class RefChimeraTest {
public:
- RefChimeraTest(vector<Sequence>&);
+ RefChimeraTest(vector<Sequence>&, bool);
int printHeader(ofstream&);
int analyzeQuery(string, string, ofstream&);
int getClosestRefIndex();
int alignLength;
int bestMatch;
//ofstream chimeraReportFile;
-
+ bool aligned;
+
MothurOut* m;
};