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

[mothur.git] / parsefastaqcommand.cpp

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 06ea359e6740bd822691e9f8ab6e3e53454cc724..1331b7f47f4e131cb5a76913889d275b7ec93121 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -46,6 +46,28 @@ string ParseFastaQCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string ParseFastaQCommand::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 == "fasta") {  outputFileName =  "fasta"; }
+            else if (type == "qfile") {  outputFileName =  "qual"; }
+            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, "ParseFastaQCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 ParseFastaQCommand::ParseFastaQCommand(){      
        try {
@@ -132,8 +154,8 @@ int ParseFastaQCommand::execute(){
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //open Output Files
-               string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "fasta";
-               string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "qual";
+               string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + getOutputFileNameTag("fasta");
+               string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + getOutputFileNameTag("qfile");
                ofstream outFasta, outQual;
                
                if (fasta) { m->openOutputFile(fastaFile, outFasta);  outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile);      }