X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=refchimeratest.cpp;h=c084bffd40c94ef9c14a43d05de39e768dc96bea;hp=701fb9eb6a711fd82108d6694790b02992bc6816;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=8159f34321e2c771638059b59a986caca9f3ab60

diff --git a/refchimeratest.cpp b/refchimeratest.cpp
index 701fb9e..c084bff 100644
--- a/refchimeratest.cpp
+++ b/refchimeratest.cpp
@@ -24,7 +24,8 @@ RefChimeraTest::RefChimeraTest(vector<Sequence>& refs, bool aligned) : aligned(a
 	referenceSeqs.resize(numRefSeqs);
 	referenceNames.resize(numRefSeqs);
 	for(int i=0;i<numRefSeqs;i++){
-		referenceSeqs[i] = refs[i].getAligned();
+		if (aligned) { referenceSeqs[i] = refs[i].getAligned(); }
+        else { referenceSeqs[i] = refs[i].getUnaligned(); }
 		referenceNames[i] = refs[i].getName();
 	}