X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.cpp;h=bd31c193e82aa0725cc8920336ec310cc19db820;hb=c7e8c2d15bd7cedcfdf18675cb0ea1a0dcd0e3c0;hp=be0421a73097bc47aa98934ba4ae59a320e02010;hpb=791f42d21a85f794529fd4c912dcc27d873c25e8;p=mothur.git

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index be0421a..bd31c19 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -98,6 +98,28 @@ string ChimeraUchimeCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string ChimeraUchimeCommand::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 =  "uchime.chimeras"; }
+            else if (type == "accnos") {  outputFileName =  "uchime.accnos"; }
+            else if (type == "alns") {  outputFileName =  "uchime.alns"; }
+            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, "ChimeraUchimeCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 ChimeraUchimeCommand::ChimeraUchimeCommand(){	
 	try {
 		abort = true; calledHelp = true;
@@ -522,9 +544,9 @@ int ChimeraUchimeCommand::execute(){
 			int start = time(NULL);	
 			string nameFile = "";
 			if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it				
-			string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "uchime.chimera";
-			string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "uchime.accnos";
-			string alnsFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "uchime.alns";
+			string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera");
+			string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos");
+			string alnsFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + getOutputFileNameTag("alns");
 			string newFasta = m->getRootName(fastaFileNames[s]) + "temp";
 				
 			//you provided a groupfile
@@ -994,7 +1016,8 @@ int ChimeraUchimeCommand::driverGroups(SequenceParser& parser, string outputFNam
 			if (m->control_pressed) { return 0; }
 			
 			//remove file made for uchime
-			m->mothurRemove(filename);
+			if (!m->debug) {  m->mothurRemove(filename);  }
+            else { m->mothurOut("[DEBUG]: saving file: " + filename + ".\n"); }
 			
 			//append files
 			m->appendFiles((outputFName+groups[i]), outputFName); m->mothurRemove((outputFName+groups[i]));