working on pam

[mothur.git] / seqsummarycommand.cpp

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 0e3b70c1db3824084a51fb0db1c88630285878c2..70aa55d38502237388c520aeae892daf4891e73c 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -203,7 +203,7 @@ int SeqSummaryCommand::execute(){
                if (namefile != "") { nameMap = m->readNames(namefile); }
         else if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile, false);
+            ct.readTable(countfile, false, false);
             nameMap = ct.getNameMap();
         }
                
@@ -449,7 +449,8 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
 
                bool done = false;
                int count = 0;
-       
+        
+        
                while (!done) {
                                
                        if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
@@ -479,7 +480,6 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
                                        ambigBases.push_back(current.getAmbigBases());
                                        longHomoPolymer.push_back(current.getLongHomoPolymer());
                                }
-                               
                                count++;
                                outSummary << current.getName() << '\t';
                                outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';