added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / removerarecommand.cpp

diff --git a/removerarecommand.cpp b/removerarecommand.cpp
index c320fa4d8854f003486bc71c8e6b0806ec7ae0e3..24b616560de3bed794d423f4cb7a3544f0d48f5f 100644 (file)
--- a/removerarecommand.cpp
+++ b/removerarecommand.cpp
@@ -220,7 +220,7 @@ RemoveRareCommand::RemoveRareCommand(string option)  {
                        
                        string temp = validParameter.validFile(parameters, "nseqs", false);      
                        if (temp == "not found") { m->mothurOut("nseqs is a required parameter."); m->mothurOutEndLine(); abort = true; }
-                       else { convert(temp, nseqs); }
+                       else { m->mothurConvert(temp, nseqs); }
                        
                        temp = validParameter.validFile(parameters, "bygroup", false);   if (temp == "not found") { temp = "f"; }
                        byGroup = m->isTrue(temp);
@@ -251,7 +251,7 @@ int RemoveRareCommand::execute(){
                if (listfile != "")                     {               processList();          }
                if (sharedfile != "")           {               processShared();        }
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
                        
                if (outputNames.size() != 0) {
                        m->mothurOutEndLine();
@@ -353,7 +353,8 @@ int RemoveRareCommand::processList(){
                if (groupfile != "") { 
                        groupMap = new GroupMap(groupfile); groupMap->readMap(); 
                        SharedUtil util;
-                       util.setGroups(Groups, groupMap->namesOfGroups);
+                       vector<string> namesGroups = groupMap->getNamesOfGroups();
+                       util.setGroups(Groups, namesGroups);
                        m->openOutputFile(outputGroupFileName, outGroup);
                }
                
@@ -365,7 +366,7 @@ int RemoveRareCommand::processList(){
                        
                        //for each bin
                        for (int i = 0; i < list->getNumBins(); i++) {
-                               if (m->control_pressed) {  if (groupfile != "") { delete groupMap; outGroup.close(); remove(outputGroupFileName.c_str()); } out.close();  remove(outputFileName.c_str());  return 0; }
+                               if (m->control_pressed) {  if (groupfile != "") { delete groupMap; outGroup.close(); m->mothurRemove(outputGroupFileName); } out.close();  m->mothurRemove(outputFileName);  return 0; }
                                
                                //parse out names that are in accnos file
                                string binnames = list->get(i);
@@ -624,7 +625,7 @@ int RemoveRareCommand::processRabund(){
 //**********************************************************************************************************************
 int RemoveRareCommand::processShared(){
        try {
-               m->Groups = Groups;
+               m->setGroups(Groups);
                
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }