fixes while testing 1.33.0

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 2a163516952c27f8a3dc7411536023f69e1f5b08..33349decab52e90be19c928b44b9b07c8f6c710a 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -395,7 +395,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                
                if(line->start == 0){
                        flowFile >> numFlows; m->gobble(flowFile);
-                       scrapFlowFile << maxFlows << endl;
+                       scrapFlowFile << numFlows << endl;
                        trimFlowFile << maxFlows << endl;
                        if(allFiles){
                                for(int i=0;i<thisBarcodePrimerComboFileNames.size();i++){
@@ -599,6 +599,7 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
                                else if(type == "REVERSE"){
                                        string oligoRC = reverseOligo(oligo);
                                        revPrimer.push_back(oligoRC);
+                    if (m->debug) { m->mothurOut("[DEBUG]: reverse oligos = " + oligoRC + ".\n"); }
                                }
                                else if(type == "BARCODE"){
                                        oligosFile >> group;
@@ -637,8 +638,7 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
                        primers[""] = 0;
                        primerNameVector.push_back("");                 
                }
-               
-               
+
                outFlowFileNames.resize(barcodeNameVector.size());
                for(int i=0;i<outFlowFileNames.size();i++){
                        outFlowFileNames[i].assign(primerNameVector.size(), "");