Fix "one before begin of" pointer formation

[SoapZA]

• Forming a pointer "one before" the start of a range is UB: https://devblogs.microsoft.com/oldnewthing/20211112-00/?p=105908
• GCC 13's UBSAN detects this now: https://gcc.gnu.org/cgit/gcc/commit?id=28896b38fabce8
• By using a (signed) index, we can avoid forming invalid pointers.

Fixes #233

[SoapZA]

@Martinsos @blawrence-ont @armintoepfer

[blawrence-ont]

LGTM, but are the changes necessarily required in myersCalcEditDistanceNW()? I don't immediately see where the pointer arithmetic can break down in that function.

Also I don't think that me approving this PR does anything really...

[SoapZA]

I just did it for consistency, but yes, that function didn't fail. Using indices is a bit debug friendlier on operator[] if this code is ever switched to use std::vector

[Martinsos]

@SoapZA thanks for this -> I will have to take some time to properly study this stuff, but I will do it! Hopefully in the next weeks.
In the meantime, any additional context helps. @SoapZA , how confident are you about the changes done in this PR -> are you confident they don't change behaviour in any way, or performance?

[SoapZA]

Logically, I'm pretty sure these don't have an impact, since changing a pointer + offset to just offset and then subscripting on the pointer doesn't change the addressing logic (and makes moving to unique_ptr<int[]> in future much easier).

Performance-wise, I haven't checked, but since the compiler can see the pointer[index] logic everywhere, it will likely optimize this away, is my guess.

[Martinsos]

Thanks @SoapZA , merged!

[Martinsos]

@SoapZA would you be interested in being added to Edlib as collaborator? You have contributed quite a bit in the last years and seem to know C/C++ quite well + you are active in the field of bioinformatics, would be great to have you involved. I have been the only maintainer from the very start and it would be good to add more people. No obligations or anything, it would just make it easier for you to contribute if you wish, and be able to do things even if I am occupied or something.

[SoapZA]

@Martinsos that would be great!