added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / nmdscommand.cpp

diff --git a/nmdscommand.cpp b/nmdscommand.cpp
index da82784f56124d5a360294fb9cc7c4b6b1114307..e2a3712a410738b0396884accc41bdd555caa735 100644 (file)
--- a/nmdscommand.cpp
+++ b/nmdscommand.cpp
@@ -141,22 +141,22 @@ NMDSCommand::NMDSCommand(string option)  {
                        }
                        
                        string temp = validParameter.validFile(parameters, "mindim", false);    if (temp == "not found") {      temp = "2";     }
-                       convert(temp, mindim);
+                       m->mothurConvert(temp, mindim);
                        
                        temp = validParameter.validFile(parameters, "maxiters", false); if (temp == "not found") {      temp = "500";   }
-                       convert(temp, maxIters);
+                       m->mothurConvert(temp, maxIters);
                        
                        temp = validParameter.validFile(parameters, "iters", false);    if (temp == "not found") {      temp = "10";    }
-                       convert(temp, iters);
+                       m->mothurConvert(temp, iters);
                        
                        temp = validParameter.validFile(parameters, "maxdim", false);   if (temp == "not found") {      temp = "2";     }
-                       convert(temp, maxdim);
+                       m->mothurConvert(temp, maxdim);
                        
                        temp = validParameter.validFile(parameters, "epsilon", false);  if (temp == "not found") {      temp = "0.000000000001";        }
-                       convert(temp, epsilon); 
+                       m->mothurConvert(temp, epsilon); 
                        
                        if (mindim < 1) { m->mothurOut("mindim must be at least 1."); m->mothurOutEndLine(); abort = true; }
-                       if (maxdim < mindim) { m->mothurOut("maxdim must be greater than mindim."); m->mothurOutEndLine(); abort = true; }
+                       if (maxdim < mindim) { maxdim = mindim; }
                }
                
        }