1.23.0

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 0512be1a70b1d12b0667f5945e4d1acb5b4768d8..cfcad1514ca629823081f54e35156934275644b1 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -383,7 +383,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 
@@ -441,34 +441,34 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        
                        
                        temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
-                       convert(temp, ksize);
+                       m->mothurConvert(temp, ksize);
                                                
                        temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "50"; }                       
-                       convert(temp, window);
+                       m->mothurConvert(temp, window);
                        
                        temp = validParameter.validFile(parameters, "match", false);                    if (temp == "not found") { temp = "5"; }
-                       convert(temp, match);
+                       m->mothurConvert(temp, match);
                        
                        temp = validParameter.validFile(parameters, "mismatch", false);                 if (temp == "not found") { temp = "-4"; }
-                       convert(temp, mismatch);
+                       m->mothurConvert(temp, mismatch);
                        
                        temp = validParameter.validFile(parameters, "divergence", false);               if (temp == "not found") { temp = "1.007"; }
-                       convert(temp, divR);
+                       m->mothurConvert(temp, divR);
                        
                        temp = validParameter.validFile(parameters, "minsim", false);                   if (temp == "not found") { temp = "90"; }
-                       convert(temp, minSimilarity);
+                       m->mothurConvert(temp, minSimilarity);
                        
                        temp = validParameter.validFile(parameters, "mincov", false);                   if (temp == "not found") { temp = "70"; }
-                       convert(temp, minCoverage);
+                       m->mothurConvert(temp, minCoverage);
                        
                        temp = validParameter.validFile(parameters, "minbs", false);                    if (temp == "not found") { temp = "90"; }
-                       convert(temp, minBS);
+                       m->mothurConvert(temp, minBS);
                        
                        temp = validParameter.validFile(parameters, "minsnp", false);                   if (temp == "not found") { temp = "10"; }
-                       convert(temp, minSNP);
+                       m->mothurConvert(temp, minSNP);
 
                        temp = validParameter.validFile(parameters, "parents", false);                  if (temp == "not found") { temp = "3"; }
-                       convert(temp, parents); 
+                       m->mothurConvert(temp, parents); 
                        
                        temp = validParameter.validFile(parameters, "realign", false);                  if (temp == "not found") { temp = "t"; }
                        realign = m->isTrue(temp); 
@@ -482,13 +482,13 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        search = validParameter.validFile(parameters, "search", false);                 if (search == "not found") { search = "blast"; }
                        
                        temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }             
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters); 
                         
                        temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "5"; }
-                       convert(temp, increment);
+                       m->mothurConvert(temp, increment);
                        
                        temp = validParameter.validFile(parameters, "numwanted", false);                if (temp == "not found") { temp = "15"; }               
-                       convert(temp, numwanted);
+                       m->mothurConvert(temp, numwanted);
                        
                        blastlocation = validParameter.validFile(parameters, "blastlocation", false);   
                        if (blastlocation == "not found") { blastlocation = ""; }