X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pipelinepdscommand.cpp;h=968ba4f66a9d233a14e5f579e9563ac4d9bbd706;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=d1309edde7631d2c8edb0f54c67be9cf02e671d2;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index d1309ed..968ba4f 100644
--- 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;  }