add condition to BSW in case of reversing

[gayoung-MetisX]

Hi, I make a pull request (#361 )for below issue.

It calculated h from beg to end. Because of the applying band, sometimes beg can grow bigger than end. Then skip i and run i+1 with the e-h value of i-1, not i's. It could cause misalignment. So, I added break condition.

example) w = 81, qlen = 72 if i = 165, i-w = 84 > beg = 84 end = 72