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

[mothur.git] / bootstrapsharedcommand.cpp

diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp
index 2835061392732dfa402f626a3d339726a601435a..9ffd2b73f0935df7ea46402f5555fb9ea9372ada 100644 (file)
--- a/bootstrapsharedcommand.cpp
+++ b/bootstrapsharedcommand.cpp
@@ -104,6 +104,7 @@ int BootSharedCommand::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, "treegroup");
@@ -120,7 +121,7 @@ int BootSharedCommand::execute(){
                tmap->makeSim(globaldata->gGroupmap);
                globaldata->gTreemap = tmap;
                        
-               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){                       
                                
@@ -129,10 +130,10 @@ int BootSharedCommand::execute(){
                                
                                processedLabels.insert(order->getLabel());
                                userLabels.erase(order->getLabel());
-                               
-                       //you have a label the user want that is smaller than this line and the last line has not already been processed 
+                               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
                        if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
                                                                                        
                                cout << lastOrder->getLabel() << '\t' << count << endl;