classify.seqs allows sequences to be in taxonomy file that are not in template. ...

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 6a3535fb4af55ee1b217c9a18c4fc83e08db7539..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
@@ -441,6 +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';       }