fixed bug with shhh.flow from file path name in write functions, added "smart" featur...

[mothur.git] / summaryqualcommand.cpp

diff --git a/summaryqualcommand.cpp b/summaryqualcommand.cpp
index 421a8f2ad36c64e218aa68a4eb6fd8dc651362d0..2a40e0862ba0b0444db035246cdcb95409fe4923 100644 (file)
--- a/summaryqualcommand.cpp
+++ b/summaryqualcommand.cpp
@@ -111,7 +111,7 @@ SummaryQualCommand::SummaryQualCommand(string option)  {
                        
                        //check for required parameters
                        qualfile = validParameter.validFile(parameters, "qfile", true);
-                       if (qualfile == "not open") { abort = true; }
+                       if (qualfile == "not open") { qualfile = ""; abort = true; }
                        else if (qualfile == "not found") {                             
                                qualfile = m->getQualFile(); 
                                if (qualfile != "") { m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
@@ -131,7 +131,12 @@ SummaryQualCommand::SummaryQualCommand(string option)  {
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       m->mothurConvert(temp, processors);                     
+                       m->mothurConvert(temp, processors);     
+                       
+                       if (namefile == "") {
+                               vector<string> files; files.push_back(qualfile);
+                               parser.getNameFile(files);
+                       }
                }
        }
        catch(exception& e) {