sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / chimerabellerophoncommand.cpp

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 82400112bc8770ca2ded637853028d86e6aede99..bb119e41c8e5b40dd681793c43c10f4c6f7e6c61 100644 (file)
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -13,14 +13,14 @@
 //**********************************************************************************************************************
 vector<string> ChimeraBellerophonCommand::setParameters(){     
        try {
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "none","none","none",false,true); parameters.push_back(pfasta);
-               CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfilter);
-               CommandParameter pcorrection("correction", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcorrection);
-               CommandParameter pwindow("window", "Number", "", "0", "", "", "",false,false); parameters.push_back(pwindow);
-               CommandParameter pincrement("increment", "Number", "", "25", "", "", "",false,false); parameters.push_back(pincrement);
-               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 pfasta("fasta", "InputTypes", "", "", "none","none","none","chimera-accnos",false,true,true); parameters.push_back(pfasta);
+               CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfilter);
+               CommandParameter pcorrection("correction", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pcorrection);
+               CommandParameter pwindow("window", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pwindow);
+               CommandParameter pincrement("increment", "Number", "", "25", "", "", "","",false,false); parameters.push_back(pincrement);
+               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);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -57,25 +57,20 @@ string ChimeraBellerophonCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string ChimeraBellerophonCommand::getOutputFileNameTag(string type, string inputName=""){      
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string ChimeraBellerophonCommand::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 =  "bellerophon.chimeras"; }
-            else if (type == "accnos") {  outputFileName =  "bellerophon.accnos"; }
-            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, "ChimeraBellerophonCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "chimera") {  pattern = "[filename],bellerophon.chimeras"; } 
+        else if (type == "accnos") {  pattern = "[filename],bellerophon.accnos"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ChimeraBellerophonCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 ChimeraBellerophonCommand::ChimeraBellerophonCommand(){        
@@ -242,9 +237,11 @@ int ChimeraBellerophonCommand::execute(){
                        
                        chimera = new Bellerophon(fastaFileNames[i], filter, correction, window, increment, processors, outputDir);     
                        
-                       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");
-                       string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) +  getOutputFileNameTag("accnos");
+                       if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]);  }//if user entered a file with a path then preserve it       
+            map<string, string> variables; 
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]));
+                       string outputFileName = getOutputFileName("chimera", variables);
+                       string accnosFileName = getOutputFileName("accnos", variables);
                        
                        chimera->getChimeras();