nx_align_match_test.nx

nx_align_match_test.nx -- end-to-end seed-pipeline KAT. Builds the full chain: pack reference + query DNA, extract minimizers from each, match query-vs-reference, assert exact (q_pos, r_pos) pairs come out. Demonstrates G1.0+G1.1+G1.2 + nx_sequence composition as a single coherent pipeline. Reference: "ACGTACGTAC" (10 bases), k=4 w=3 minimizers: (0x1B, 0), (0x6C, 1), (0x1B, 4) Query: "GTACGT" (6 bases), k=4 w=3 k-mers / canonical at pos 0..2: pos 0: GTAC = 0xB1 (palindrome) pos 1: TACG = 0xC6 / rc CGTA 0x6C -> canon 0x6C pos 2: ACGT = 0x1B (palindrome) 1 window, leftmost min of [0xB1, 0x6C, 0x1B] = 0x1B at pos 2. minimizers: (0x1B, 2) Match: query value 0x1B hits reference 0x1B at r_pos 0 and r_pos 4. pairs: (q=2, r=0), (q=2, r=4) count = 2 expect_exit: 0 license_tier: ORIGINAL