changed dups parameter to dereplicate in chimera.uchime.

[mothur.git] / libshuffcommand.cpp

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 1e8102f49f40753d239f8188f1a88cc9e3578587..7f8cd9b721fe50e82f4fdf2553e51a6d53b86a22 100644 (file)
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -65,6 +65,27 @@ string LibShuffCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string LibShuffCommand::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 == "coverage")             {   outputFileName =  "libshuff.coverage";       }
+            else if (type == "libshuffsummary")      {   outputFileName =  "libshuff.summary";   }
+            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, "LibShuffCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 LibShuffCommand::LibShuffCommand(){    
        try {
                abort = true; calledHelp = true; 
@@ -170,13 +191,13 @@ LibShuffCommand::LibShuffCommand(string option)  {
                                
                        string temp;
                        temp = validParameter.validFile(parameters, "iters", false);                            if (temp == "not found") { temp = "10000"; }
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);                           if (temp == "not found") { temp = "1.0"; }
-                       convert(temp, cutOff); 
+                       m->mothurConvert(temp, cutOff); 
                        
                        temp = validParameter.validFile(parameters, "step", false);                             if (temp == "not found") { temp = "0.01"; }
-                       convert(temp, step); 
+                       m->mothurConvert(temp, step); 
                        
                        temp = validParameter.validFile(parameters, "sim", false);                              if (temp == "not found") { temp = "F"; }
                        sim = m->isTrue(temp); 
@@ -341,7 +362,7 @@ int LibShuffCommand::printCoverageFile() {
        try {
 
                ofstream outCov;
-               summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "libshuff.coverage";
+               summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("coverage");
                m->openOutputFile(summaryFile, outCov);
                outputNames.push_back(summaryFile); outputTypes["coverage"].push_back(summaryFile);
                outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
@@ -437,7 +458,7 @@ int LibShuffCommand::printSummaryFile() {
        try {
 
                ofstream outSum;
-               summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "libshuff.summary";
+               summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("libshuffsummary");
                m->openOutputFile(summaryFile, outSum);
                outputNames.push_back(summaryFile); outputTypes["libshuffsummary"].push_back(summaryFile);