Extended gap for Smith-Waterman #2
Description
The best local alignment should take into account the possibility to open the gap and extend it at the cost of gap extension penalty which is typically smaller than gap opening penalty. At the moment this takes into account only gap extension if the gap was open at the previous step. However, sometime it is better to open the gap a few steps before and then extend it up to the current position which may lead to the different optimal path for alignment two sequences.
The bug is not critical and can be found for extreme cases as GAP_EXTENSION=0