* issues at the 5' end of the alignment seem to take care of themselves in the traceback.
*
*/
-using namespace std;
#include "alignmentcell.hpp"
#include "overlap.hpp"
int rowIndex = maxRow(alignment, band); // get the index for the row with the highest right hand side score
int colIndex = maxColumn(alignment, band); // get the index for the column with the highest bottom row score
-
+
int row = lB-1;
int column = lA-1;