nx_sequence_fm_test.nx

nx_sequence_fm_test.nx -- KAT for FM-index construction + backward search. Canonical "BANANA$" reference (Ferragina-Manzini 2000, textbook across every IR / bioinformatics intro): Suffixes (sorted lexicographically, $=0x24 < A < B < N): 6 $ 5 A$ 3 ANA$ 1 ANANA$ 0 BANANA$ 4 NA$ 2 NANA$ SA = [6, 5, 3, 1, 0, 4, 2] BWT = [A, N, N, B, $, A, A] = "ANNB$AA" C[$] = 0 ; C[A] = 1 ; C[B] = 4 ; C[N] = 5 ; C[anything > N] = 7 fm_count("ANA") = 2 (positions 1, 3) fm_count("BAN") = 1 (position 0) fm_count("NAB") = 0 (not in text) fm_count("A") = 3 Plus DNA "ACGT$" KAT and a not-in-text refusal. expect_exit: 0 license_tier: ORIGINAL