- if (debugOnly) { return 0; }
-
- commandFactory = CommandFactory::getInstance();
-
- m->mothurOut("Mothur's directories:"); m->mothurOutEndLine();
-
- //redirect output
- if ((output == "clear") || (output == "")) { output = ""; commandFactory->setOutputDirectory(output); }
- else if (output == "default") {
- string exepath = m->argv;
- output = exepath.substr(0, (exepath.find_last_of('m')));
-
- m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
- commandFactory->setOutputDirectory(output);
- }else {
- if (m->dirCheck(output)) {
- m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
- commandFactory->setOutputDirectory(output);
+ if (debugOnly) { }
+ else {
+ commandFactory = CommandFactory::getInstance();
+
+ m->mothurOut("Mothur's directories:"); m->mothurOutEndLine();
+
+ //redirect output
+ if ((output == "clear") || (output == "")) { output = ""; commandFactory->setOutputDirectory(output); }
+ else if (output == "default") {
+ string exepath = m->argv;
+ output = exepath.substr(0, (exepath.find_last_of('m')));
+
+ m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
+ commandFactory->setOutputDirectory(output);
+ }else {
+ if (m->dirCheck(output)) {
+ m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
+ commandFactory->setOutputDirectory(output);
+ }