mods to shhh.seqs and trim.flows to fix eye candy output

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 05ed31ebd880af06984fa87cba97349df3f5e8c4..6ee865516bee6851fadf28f81e70bb249c35562d 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -124,14 +124,6 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                                        if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
                                }
                                
-                               
-//                             it = parameters.find("group");
-//                             //user has given a template file
-//                             if(it != parameters.end()){ 
-//                                     path = m->hasPath(it->second);
-//                                     //if the user has not given a path then, add inputdir. else leave path alone.
-//                                     if (path == "") {       parameters["group"] = inputDir + it->second;            }
-//                             }
                        }
                        
                        
@@ -157,10 +149,10 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        // ...at some point should added some additional type checking...
                        
                        string temp;
-                       temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "360"; }
+                       temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "450"; }
                        convert(temp, minFlows);  
 
-                       temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "720"; }
+                       temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "450"; }
                        convert(temp, maxFlows);  
                        
                        
@@ -283,7 +275,7 @@ int TrimFlowsCommand::execute(){
                                        if (pFile==NULL) perror ("Error opening file");
                                        else{
                                                fseek (pFile, 0, SEEK_END);
-                                               size=ftell (pFile);
+                                               size=ftell(pFile);
                                                fclose (pFile);
                                        }
 
@@ -292,6 +284,8 @@ int TrimFlowsCommand::execute(){
                                        }
                                        else{
                                                output << barcodePrimerComboFileNames[i][j] << endl;
+                                               outputNames.push_back(barcodePrimerComboFileNames[i][j]);
+                                               outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
                                        }
                                }
                        }
@@ -306,14 +300,14 @@ int TrimFlowsCommand::execute(){
                        output.close();
                }
                outputTypes["flow.files"].push_back(flowFilesFileName);
-               outputNames.push_back(flowFileName);
+               outputNames.push_back(flowFilesFileName);
                
-               //set fasta file as new current fastafile
-               string current = "";
-               itTypes = outputTypes.find("fasta");
-               if (itTypes != outputTypes.end()) {
-                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
-               }
+//             set fasta file as new current fastafile
+//             string current = "";
+//             itTypes = outputTypes.find("fasta");
+//             if (itTypes != outputTypes.end()) {
+//                     if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+//             }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -581,8 +575,6 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
                                                fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
                                        }
                                        
-                                       outputNames.push_back(fileName);
-                                       outputTypes["flow"].push_back(fileName);
                                        outFlowFileNames[itBar->second][itPrimer->second] = fileName;
                                        
                                        ofstream temp;