worked on chimeras

[mothur.git] / chimeraseqscommand.cpp

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index 08c02a8ecc64afecb5693e7f834b02b4759c1199..aaed3bab7b56b14460d06de90c9551df70c4351d 100644 (file)
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -22,7 +22,7 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantiles" };
+                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile" };
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -48,9 +48,9 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                        if (consfile == "not open") { abort = true; }
                        else if (consfile == "not found") { consfile = "";  }   
                        
-                       quanfile = validParameter.validFile(parameters, "quantiles", true);
+                       quanfile = validParameter.validFile(parameters, "quantile", true);
                        if (quanfile == "not open") { abort = true; }
-                       else if (quanfile == "not found") { consfile = "";  }   
+                       else if (quanfile == "not found") { quanfile = "";  }   
                        
 
                        string temp;
@@ -71,7 +71,7 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                                
                        method = validParameter.validFile(parameters, "method", false);         if (method == "not found") { method = "pintail"; }
                        
-                       if ((method == "pintail") && (templatefile == "") && (consfile == "")) { mothurOut("You must provide a template or conservation file with the pintail method."); mothurOutEndLine(); abort = true;  }
+                       if ((method == "pintail") && (templatefile == "")) { mothurOut("You must provide a template file with the pintail method."); mothurOutEndLine(); abort = true;  }
                        
 
                }