Note on ends-free BiWFA

[smarco]

Hi,

I would like to highlight that the BiWFA can be applied to any ends-free alignment variation. If you think about it, you only need to change the initial conditions; that is, WF_0 of forward and reverse alignment need to allow starting at any diagonal (with offset zero).

Although, I'm not sure about how performant will this be compared to the regular WFA ends-free (i.e., for different sequence lengths, errors, and ends-free init length), from the algorithmic standpoint, I'm sure it is doable. In fact, I started to put that code into BiWFA, although I stopped for the sake of releasing a simpler code.

Cheers,

[lh3]

Yes, you are right. I have removed the claim from README.

In practice, I guess it may be faster to use the standard WFA to find alignment ends and then reconstruct the base alignment with global BiWFA.

[smarco]

Yes, precisely. I have the same intuition.