added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / countseqscommand.cpp

diff --git a/countseqscommand.cpp b/countseqscommand.cpp
index a7890b878a7f1210137e683e4a1311a02439eb49..9cdd033ac29609d6f763f52597a4809fea204326 100644 (file)
--- a/countseqscommand.cpp
+++ b/countseqscommand.cpp
@@ -157,7 +157,8 @@ int CountSeqsCommand::execute(){
                        
                        //make sure groups are valid. takes care of user setting groupNames that are invalid or setting groups=all
                        SharedUtil* util = new SharedUtil();
-                       util->setGroups(Groups, groupMap->namesOfGroups);
+                       vector<string> nameGroups = groupMap->getNamesOfGroups();
+                       util->setGroups(Groups, nameGroups);
                        delete util;
                        
                        //sort groupNames so that the group title match the counts below, this is needed because the map object automatically sorts
@@ -222,7 +223,7 @@ int CountSeqsCommand::execute(){
                
                if (groupfile != "") { delete groupMap; }
                
-               if (m->control_pressed) { remove(outputFileName.c_str()); return 0; }
+               if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Name: "); m->mothurOutEndLine();