671d2..968ba4f66a9d233a14e5f579e9563ac4d9bbd706 100644 (file)
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -94,6 +94,7 @@ PipelineCommand::PipelineCommand(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();
@@ -179,7 +180,7 @@ PipelineCommand::PipelineCommand(string option) {
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        if (pipeFilename != "") {
                                abort = readUsersPipeline();
@@ -187,6 +188,7 @@ PipelineCommand::PipelineCommand(string option) {
                                sffFile = validParameter.validFile(parameters, "sff", true);
                                if (sffFile == "not found") { m->mothurOut("sff is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true;  }
                                else if (sffFile == "not open") { sffFile = ""; abort = true; }
+                               else { m->setSFFFile(sffFile); }
                                        
                                oligosFile = validParameter.validFile(parameters, "oligos", true);
                                if (oligosFile == "not found") { m->mothurOut("oligos is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true;  }