X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=refchimeratest.h;h=41df4ebba55842eae2c36ff9f02af303d20b64c7;hp=d4983e05c07ca3b134811f5595290a472af477a4;hb=3c5a709812a966bf3cabc8bb15f86f0c36cf1e34;hpb=e321831a217a5c87550e930995816c9930f85f02

diff --git a/refchimeratest.h b/refchimeratest.h
index d4983e0..41df4eb 100644
--- a/refchimeratest.h
+++ b/refchimeratest.h
@@ -16,7 +16,7 @@
 class RefChimeraTest {
 	
 public:
-	RefChimeraTest(vector<Sequence>&);
+	RefChimeraTest(vector<Sequence>&, bool);
 	int printHeader(ofstream&);
 	int analyzeQuery(string, string, ofstream&);
 	int getClosestRefIndex();
@@ -34,7 +34,8 @@ private:
 	int alignLength;
 	int bestMatch;
 	//ofstream chimeraReportFile;
-	
+	bool aligned;
+    
 	MothurOut* m;
 };