changed dups parameter to dereplicate in chimera.uchime.

[mothur.git] / makefastqcommand.cpp

diff --git a/makefastqcommand.cpp b/makefastqcommand.cpp
index 82f730159c000888e544308ddfb58289a3363fc2..c6dcf2c83092303abdd685848efe9c875ca75976 100644 (file)
--- a/makefastqcommand.cpp
+++ b/makefastqcommand.cpp
@@ -46,6 +46,26 @@ string MakeFastQCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string MakeFastQCommand::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 == "fastq")             {   outputFileName =  "fastq";         }
+            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, "MakeFastQCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 MakeFastQCommand::MakeFastQCommand(){  
        try {
                abort = true; calledHelp = true; 
@@ -145,7 +165,7 @@ int MakeFastQCommand::execute(){
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                
-               string outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "fastq";
+               string outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fastq");
                outputNames.push_back(outputFile); outputTypes["fastq"].push_back(outputFile);
                
                ofstream out;
@@ -181,7 +201,7 @@ int MakeFastQCommand::execute(){
                qFile.close();
                out.close();
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -201,7 +221,7 @@ string MakeFastQCommand::convertQual(vector<int> qual) {
        try {
                string qualScores;
                
-               int controlChar = int('!');
+               int controlChar = int('@');
                
                for (int i = 0; i < qual.size(); i++) { 
                        int temp = qual[i] + controlChar;