sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 7140b56c6b5866321a763675b7b4f75bd1d618e7..5a5d445cb8624386e90d4c714c1f460f1be0d509 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -1533,7 +1533,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                        // get rest of line in case there is a primer name
                                        while (!inOligos.eof()) {       
                                                char c = inOligos.get(); 
-                                               if (c == 10 || c == 13){        break;  }
+                                               if (c == 10 || c == 13 || c == -1){     break;  }
                                                else if (c == 32 || c == 9){;} //space or tab
                                                else {  group += c;  }
                                        } 
@@ -1648,7 +1648,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
         if (hasPairedBarcodes || hasPrimer) {
             pairedOligos = true;
             if ((primers.size() != 0) || (barcodes.size() != 0) || (linker.size() != 0) || (spacer.size() != 0) || (revPrimer.size() != 0)) { m->control_pressed = true;  m->mothurOut("[ERROR]: cannot mix paired primers and barcodes with non paired or linkers and spacers, quitting."); m->mothurOutEndLine();  return 0; }
-        }
+        }else if (reorient) { m->mothurOut("[Warning]: cannot use checkorient without paired barcodes or primers, ignoring.\n"); m->mothurOutEndLine(); reorient = false; }
         
                if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }
         
@@ -1852,7 +1852,13 @@ bool TrimSeqsCommand::keepFirstTrim(Sequence& sequence, QualityScores& qscores){
                if(qscores.getName() != ""){
                        qscores.trimQScores(-1, keepFirst);
                }
+
+//        sequence.printSequence(cout);cout << endl;
+        
                sequence.trim(keepFirst);
+        
+//        sequence.printSequence(cout);cout << endl << endl;;
+
                return success;
        }
        catch(exception& e) {