Function smith_waterman 

pub fn smith_waterman(
    query: &[u8],
    target: &[u8],
    gap: GapPenalty,
    score_fn: impl Fn(u8, u8) -> i32,
) -> AlignmentResult

Smith-Waterman local alignment with affine gap penalties. Allocates O(m×n) DP tables — caller should respect MAX_SEQ_LEN.