sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / chimeracheckcommand.cpp

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 6a4732cf72cd4222e539beb93c6b0b45226d2a08..6caa606dc10ee387cd2eb829d264a7d17f0ee670 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -13,16 +13,16 @@
 //**********************************************************************************************************************
 vector<string> ChimeraCheckCommand::setParameters(){   
        try {
-               CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
-               CommandParameter psvg("svg", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psvg);
-               CommandParameter pincrement("increment", "Number", "", "10", "", "", "",false,false); parameters.push_back(pincrement);
-               CommandParameter pksize("ksize", "Number", "", "7", "", "", "",false,false); parameters.push_back(pksize);
-               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-               CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
+               CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera",false,true,true); parameters.push_back(pfasta);
+               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pname);
+               CommandParameter psvg("svg", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psvg);
+               CommandParameter pincrement("increment", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pincrement);
+               CommandParameter pksize("ksize", "Number", "", "7", "", "", "","",false,false); parameters.push_back(pksize);
+               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+               CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
 
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -65,24 +65,19 @@ string ChimeraCheckCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string ChimeraCheckCommand::getOutputFileNameTag(string type, string inputName=""){    
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string ChimeraCheckCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //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);
-       }
+        if (type == "chimera") {  pattern = "[filename],chimeracheck.chimeras"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ChimeraCheckCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 ChimeraCheckCommand::ChimeraCheckCommand(){    
@@ -362,7 +357,9 @@ 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])) + getOutputFileNameTag("chimera");
+            map<string, string> variables;
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]));
+                       string outputFileName = getOutputFileName("chimera", variables);
                        outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
                        
                #ifdef USE_MPI