feat: add Sankoff parsimony model and directory locking

Implements a calibrated 16-state Sankoff substitution cost matrix and CLI pipeline for evolutionary distance computation, including empirical calibration via saturation-filtered SNP counts. Refactors the sibling scanning stage to use batched transforms for improved synchronization efficiency. Introduces an OS-level advisory directory lock across all index-modifying commands to prevent concurrent write corruption. Updates dependencies and exposes new Sankoff utilities in the public API.
2026-08-12 20:05:10 +02:00
parent 14aa82521d
commit 55d7fa2067
17 changed files with 1494 additions and 180 deletions
@@ -0,0 +1,27 @@
+ratio_ceiling: 0.5
+flank_length_m: 15
+p_hat: 0.010713940022064144
+p_hat_variance: 3.2110559785689563e-10
+n_pairs_included: 158
+n_loci_total: 33008305
+mean_sub_cost: 1.4764371767846869
+c_ctx: 1.7343663443925388
+substitutions:
+- pair: A/C
+  count: 27810
+  cost: 2.5439415226130238
+- pair: A/G
+  count: 130153
+  cost: 1.0
+- pair: A/T
+  count: 24555
+  cost: 2.6684722241428322
+- pair: C/G
+  count: 19637
+  cost: 2.892062911764701
+- pair: C/T
+  count: 124878
+  cost: 1.0413902163542994
+- pair: G/T
+  count: 26616
+  cost: 2.5878424665170052