working on windows paralellization, added trimOligos class to be used by trim.flows...

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index bc2dd481e5589ea5ba8b319aa707ecf3a3eea463..3fa622f01ff2fc334f5cbb9d79851a9ca7f8b30c 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -162,6 +162,7 @@ int DeconvoluteCommand::execute() {
                map<string, string>::iterator itStrings;
                set<string> nameInFastaFile; //for sanity checking
                set<string>::iterator itname;
+               vector<string> nameFileOrder;
                int count = 0;
                while (!in.eof()) {
                        
@@ -189,8 +190,9 @@ int DeconvoluteCommand::execute() {
                                                        m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file, and not in your namefile, please correct."); m->mothurOutEndLine();
                                                }else {
                                                        sequenceStrings[seq.getAligned()] = itNames->second;
+                                                       nameFileOrder.push_back(seq.getAligned());
                                                }
-                                       }else { sequenceStrings[seq.getAligned()] = seq.getName();      }
+                                       }else { sequenceStrings[seq.getAligned()] = seq.getName();      nameFileOrder.push_back(seq.getAligned()); }
                                }else { //this is a dup
                                        if (oldNameMapFName != "") {
                                                itNames = nameMap.find(seq.getName());
@@ -222,17 +224,22 @@ int DeconvoluteCommand::execute() {
                ofstream outNames;
                m->openOutputFile(outNameFile, outNames);
                
-               for (itStrings = sequenceStrings.begin(); itStrings != sequenceStrings.end(); itStrings++) {
+               for (int i = 0; i < nameFileOrder.size(); i++) {
+               //for (itStrings = sequenceStrings.begin(); itStrings != sequenceStrings.end(); itStrings++) {
                        if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); outNames.close(); m->mothurRemove(outNameFile); return 0; }
                        
-                       //get rep name
-                       int pos = (itStrings->second).find_first_of(',');
+                       itStrings = sequenceStrings.find(nameFileOrder[i]);
                        
-                       if (pos == string::npos) { // only reps itself
-                               outNames << itStrings->second << '\t' << itStrings->second << endl;
-                       }else {
-                               outNames << (itStrings->second).substr(0, pos) << '\t' << itStrings->second << endl;
-                       }
+                       if (itStrings != sequenceStrings.end()) {
+                               //get rep name
+                               int pos = (itStrings->second).find_first_of(',');
+                       
+                               if (pos == string::npos) { // only reps itself
+                                       outNames << itStrings->second << '\t' << itStrings->second << endl;
+                               }else {
+                                       outNames << (itStrings->second).substr(0, pos) << '\t' << itStrings->second << endl;
+                               }
+                       }else{ m->mothurOut("[ERROR]: mismatch in namefile print."); m->mothurOutEndLine(); m->control_pressed = true; }
                }
                outNames.close();