working on chimera.slayer

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index cf219951f08e314f57ebb2e6c27985d3f5409167..11193329c604d13a20d4094a08292954eb2c54bd 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -342,7 +342,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        temp = validParameter.validFile(parameters, "parents", false);                  if (temp == "not found") { temp = "3"; }
                        convert(temp, parents); 
                        
-                       temp = validParameter.validFile(parameters, "realign", true);                   if (temp == "not found") { temp = "t"; }
+                       temp = validParameter.validFile(parameters, "realign", false);                  if (temp == "not found") { temp = "t"; }
                        realign = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "trim", false);                             if (temp == "not found") { temp = "f"; }
@@ -374,7 +374,6 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
 
 int ChimeraSlayerCommand::execute(){
        try{
-               
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                for (int s = 0; s < fastaFileNames.size(); s++) {