fixes while testing 1.33.0

[mothur.git] / sequencecountparser.cpp

diff --git a/sequencecountparser.cpp b/sequencecountparser.cpp
index 4ba60918bd7f064ad3bfb71c08574ce4c2c167aa..5349da09ff719a5ac07a85ecb4015c44d41121ee 100644 (file)
--- a/sequencecountparser.cpp
+++ b/sequencecountparser.cpp
@@ -16,7 +16,7 @@ SequenceCountParser::SequenceCountParser(string countfile, string fastafile) {
                
                //read count file
                CountTable countTable;
-               countTable.readTable(countfile);
+               countTable.readTable(countfile, true, false);
                
                //initialize maps
                namesOfGroups = countTable.getNamesOfGroups();
@@ -206,7 +206,7 @@ int SequenceCountParser::getSeqs(string g, string filename, bool uchimeFormat=fa
                                        
                                        if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }
                                        
-                                       out << ">" << nameVector[i].name  << "/ab=" << nameVector[i].numIdentical << "/" << endl << nameVector[i].seq << endl;
+                                       out << ">" << nameVector[i].name << "/ab=" << nameVector[i].numIdentical << "/" << endl << nameVector[i].seq << endl; //
                                }
                                
                        }else {