shhh.seqs and trim.flows modifications.

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 960a59d3950e92590063f348f890c267a3123e12..8184327e5bbfe33afa534cfc6515627d05403324 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -221,10 +221,10 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        convert(temp, tdiffs);
                        if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
                        
-                       temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found") { temp = "T";          }
+                       temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found"){ temp = "T";           }
                        allFiles = m->isTrue(temp);
                        
-                       temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found") { temp = "1"; }
+                       temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){ temp = "1";           }
                        convert(temp, processors); 
                        
                        if(oligoFileName == ""){        allFiles = 0;           }
@@ -322,6 +322,7 @@ int TrimFlowsCommand::execute(){
                        output.close();
                }
                outputTypes["flow.files"].push_back(flowFilesFileName);
+               outputNames.push_back(flowFileName);
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -431,15 +432,13 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                                if(fasta)       {       currSeq.printSequence(fastaFile);       }
                                
                                if(allFiles){
-//                                     string fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + barcodePrimerCombos[barcodeIndex][primerIndex] + ".flow";
                                        ofstream output;
                                        m->openOutputFileAppend(barcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
                                        output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
                                        
                                        flowData.printFlows(output);
                                        output.close();
-                               }
-                               
+                               }                               
                        }
                        else{
                                flowData.printFlows(scrapFlowFile, trashCode);