Improve speed of basic search

[Martinsos]

Before, in v1.0 branch, opal was 1.5 times faster than now! I have to speed up the parts that I can and isolate all functionalities that are not needed in basic search and are making it slower.

[Martinsos]

I did not find anything specially useful using profiler: I think I should proceed by:

• providing a flag not to search for end location (done with 9075caf) -> biiiig speedup!
• going through code very carefully and improving every possible bit
• resolve Slowdown after new feature #11 -> discover what caused that slowdown and fix it
• consider implementing Process multiple cells in one iteration, add padding to database sequences, optimize for cache #3

[Martinsos]

It seems like slowdown in #11 is caused by not breaking from for loop that checks for overflow! If overflow is found and I break from loop when using buckets mode, it will have better time than when not breaking immediately but little bit later. I did not fix this yet, I should explore why this actually has effect on speed that is noticable!

[Martinsos]

Important: fix I mentioned for #11, it does not seem to help for most of the tests, only for few of them. I will leave the change however.

[Martinsos]

This fix for #11 makes almost no sense! There is almost no code executed if I do not break so early, so why is there change in performance? I have no idea and that is somewhat frustrating, but I have to continue.