X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=aligncommand.cpp;h=f757a7920bb337883a2a7773f35ed533d2186c80;hp=f9c0436c62874864279e533a3258d72bf2f6cf2d;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=c48d91112209b841444923670dca5454da0e2a4d

diff --git a/aligncommand.cpp b/aligncommand.cpp
index f9c0436..f757a79 100644
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -558,6 +558,7 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
 			if (m->control_pressed) {  break; }
 			
 			Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
+            cout  << candidateSeq->getAligned() << endl;
 			report.setCandidate(candidateSeq);
 
 			int origNumBases = candidateSeq->getNumBases();