changed reading of name file to use buffered reads. note the splitAtWhiteSpace functi...

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index c019a70e4a2a7d35374192b3f8cca11787e7ecef..6f5bb979a4d45b9fc3d8201848aa9f6b2d2dddb7 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -687,6 +687,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                                currQual.printQScores(trimQualFile);
                                        }
                                        
+                    
                                        if(nameFile != ""){
                                                map<string, string>::iterator itName = nameMap.find(currSeq.getName());
                                                if (itName != nameMap.end()) {  trimNameFile << itName->first << '\t' << itName->second << endl; }
@@ -708,11 +709,13 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                                        
                                                        outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
                                                        
+                            int numRedundants = 0;
                                                        if (nameFile != "") {
                                                                map<string, string>::iterator itName = nameMap.find(currSeq.getName());
                                                                if (itName != nameMap.end()) { 
                                                                        vector<string> thisSeqsNames; 
                                                                        m->splitAtChar(itName->second, thisSeqsNames, ',');
+                                    numRedundants = thisSeqsNames.size()-1; //we already include ourselves below
                                                                        for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
                                                                                outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
                                                                        }
@@ -720,8 +723,8 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                                        }
                                                        
                                                        map<string, int>::iterator it = groupCounts.find(thisGroup);
-                                                       if (it == groupCounts.end()) {  groupCounts[thisGroup] = 1; }
-                                                       else { groupCounts[it->first]++; }
+                                                       if (it == groupCounts.end()) {  groupCounts[thisGroup] = 1 + numRedundants; }
+                                                       else { groupCounts[it->first] += (1 + numRedundants); }
                                                                
                                                }
                                        }