Wavefront expansion global alignment algorithm or wavefront alignment (WFA).

Takes two parameters text and pattern of length tlen and qlen respectively.

It then cuts across 3 DP tables (I, D and M, as in Smith, Waterman and Gotoh) using negative gradient diagonal lines as in (Myers ... and Marco 2020).

The central diagonal (A_k) is computed A_k := tlen - qlen. When tlen === qlen, A_k === 0 and runs from the top left cell to the bottom right cell. Diagonals below the central diagonal are negative diagonals and diagonals above it are positive diagonals.

The aim of the alignment algorithm is to move along the A_k from the top left cell (0,0) to the bottom right cell (tlen, qlen).

The movement is made in steps called offsets. An offset is the number of steps made along a diagonal starting from the start of the diagonal.

(v,h) is a cell in the matrix.

v = offset - k
h = offset
A_k = (tlen-qlen) The central diagonal

Rust implementation of ekg/wflambda. Moved in from urbanslug/wflambda.

A generalization of WFA that runs on regions (abstract bases) using a custom match & traceback lambdas.

cargo doc --open

Santiago Marco-Sola, Juan Carlos Moure, Miquel Moreto, Antonio Espinosa. "Fast gap-affine pairwise alignment using the wavefront algorithm." Bioinformatics, 2020.