sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / makegroupcommand.cpp

diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp
index e32af2152e1bd3d420a0a94dac738a97c19c24af..68b1e84d0e7e6eb811971128d14490832ad390ae 100644 (file)
--- a/makegroupcommand.cpp
+++ b/makegroupcommand.cpp
@@ -14,10 +14,11 @@
 //**********************************************************************************************************************
 vector<string> MakeGroupCommand::setParameters(){      
        try {
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","group",false,true,true); parameters.push_back(pfasta);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pgroups);
+               CommandParameter poutput("output", "String", "", "", "", "", "","",false,false); parameters.push_back(poutput);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -47,6 +48,21 @@ string MakeGroupCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string MakeGroupCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "group") {  pattern = "[filename],groups"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "MakeGroupCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 MakeGroupCommand::MakeGroupCommand(){  
        try {
                abort = true; calledHelp = true; 
@@ -164,8 +180,10 @@ MakeGroupCommand::MakeGroupCommand(string option)  {
                                }
                                
                                //prevent giantic file name
-                               if (fastaFileNames.size() > 3) { filename = outputDir + "merge.groups"; }
-                               else {  filename += "groups";  }
+                map<string, string> variables; 
+                variables["[filename]"] = filename;
+                               if (fastaFileNames.size() > 3) { variables["[filename]"] = outputDir + "merge"; }
+                               filename = getOutputFileName("group",variables);  
                                
                                //make sure there is at least one valid file left
                                if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
@@ -224,7 +242,7 @@ int MakeGroupCommand::execute(){
                out.close();
                
                m->mothurOutEndLine();
-               m->mothurOut("Output File Name: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename); 
+               m->mothurOut("Output File Names: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename); 
                m->mothurOutEndLine();
                
                //set group file as new current groupfile