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

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index fd28e841faee71bf35ed49a3f6ff21e4455cb8fa..d2333d74c6890f8d1c5563e22e9f27ba633046f2 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -140,12 +140,13 @@ int CollectSharedCommand::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;
                                
                //set users groups
                util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "collect");
                util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
 
-               while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+               while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
                                
@@ -157,6 +158,7 @@ int CollectSharedCommand::execute(){
                                cout << order->getLabel() << '\t' << count << endl;
                                processedLabels.insert(order->getLabel());
                                userLabels.erase(order->getLabel());
+                               userLines.erase(count);
 
                        //you have a label the user want that is smaller than this line and the last line has not already been processed 
                        }