# The BiWFA meeting condition

cross references: BiWFA GitHub issue

It seems that getting the meeting/overlap condition of BiWFA (Marco-Sola et al. (2023), Algorithm 1 and Lemma 2.1) correct is tricky.

Let $$p := \max(x, o+e)$$ be the maximal cost of any edge in the edit graph. As in the BiWFA paper, let $$s_f$$ and $$s_r$$ be the distances of the forward and reverse fronts computed so far.

We prove the following lemma:

Lemma Once BiWFA has expanded the forward and reverse fronts up to $$s_f$$ and $$s_r$$ and has found some path of cost $$s \leq s_f + s_r$$, expanding the fronts until $$s’_f + s’_r \geq s+p+o$$ is guaranteed to find a shortest path.

Proof

1. Increment $$s_f$$ and $$s_r$$ up to the point (but excluding) where $$s’_f + s’_r = s + p + o$$.

2. Let $$\pi$$ be a shortest path in the edit graph of cost $$s_\pi$$.

3. Let $$I$$ be the interval of distances on the path $$\pi$$ from the start that are covered by both the forward and reverse fronts. (This probably needs a more formal definition.)

4. $$I = [s_\pi -s’_r+o, s’_f)$$ or $$I = (s_\pi - s’_r+o, s’_f]$$ is covered both in the forward and reverse direction for all (affine) layers ($$M$$, $$I$$, $$D$$). The side on which $$I$$ is open depends on whether $$s’_f$$ or $$s’_r$$ was incremented last.

5. Since $$s_\pi \leq s$$, we have

\begin{align} |I| &= s’_f - (s_\pi - s’_r + o)\\ &= s’_f + s’_r - s_\pi - o \\ &= s+p+o - s_\pi - o \\ &= s-s_\pi +p \\ &\geq p. \end{align}

6. Each edge in the edit graph has cost at most $$p = \max(x, o+e)$$.

7. $$\pi$$ contains at least one node every $$p$$ fronts, as long as $$s_f \leq s_\pi$$ and $$s_r \leq s_\pi$$.

8. Since the interval $$I$$ has size $$p$$ it contains at least one node of $$\pi$$.

9. Thus, the forward and reverse wavefronts overlap sufficiently to find a shortest path.

## References

Marco-Sola, Santiago, Jordan M Eizenga, Andrea Guarracino, Benedict Paten, Erik Garrison, and Miquel Moreto. 2023. “Optimal Gap-Affine Alignment in O(s) Space.” Edited by Pier Luigi Martelli. Bioinformatics 39 (2). https://doi.org/10.1093/bioinformatics/btad074.