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