some changes to trim.flows

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 8184327e5bbfe33afa534cfc6515627d05403324..bb8d3863ea56b52dfea6c772dbf0beb397810849 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -16,7 +16,7 @@ vector<string> TrimFlowsCommand::getValidParameters(){
        try {
                string Array[] =  {"flow", "maxflows", "minflows",
                        "fasta", "minlength", "maxlength", "maxhomop", "signal", "noise"
-                       "oligos", "pdiffs", "bdiffs", "tdiffs", 
+                       "oligos", "pdiffs", "bdiffs", "tdiffs",  "order",
                        "allfiles", "processors",
                        "outputdir","inputdir"
                
@@ -106,7 +106,7 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        //valid paramters for this command
                        string AlignArray[] =  {"flow", "maxflows", "minflows",
                                "fasta", "minlength", "maxlength", "maxhomop", "signal", "noise",
-                               "oligos", "pdiffs", "bdiffs", "tdiffs", 
+                               "oligos", "pdiffs", "bdiffs", "tdiffs", "order",
                                "allfiles", "processors",
                
                                //                      "group",
@@ -226,7 +226,13 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){ temp = "1";           }
                        convert(temp, processors); 
-                       
+       
+                       flowOrder = validParameter.validFile(parameters, "order", false);
+                       if (flowOrder == "not found"){ flowOrder = "TACG";              }
+                       else if(flowOrder.length() != 4){
+                               m->mothurOut("The value of the order option must be four bases long\n");
+                       }
+
                        if(oligoFileName == ""){        allFiles = 0;           }
 
                        numFPrimers = 0;
@@ -367,7 +373,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                        }
                }
                
-               FlowData flowData(numFlows, signal, noise, maxHomoP);
+               FlowData flowData(numFlows, signal, noise, maxHomoP, flowOrder);
                
                ofstream fastaFile;
                if(fasta){      m->openOutputFile(fastaFileName, fastaFile);    }