Add flag to choose if end location is needed (to make search faster)

[Martinsos]

When I added functionality for finding end location of alignment (#13), search got slower for about 20%, maybe even more, although I did my best not to slow it down. One possible fix for this, if it can be fixed, would be to introduce a flag that will enable user to choose if he needs end location of alignment or not. I hope that search will be as quick as before when this flag is negative, although I am not sure this will actually help (because we will probably have to put if in core loop, and that may slow things down even more -> or it may help as it will have constant value, I am not sure how smart is compiler or whoever).

[Martinsos]

I did this and it really did help a lot (~30%)!