fixes while testing 1.33.0

[mothur.git] / venncommand.cpp

diff --git a/venncommand.cpp b/venncommand.cpp
index 3767687bff20dd66f754d8e55920135d7609fe68..0327d53b6d0d85c737d4b6e17d0666afa183efdd 100644 (file)
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -214,10 +214,19 @@ VennCommand::VennCommand(string option)  {
                        temp = validParameter.validFile(parameters, "nseqs", false);            if (temp == "not found"){       temp = "f";                             }
                        nseqs = m->isTrue(temp); 
 
-                       temp = validParameter.validFile(parameters, "permute", false);          if (temp == "not found"){       temp = "4";                             }
+                       temp = validParameter.validFile(parameters, "permute", false);
+            if (temp == "not found"){  temp = "4";                             }
+            else {
+                if ((temp == "1") || (temp == "2") || (temp == "3") || (temp == "4")) {}
+                else {
+                    bool permTrue = m->isTrue(temp);
+                    if (permTrue) { temp = "4"; }
+                    else { }
+                }
+            }
                        m->mothurConvert(temp, perm);
             if ((perm == 1) || (perm == 2) || (perm == 3) || (perm == 4)) { }
-            else { m->mothurOut("[ERROR]: Not a valid permute value.  Valid values are 1, 2, 3, and 4."); m->mothurOutEndLine(); abort = true;  }
+            else { m->mothurOut("[ERROR]: Not a valid permute value.  Valid values are 1, 2, 3, 4 and true."); m->mothurOutEndLine(); abort = true;  }
             
             temp = validParameter.validFile(parameters, "sharedotus", false);          if (temp == "not found"){       temp = "t";                             }
                        sharedOtus = m->isTrue(temp);