How to set match score ?

[fkallen]

There is no option to set the match score.

// Initialize the alignment parameters (*after* the sequences have been
// added)
affine_penalties_t penalties = {.x = 2, .o = 3, .e = 1};
wfagpu_initialize_parameters(&aligner, penalties);

[quim0]

The original WFA algorithm requires the match score to be 0. Later, Eizenga proposed a score transformation that allows the match score to be set to values < 0. I’ll try to find some time to implement this.

Do you plan to use this feature for benchmarking the library or for integrating it into a tool? Keep in mind that applying the score transformation may introduce some performance overhead, as higher penalties can lead to more WFA "steps".