fixed bug with aligner and longest base. added deunique.seqs command.

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index b4af28a2990a44d69527d4c5cb7e5984d8b73033..63a117d5064cc8178051017173bacdfd80cb6b3a 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -562,10 +562,11 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
                                                                
                                Sequence temp = templateDB->findClosestSequence(candidateSeq);
                                Sequence* templateSeq = &temp;
-                               
+                       
                                float searchScore = templateDB->getSearchScore();
                                                                
                                Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
+               
                                Sequence* copy;
                                
                                Nast* nast2;
@@ -580,6 +581,7 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
                                        string wasBetter =  "";
                                        //if the user wants you to try the reverse
                                        if (flip) {
+                               
                                                //get reverse compliment
                                                copy = new Sequence(candidateSeq->getName(), originalUnaligned);
                                                copy->reverseComplement();