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

[mothur.git] / parselistcommand.cpp

diff --git a/parselistcommand.cpp b/parselistcommand.cpp
index 20f92f73b3e8107bd47a1e99f253779e67d2a423..c0622f219cc252be7ca0bf29d28ac349cddb3357 100644 (file)
--- a/parselistcommand.cpp
+++ b/parselistcommand.cpp
@@ -99,6 +99,7 @@ int ParseListCommand::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;
 
                        //read in group map info.
                        groupMap = new GroupMap(globaldata->getGroupFile());
@@ -112,7 +113,7 @@ int ParseListCommand::execute(){
                                                
                        //parses and sets each groups listvector
                        //as long as you are not at the end of the file or done wih the lines you want
-                       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){
                                        cout << list->getLabel() << '\t' << count << endl;
@@ -120,6 +121,7 @@ int ParseListCommand::execute(){
                                        
                                        processedLabels.insert(list->getLabel());
                                        userLabels.erase(list->getLabel());
+                                       userLines.erase(count);
                                }
                                
                                if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {