*/
-#include "mothur.h"
-#include "mothurout.h"
/**************************************************************************************************/
MothurOut* m;
- string queryName, templateName, searchMethod, alignmentMethod;
+ string queryName, templateName, searchMethod, alignmentMethod, dummySearchScore;
int queryLength, templateLength, queryStart, queryEnd, templateStart, templateEnd, pairwiseAlignmentLength, gapsInQuery, gapsInTemplate, longestInsert;
float searchScore, simBtwnQueryAndTemplate;