added sff.multiple command. fixed issue with windows paralellization in chimera...

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 2d77d28d367c8c9cf0be0e8b0094817f4adb1ee9..d7ca230449fbebd3488a512c5fbd25d3159c1156 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -118,7 +118,7 @@ SffInfoCommand::SffInfoCommand(){
 SffInfoCommand::SffInfoCommand(string option)  {
        try {
                abort = false; calledHelp = false;   
-               hasAccnos = false;
+               hasAccnos = false; hasOligos = false;
         split = 1;
                
                //allow user to run help
@@ -583,7 +583,6 @@ int SffInfoCommand::extractSffInfo(string input, string accnos, string oligos){
             //create new common headers for each file with the correct number of reads
             adjustCommonHeader(header);
             
-            map<string, string> uniqueSffNames;// so we don't add the same sff multiple times
                        map<string, string>::iterator it;
                        set<string> namesToRemove;
                        for(int i=0;i<filehandles.size();i++){
@@ -594,12 +593,7 @@ int SffInfoCommand::extractSffInfo(string input, string accnos, string oligos){
                                                                m->mothurRemove(filehandles[i][j]);
                                 m->mothurRemove(filehandlesHeaders[i][j]);
                                                                namesToRemove.insert(filehandles[i][j]);
-                            }else{     
-                                                               it = uniqueSffNames.find(filehandles[i][j]);
-                                                               if (it == uniqueSffNames.end()) {       
-                                                                       uniqueSffNames[filehandles[i][j]] = barcodeNameVector[i];       
-                                                               }       
-                                                       }
+                            }
                                                }
                                        }
                                }