added get.rabund and get.sabund command and fixed bug introduced by line by line...

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index e7fda2e5dedcd8052b3c610931964377e356a7af..9bc0c0f2239282193748a651389af8c238b1daa2 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -144,14 +144,16 @@ int SummaryCommand::execute(){
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
                set<string> processedLabels;
                set<string> userLabels = globaldata->labels;
+               set<int> userLines = globaldata->lines;
                
-               while((sabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+               while((sabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
                        
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){                      
        
                                cout << sabund->getLabel() << '\t' << count << endl;
                                processedLabels.insert(sabund->getLabel());
                                userLabels.erase(sabund->getLabel());
+                               userLines.erase(count);
 
                                
                                outputFileHandle << sabund->getLabel();