line and label no longer persist between commands. Added phylip formated output...

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 0a742ea562852e8097485bea5a67200f6d8524c8..6a09ada5d3e8e4141c56a0c0ef4943beae6ef815 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -164,6 +164,11 @@ int SummarySharedCommand::execute(){
                        outputFileHandle.close();  remove(outputFileName.c_str());
                        if (mult == true) {  outAll.close();  remove(outAllFileName.c_str());  }
                        return 0;
+               //if you only have 2 groups you don't need a .sharedmultiple file
+               }else if ((lookup.size() == 2) && (mult == true)) { 
+                       mult = false;
+                       outAll.close();  
+                       remove(outAllFileName.c_str());
                }
                                        
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.