sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / matrixoutputcommand.cpp

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 3844e18c1e687ef47fae1dda09d10e61973ab798..310e32bf23e048c73ae37579ac2e8e2d1cb8b0ff 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -18,7 +18,7 @@ vector<string> MatrixOutputCommand::setParameters(){
         CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
                CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
                CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
-               CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "","",false,false); parameters.push_back(poutput);
+               CommandParameter poutput("output", "Multiple", "lt-square-column", "lt", "", "", "","",false,false); parameters.push_back(poutput);
         CommandParameter pmode("mode", "Multiple", "average-median", "average", "", "", "","",false,false); parameters.push_back(pmode);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
         CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
@@ -45,7 +45,7 @@ string MatrixOutputCommand::getHelpString(){
         helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
         helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group.\n";
                helpString += "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
-               helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n";
+               helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, column and square. The default is lt.\n";
         helpString += "The mode parameter allows you to specify if you want the average or the median values reported when subsampling. Options are average, and median. The default is average.\n";
                helpString += "Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n";
                helpString += "The default value for groups is all the groups in your groupfile.\n";
@@ -156,7 +156,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                        }
                        
                        output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "lt"; }
-                       if ((output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
+                       if ((output != "lt") && (output != "square") && (output != "column")) { m->mothurOut(output + " is not a valid output form. Options are lt, column and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
             
             mode = validParameter.validFile(parameters, "mode", false);                if(mode == "not found"){        mode = "average"; }
                        if ((mode != "average") && (mode != "median")) { m->mothurOut(mode + " is not a valid mode. Options are average and medina. I will use average."); m->mothurOutEndLine(); output = "average"; }
@@ -449,11 +449,9 @@ void MatrixOutputCommand::printSims(ostream& out, vector< vector<double> >& simM
        try {
                
                out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-               
-               //output num seqs
-               out << simMatrix.size() << endl;
-               
+                               
                if (output == "lt") {
+            out << simMatrix.size() << endl;
                        for (int b = 0; b < simMatrix.size(); b++)      {
                                out << lookup[b]->getGroup() << '\t';
                                for (int n = 0; n < b; n++)     {
@@ -461,7 +459,14 @@ void MatrixOutputCommand::printSims(ostream& out, vector< vector<double> >& simM
                                }
                                out << endl;
                        }
+        }else if (output == "column") {
+            for (int b = 0; b < simMatrix.size(); b++) {
+                for (int n = 0; n < b; n++)    {
+                    out << lookup[b]->getGroup() << '\t' << lookup[n]->getGroup() << '\t' << simMatrix[b][n] << endl;
+                }
+            }
                }else{
+            out << simMatrix.size() << endl;
                        for (int b = 0; b < simMatrix.size(); b++)      {
                                out << lookup[b]->getGroup() << '\t';
                                for (int n = 0; n < simMatrix[b].size(); n++)   {
@@ -629,6 +634,9 @@ int MatrixOutputCommand::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]->end-pDataArray[i]->start)) {
+                        m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " 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 k = 0; k < calcDists.size(); k++) {