metastats in progress

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 1cbb91a2da487a7f0aa00a0689d393297ba592c0..89ea3f9c8b44c782e2a9ebd8588c548c61f9e81a 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -203,8 +203,8 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        // ...at some point should added some additional type checking...
                        string temp;
                        temp = validParameter.validFile(parameters, "flip", false);
-                       if (temp == "not found"){       flip = 0;       }
-                       else if(m->isTrue(temp))        {       flip = 1;       }
+                       if (temp == "not found")    {   flip = 0;       }
+                       else {  flip = m->isTrue(temp);         }
                
                        temp = validParameter.validFile(parameters, "oligos", true);
                        if (temp == "not found"){       oligoFile = "";         }