sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / metastatscommand.cpp

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index 4744424d426d61243894d4779fa60dcd20781be3..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);          }
@@ -61,6 +61,21 @@ string MetaStatsCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string MetaStatsCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        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 {
                abort = true; calledHelp = true;
@@ -416,6 +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]);
@@ -449,7 +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 + ".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];
@@ -483,25 +505,16 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
                                outputNames.pop_back();
                        }else {
                 
-                ofstream outTemp;
-                string tempOut = outputDir + "data." + setA + "-" + setB + ".matrix";
-                m->openOutputFile(tempOut, outTemp);
-                for (int i = 0; i < subset.size(); i++) { outTemp << '\t' << subset[i]->getGroup(); }
-                outTemp << endl;
-                
-                
                                //fill data
                                for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
                                        //data[j] = new double[subset.size()];
                                        data2[j].resize(subset.size(), 0.0);
-                    outTemp << "OTU" << (j+1);
+                   
                                        for (int i = 0; i < subset.size(); i++) {
                                                data2[j][i] = (subset[i]->getAbundance(j));
-                        outTemp << '\t' << subset[i]->getAbundance(j);
                                        }
-                    outTemp << endl;
                                }
-                               outTemp.close();
+                               
                                m->mothurOut("Comparing " + setA + " and " + setB + "..."); m->mothurOutEndLine(); 
                                //metastat_main(output, thisLookUp[0]->getNumBins(), subset.size(), threshold, iters, data, setACount);