changed dups parameter to dereplicate in chimera.uchime.

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index d45f20cae1f0516c014d42cf7e6afaef57d2a1a2..296a6fe37d0449bb719d69c4001429583bcb74ee 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -28,7 +28,7 @@ vector<string> TrimFlowsCommand::setParameters(){
                CommandParameter psignal("signal", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(psignal);
                CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pnoise);
                CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "",false,false); parameters.push_back(pallfiles);
-               CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder);
+               CommandParameter porder("order", "String", "", "TACG", "", "", "",false,false); parameters.push_back(porder);
                CommandParameter pfasta("fasta", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfasta);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
@@ -347,7 +347,7 @@ int TrimFlowsCommand::execute(){
                        
                        output.close();
                }
-               outputTypes["flow.files"].push_back(flowFilesFileName);
+               outputTypes["file"].push_back(flowFilesFileName);
                outputNames.push_back(flowFilesFileName);
                
 //             set fasta file as new current fastafile
@@ -423,11 +423,9 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                        string trashCode = "";
                        
                        flowData.getNext(flowFile); 
-                       //cout << "driver good bit " << flowFile.good() << endl;        
                        flowData.capFlows(maxFlows);    
                        
                        Sequence currSeq = flowData.getSequence();
-                       
                        if(!flowData.hasMinFlows(minFlows)){    //screen to see if sequence is of a minimum number of flows
                                success = 0;
                                trashCode += 'l';
@@ -443,6 +441,8 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                 
             }
             
+            if (m->debug) { m->mothurOut("[DEBUG]: " + currSeq.getName() + " " + currSeq.getUnaligned() + "\n"); }
+            
                        if(barcodes.size() != 0){
                                success = trimOligos.stripBarcode(currSeq, barcodeIndex);
                                if(success > bdiffs)            {       trashCode += 'b';       }