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

[mothur.git] / binsequencecommand.cpp

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index c21757850b858d4a53173619da911ffcab5d24a3..8f0bb9fd45b34fbaa6d72b81f9d42e7658d2ee3a 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -77,9 +77,10 @@ int BinSeqCommand::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((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+               while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
                        
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){
                                
@@ -88,7 +89,7 @@ int BinSeqCommand::execute(){
                                                        
                                processedLabels.insert(list->getLabel());
                                userLabels.erase(list->getLabel());
-
+                               userLines.erase(count);
                        }
                        
                        if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {