fix trim.seqs / qualscores bug

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index abfe15a17a18d9e203be7bc4bfaac0fd0e6b4a0f..49aca824ea46fb18c5845e4caa5bab0aca5db305 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -352,7 +352,6 @@ int TrimSeqsCommand::execute(){
                if (m->control_pressed) {  return 0; }                  
                        
                if(allFiles){
-                       //clear out all old group files
                        map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
                        map<string, string>::iterator it;
                        set<string> namesToRemove;
@@ -407,10 +406,10 @@ int TrimSeqsCommand::execute(){
                //output group counts
                m->mothurOutEndLine();
                int total = 0;
-               for (int i = 0; i < barcodeNameVector.size(); i++) {
-                       if ((barcodeNameVector[i] != "") && (groupCounts[i] != 0)) { total += groupCounts[i]; m->mothurOut("Group " + barcodeNameVector[i] + " contains " + toString(groupCounts[i]) + " sequences."); m->mothurOutEndLine(); }
-               }
-               if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
+//             for (int i = 0; i < barcodeNameVector.size(); i++) {
+//                     if ((barcodeNameVector[i] != "") && (groupCounts[i] != 0)) { total += groupCounts[i]; m->mothurOut("Group " + barcodeNameVector[i] + " contains " + toString(groupCounts[i]) + " sequences."); m->mothurOutEndLine(); }
+//             }
+//             if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
                
                        if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } return 0;     }