changing command name classify.shared to classifyrf.shared

[mothur.git] / refchimeratest.cpp

diff --git a/refchimeratest.cpp b/refchimeratest.cpp
index 701fb9eb6a711fd82108d6694790b02992bc6816..c084bffd40c94ef9c14a43d05de39e768dc96bea 100644 (file)
--- 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();
        }