sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / metastatscommand.cpp

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index b5b01e7f97166ed80143d349b9ae8c340d53e654..9dff3543f49efa25037ce7fb3dd9eeeebbe8c787 100644 (file)
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -14,16 +14,16 @@
 //**********************************************************************************************************************
 vector<string> MetaStatsCommand::setParameters(){      
        try {
-               CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
-               CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
-               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-               CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
-               CommandParameter pthreshold("threshold", "Number", "", "0.05", "", "", "",false,false); parameters.push_back(pthreshold);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter psets("sets", "String", "", "", "", "", "",false,false); parameters.push_back(psets);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","metastats",false,true,true); parameters.push_back(pshared);
+               CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
+               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+               CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+               CommandParameter pthreshold("threshold", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(pthreshold);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter psets("sets", "String", "", "", "", "", "","",false,false); parameters.push_back(psets);
+               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);          }
@@ -61,26 +61,20 @@ string MetaStatsCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string MetaStatsCommand::getOutputFileNameTag(string type, string inputName=""){       
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string MetaStatsCommand::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 == "metastats")        {   outputFileName = "metastats";       }
-            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, "MetaStatsCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "metastats") {  pattern = "[filename],[distance],[group],metastats"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "MetaStatsCommand", "getOutputPattern");
+        exit(1);
+    }
 }
-
 //**********************************************************************************************************************
 MetaStatsCommand::MetaStatsCommand(){  
        try {
@@ -437,6 +431,9 @@ int MetaStatsCommand::process(vector<SharedRAbundVector*>& thisLookUp){
                     
                     //Close all thread handles and free memory allocations.
                     for(int i=0; i < pDataArray.size(); i++){
+                        if (pDataArray[i]->count != (pDataArray[i]->num)) {
+                            m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->num) + " groups assigned to it, quitting. \n"); m->control_pressed = true; 
+                        }
                         for (int j = 0; j < pDataArray[i]->thisLookUp.size(); j++) {  delete pDataArray[i]->thisLookUp[j];  } 
                         for (int j = 0; j < pDataArray[i]->outputNames.size(); j++) {  
                             outputNames.push_back(pDataArray[i]->outputNames[j]);
@@ -470,7 +467,11 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
                        string setB = namesOfGroupCombos[c][1];
                
                        //get filename
-                       string outputFileName = outputDir +  m->getRootName(m->getSimpleName(sharedfile)) + thisLookUp[0]->getLabel() + "." + setA + "-" + setB + "." + getOutputFileNameTag("metastats");
+            map<string, string> variables; 
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+            variables["[distance]"] = thisLookUp[0]->getLabel();
+            variables["[group]"] = setA + "-" + setB;
+                       string outputFileName = getOutputFileName("metastats",variables);
                        outputNames.push_back(outputFileName); outputTypes["metastats"].push_back(outputFileName);
                        //int nameLength = outputFileName.length();
                        //char * output = new char[nameLength];