X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.cpp;fp=qualityscores.cpp;h=0c55650b33149148c80374a0b8c03d41a7a4ea53;hb=fe08eacea5a2d34cd4bd27e8451fd2872102a80a;hp=1f86efc51304cc81fa2f359c8b2c996da52e8c30;hpb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;p=mothur.git

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 1f86efc..0c55650 100644
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -200,7 +200,7 @@ bool QualityScores::stripQualThreshold(Sequence& sequence, double qThreshold){
 		
 		if(seqName != sequence.getName()){
 			m->mothurOut("sequence name mismatch btwn fasta: " + sequence.getName() + " and qual file: " + seqName);
-			m->mothurOutEndLine();	
+			m->mothurOutEndLine();	m->control_pressed = true;
 		}
 		
 		int end;