}
}
//**********************************************************************************************************************
+string ChimeraCheckCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "chimera") { outputFileName = "chimeracheck.chimeras"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraCcodeCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
ChimeraCheckCommand::ChimeraCheckCommand(){
try {
abort = true; calledHelp = true;
if (m->control_pressed) { delete chimera; return 0; }
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]); }//if user entered a file with a path then preserve it
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "chimeracheck.chimeras";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + getOutputFileNameTag("chimera");
outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
#ifdef USE_MPI