added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / chimeracheckcommand.cpp

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index cc486d3ab690fd655c1de8a22ae406eafc2c242f..87f51e7c95c136403024c593e681a844ca18d006 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -65,6 +65,26 @@ string ChimeraCheckCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+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;
@@ -342,7 +362,7 @@ int ChimeraCheckCommand::execute(){
                        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