sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 85eb448916d5058b80ea7dade2b98d3f5e3148f9..e82d1f6600e0b83f79154634ddfbda43d7542d91 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -190,7 +190,9 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
             temp = validParameter.validFile(parameters, "iters", false);                       if (temp == "not found") { temp = "1000"; }
                        m->mothurConvert(temp, iters); 
             
-            output = validParameter.validFile(parameters, "output", false);            if(output == "not found"){      output = "lt"; }
+            output = validParameter.validFile(parameters, "output", false);            
+            if(output == "not found"){ output = "lt"; }
+            else { createPhylip = true; }
                        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"; }
             
             temp = validParameter.validFile(parameters, "subsample", false);           if (temp == "not found") { temp = "F"; }
@@ -740,6 +742,9 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                 
                 //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; 
+                    }
                     m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName);
                     m->mothurRemove((sumFileName + toString(processIDS[i]) + ".temp"));
                     
@@ -789,6 +794,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                         variables["[calc]"] = sumCalculators[i]->getName();
                         variables["[distance]"] = thisLookup[0]->getLabel();
                         variables["[outputtag]"] = output;
+                        variables["[tag2]"] = "";
                         string distFileName = getOutputFileName("phylip",variables);
                         outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
                         ofstream outDist;
@@ -804,60 +810,12 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
             for (int i = 0; i < calcDists.size(); i++) {  calcDists[i].clear(); }
                }
 
-        if (iters != 1) {
+        if (iters != 0) {
             //we need to find the average distance and standard deviation for each groups distance
-            
-            vector< vector<seqDist>  > calcAverages; calcAverages.resize(sumCalculators.size()); 
-            for (int i = 0; i < calcAverages.size(); i++) {  //initialize sums to zero.
-                calcAverages[i].resize(calcDistsTotals[0][i].size());
-                
-                for (int j = 0; j < calcAverages[i].size(); j++) {
-                    calcAverages[i][j].seq1 = calcDists[i][j].seq1;
-                    calcAverages[i][j].seq2 = calcDists[i][j].seq2;
-                    calcAverages[i][j].dist = 0.0;
-                }
-            }
-            
-            for (int thisIter = 0; thisIter < iters; thisIter++) { //sum all groups dists for each calculator
-                for (int i = 0; i < calcAverages.size(); i++) {  //initialize sums to zero.
-                    for (int j = 0; j < calcAverages[i].size(); j++) {
-                        calcAverages[i][j].dist += calcDistsTotals[thisIter][i][j].dist;
-                    }
-                }
-            }
-            
-            for (int i = 0; i < calcAverages.size(); i++) {  //finds average.
-                for (int j = 0; j < calcAverages[i].size(); j++) {
-                    calcAverages[i][j].dist /= (float) iters;
-                }
-            }
+            vector< vector<seqDist>  > calcAverages = m->getAverages(calcDistsTotals);
             
             //find standard deviation
-            vector< vector<seqDist>  > stdDev; stdDev.resize(sumCalculators.size());
-            for (int i = 0; i < stdDev.size(); i++) {  //initialize sums to zero.
-                stdDev[i].resize(calcDistsTotals[0][i].size());
-                
-                for (int j = 0; j < stdDev[i].size(); j++) {
-                    stdDev[i][j].seq1 = calcDists[i][j].seq1;
-                    stdDev[i][j].seq2 = calcDists[i][j].seq2;
-                    stdDev[i][j].dist = 0.0;
-                }
-            }
-            
-            for (int thisIter = 0; thisIter < iters; thisIter++) { //compute the difference of each dist from the mean, and square the result of each
-                for (int i = 0; i < stdDev.size(); i++) {  
-                    for (int j = 0; j < stdDev[i].size(); j++) {
-                        stdDev[i][j].dist += ((calcDistsTotals[thisIter][i][j].dist - calcAverages[i][j].dist) * (calcDistsTotals[thisIter][i][j].dist - calcAverages[i][j].dist));
-                    }
-                }
-            }
-            
-            for (int i = 0; i < stdDev.size(); i++) {  //finds average.
-                for (int j = 0; j < stdDev[i].size(); j++) {
-                    stdDev[i][j].dist /= (float) iters;
-                    stdDev[i][j].dist = sqrt(stdDev[i][j].dist);
-                }
-            }
+            vector< vector<seqDist>  > stdDev = m->getStandardDeviation(calcDistsTotals, calcAverages); 
             
             //print results
             for (int i = 0; i < calcDists.size(); i++) {