added modify names parameter to set.dir

[mothur.git] / removeseqscommand.cpp

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index 5c0216366a98c83bc11c776ad31b0da1086120cd..b1bc4fd508576c04126206b4e178798c088cb91d 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -469,7 +469,7 @@ int RemoveSeqsCommand::readQual(){
                                saveName = name.substr(1);
                                while (!in.eof())       {       
                                        char c = in.get(); 
-                                       if (c == 10 || c == 13){        break;  }
+                                       if (c == 10 || c == 13 || c == -1){     break;  }
                                        else { name += c; }     
                                } 
                                m->gobble(in);
@@ -557,7 +557,7 @@ int RemoveSeqsCommand::readCount(){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(outputFileName)) {
-            ct.readTable(outputFileName);
+            ct.readTable(outputFileName, true);
             ct.printTable(outputFileName);
         }
 
@@ -813,7 +813,7 @@ int RemoveSeqsCommand::readTax(){
                while(!in.eof()){
                        if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
                        
-                       in >> name;                             //read from first column
+                       in >> name;     m->gobble(in);                  //read from first column
                        in >> tax;                      //read from second column
                        
             if (!dups) {//adjust name if needed