get.oturep change and trim.seqs fix

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 818775fdd7e24678545750fcfad6596efdd666e6..44c58c31d26e66342e7a1bf73feb21f7f3919bfa 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -437,7 +437,7 @@ int GetOTURepCommand::execute(){
                        delete read; delete input; delete list; globaldata->gListVector = NULL; return 0; 
                }
                
-               if (!weighted) { readNamesFile(weighted); }
+               if ((!weighted) && (namefile != "")) { readNamesFile(weighted); }
                
                while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
@@ -565,7 +565,7 @@ void GetOTURepCommand::readNamesFile() {
                
                string name, names, sequence;
        
-               while(inNames){
+               while(!inNames.eof()){
                        inNames >> name;                        //read from first column  A
                        inNames >> names;               //read from second column  A,B,C,D
                        
@@ -599,7 +599,7 @@ void GetOTURepCommand::readNamesFile(bool w) {
                
                string name, names, sequence;
                
-               while(inNames){
+               while(!inNames.eof()){
                        inNames >> name;        m->gobble(inNames);             //read from first column  A
                        inNames >> names;                                                       //read from second column  A,B,C,D