X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=aligncommand.cpp;h=f757a7920bb337883a2a7773f35ed533d2186c80;hp=fc98c10924138a3aa168dabbc609f64bfb89f3e4;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=c85db0a4be3a1f8037a71a23ca73f9762184e28a

diff --git a/aligncommand.cpp b/aligncommand.cpp
index fc98c10..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();
@@ -644,11 +645,11 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
 			#endif
 			
 			//report progress
-			if((count) % 100 == 0){	m->mothurOut(toString(count)); m->mothurOutEndLine();		}
+			if((count) % 100 == 0){	m->mothurOutJustToScreen(toString(count) + "\n"); 		}
 			
 		}
 		//report progress
-		if((count) % 100 != 0){	m->mothurOut(toString(count)); m->mothurOutEndLine();		}
+		if((count) % 100 != 0){	m->mothurOutJustToScreen(toString(count) + "\n"); 		}
 		
 		delete alignment;
 		alignmentFile.close();