Update WFA over GBWT

[jltsiren]

Changelog Entry

To be copied to the draft changelog by merger:

• Nothing that concerns the user

Description

Update the semantics of WFA over GBWT. The endpoints of the alignment must still be on the haplotype the sequence is aligned to, but they are not included in the alignment itself. In other words, the alignment will be strictly between the endpoints. If the endpoints are identical, alignment is possible only if there is a cycle.

Also added proper error handling to the alignment object:

WFAAlignment result = extender.connect(sequence, from, to);
if (!result) {
    std::cerr << "Failure!" << std::endl;
}

Now we can tell the difference between an empty alignment (an empty sequence aligns to a path between two adjacent endpoints) and a failure.

Also added new tests for various special cases.