nx_align_score_test.nx

nx_align_score_test.nx -- end-to-end seed-and-extend pipeline KAT. Full chain composed in one test: 1. pack reference "ACGTACGTACGT" (12 bases) and query "ACGTACGT" (8 bases) 2. minimizer_extract from each (k=4 w=3) 3. minimizer_match to produce seed pairs 4. hand-sort seed pairs by (r_pos, q_pos) 5. seed_chain to find longest co-linear chain 6. score_chained_alignment to run SW over the chain region Hand-traced expected values: Reference minimizers (5): (0x1B, 0) (0x6C, 1) (0x1B, 4) (0x6C, 5) (0x1B, 8) Query minimizers (3): (0x1B, 0) (0x6C, 1) (0x1B, 4) Match pairs (outer q, inner r) = 8: q_idx 0 (v=0x1B,q_pos=0): (0,0) (0,4) (0,8) q_idx 1 (v=0x6C,q_pos=1): (1,1) (1,5) q_idx 2 (v=0x1B,q_pos=4): (4,0) (4,4) (4,8) After sort by (r,q) ascending: index 0: (q=0, r=0) index 1: (q=4, r=0) index 2: (q=1, r=1) index 3: (q=0, r=4) index 4: (q=4, r=4) index 5: (q=1, r=5) index 6: (q=0, r=8) index 7: (q=4, r=8) Chain DP picks chain length 3 at end-index 4 (leftmost tie): indices [0, 2, 4] -> seeds (q=0,r=0), (q=1,r=1), (q=4,r=4) Alignment region: q_start = 0, q_end = 4 + 4 = 8 r_start = 0, r_end = 4 + 4 = 8 q[0..8) = "ACGTACGT" == r[0..8) -> perfect 8-base match SW score (m=+2 mis=-1 gap=-2) = 8 * 2 = 16, end (8, 8) expect_exit: 0