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

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index b4de07b082fb0274c02ba71793c0e3023d192a35..22dc2e9f7ab15a671f4a3dd699ca570655b688a4 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -49,10 +49,11 @@ int SharedCommand::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;
                
                shared = new Shared();
                
-               while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+               while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
                        
                                                
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
@@ -62,6 +63,7 @@ int SharedCommand::execute(){
                                
                                        processedLabels.insert(SharedList->getLabel());
                                        userLabels.erase(SharedList->getLabel());
+                                       userLines.erase(count);
                        }
                        
                        if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastList->getLabel()) != 1)) {