added binary file operations to mothurout class. added comment to sequence class...

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index d93fb6e775392b5436b6dadbb99c88761e862de8..2c9399bda1dd363d04c1fed89ff9b12ea8c3aace 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -184,9 +184,6 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
                        string temp = validParameter.validFile(parameters, "all", false);                               if (temp == "not found") { temp = "false"; }
                        all = m->isTrue(temp);
                        
-                       temp = validParameter.validFile(parameters, "distance", false);                                 if (temp == "not found") { temp = "false"; }
-                       createPhylip = m->isTrue(temp);
-                       
             temp = validParameter.validFile(parameters, "iters", false);                       if (temp == "not found") { temp = "1000"; }
                        m->mothurConvert(temp, iters); 
             
@@ -204,6 +201,10 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
             
             if (subsample == false) { iters = 0; }
             
+            temp = validParameter.validFile(parameters, "distance", false);                                    if (temp == "not found") { temp = "false"; }
+                       createPhylip = m->isTrue(temp);
+            if (subsample) { createPhylip = true; }
+            
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
                        m->mothurConvert(temp, processors);