bug fixes

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index dd5bf3460debcc3e2fd5b6af736b0e123c7890ae..d1b9a5c43549991bd3876164a318b8d9accb54ce 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -34,7 +34,8 @@ TrimSeqsCommand::TrimSeqsCommand(){
                abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
-               outputTypes["qual"] = tempOutNames;
+               outputTypes["qfile"] = tempOutNames;
+               outputTypes["group"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
@@ -103,7 +104,8 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        //initialize outputTypes
                        vector<string> tempOutNames;
                        outputTypes["fasta"] = tempOutNames;
-                       outputTypes["qual"] = tempOutNames;
+                       outputTypes["qfile"] = tempOutNames;
+                       outputTypes["group"] = tempOutNames;
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
@@ -223,13 +225,9 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found") { temp = "1"; }
                        convert(temp, processors); 
                        
-                       if ((oligoFile != "") && (groupfile != "")) {
-                               m->mothurOut("You given both a oligos file and a groupfile, only one is allowed."); m->mothurOutEndLine(); abort = true;
-                       }
-                                                                                               
                        
-                       if(allFiles && (oligoFile == "") && (groupfile == "")){
-                               m->mothurOut("You selected allfiles, but didn't enter an oligos or group file.  Ignoring the allfiles request."); m->mothurOutEndLine();
+                       if(allFiles && (oligoFile == "")){
+                               m->mothurOut("You selected allfiles, but didn't enter an oligos.  Ignoring the allfiles request."); m->mothurOutEndLine();
                        }
                        if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
                                m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
@@ -319,15 +317,15 @@ int TrimSeqsCommand::execute(){
                if (qFileName != "") {
                        outputNames.push_back(trimQualFile);
                        outputNames.push_back(scrapQualFile);
-                       outputTypes["qual"].push_back(trimQualFile);
-                       outputTypes["qual"].push_back(scrapQualFile); 
+                       outputTypes["qfile"].push_back(trimQualFile);
+                       outputTypes["qfile"].push_back(scrapQualFile); 
                }
                
                string outputGroupFileName;
 
                if(oligoFile != ""){
                        outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
-                       outputNames.push_back(outputGroupFileName); outputTypes["groups"].push_back(outputGroupFileName);
+                       outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
                        getOligos(fastaFileNames, qualFileNames);
                }
 
@@ -928,7 +926,7 @@ void TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                        if(qFileName != ""){
                                                qualFileName = outputDir + m->getRootName(m->getSimpleName(qFileName)) + comboGroupName + ".qual";
                                                outputNames.push_back(qualFileName);
-                                               outputTypes["qual"].push_back(qualFileName);
+                                               outputTypes["qfile"].push_back(qualFileName);
                                                qualFileNames[itBar->second][itPrimer->second] = qualFileName;
                                                m->openOutputFile(qualFileName, temp);          temp.close();
                                        }