fixed trim.seqs group counts by adding back in the primer group

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 6aea7d827b5a3acab51a330958fb62bacaaa16d0..0734a887837e547be9978619b4b6f3923c33f905 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -406,12 +406,29 @@ int TrimSeqsCommand::execute(){
                //output group counts
                m->mothurOutEndLine();
                int total = 0;
-               for (int i = 0; i < barcodeNameVector.size(); i++) {
-                       if ((barcodeNameVector[i] != "") && (groupCounts[i] != 0)) { total += groupCounts[i]; m->mothurOut("Group " + barcodeNameVector[i] + " contains " + toString(groupCounts[i]) + " sequences."); m->mothurOutEndLine(); }
+               for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
+                        total += it->second; m->mothurOut("Group " + it->first + " contains " + toString(it->second) + " sequences."); m->mothurOutEndLine(); 
                }
                if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
                
-                       if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } return 0;     }
+               if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } return 0;     }
+
+               //set fasta file as new current fastafile
+               string current = "";
+               itTypes = outputTypes.find("fasta");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+               }
+               
+               itTypes = outputTypes.find("qfile");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
+               }
+               
+               itTypes = outputTypes.find("group");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+               }
 
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -579,8 +596,15 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                        }
                                        
                                        if(barcodes.size() != 0){
-                                               outGroupsFile << currSeq.getName() << '\t' << barcodeNameVector[barcodeIndex] << endl;
-                                               groupCounts[barcodeIndex]++;
+                                               string thisGroup = barcodeNameVector[barcodeIndex];
+                                               if (primers.size() != 0) { thisGroup += "." + primerNameVector[primerIndex]; }
+                                               
+                                               outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
+                                               
+                                               map<string, int>::iterator it = groupCounts.find(thisGroup);
+                                               if (it == groupCounts.end()) {  groupCounts[thisGroup] = 1; }
+                                               else { groupCounts[it->first]++; }
+                                                       
                                        }
                                        
                                        
@@ -693,8 +717,8 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                ofstream out;
                                string tempFile = filename + toString(getpid()) + ".num.temp";
                                m->openOutputFile(tempFile, out);
-                               for(int i = 0; i < groupCounts.size(); i++) {
-                                       out << groupCounts[i] << endl;
+                               for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
+                                       out << it->first << '\t' << it->second << endl;
                                }
                                out.close();
                                
@@ -761,12 +785,14 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                        ifstream in;
                        string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
                        m->openInputFile(tempFile, in);
-                       int count = 0; 
                        int tempNum;
+                       string group;
                        while (!in.eof()) { 
-                               in >> tempNum; m->gobble(in);
-                               groupCounts[count] += tempNum; 
-                               count++;
+                               in >> group >> tempNum; m->gobble(in);
+                               
+                               map<string, int>::iterator it = groupCounts.find(group);
+                               if (it == groupCounts.end()) {  groupCounts[group] = tempNum; }
+                               else { groupCounts[it->first] += tempNum; }
                        }
                        in.close(); remove(tempFile.c_str());
                        
@@ -1005,7 +1031,6 @@ void TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                }
                numFPrimers = primers.size();
                numRPrimers = revPrimer.size();
-               groupCounts.resize(barcodeNameVector.size(), 0);
 
        }
        catch(exception& e) {