unify omega pvalue staged refinement and remove omega_pvalue_niter

Author: kfuku52

csubst/csubst

@@ -533,24 +533,17 @@ def _main():
                          help='default=%(default)s: Experimental feature. Overdispersion coefficient for '
                               '--omega_pvalue_null_model nbinom. Variance is mean + alpha*mean^2. '
                               '"auto" estimates alpha from observed-vs-expected count dispersion.')
-    analyze.add_argument('--omega_pvalue_niter', metavar='INT', default=1000, type=int,
-                         help='default=%(default)s: Experimental feature. Number of randomization iterations for --calc_omega_pvalue. '
-                              'Larger values improve tail resolution but increase runtime and memory.')
     analyze.add_argument('--omega_pvalue_niter_schedule', metavar='0|N1,N2,...', default='0', type=str,
                          help='default=%(default)s: Experimental feature. Iteration schedule for staged '
-                              '--calc_omega_pvalue refinement under --omega_pvalue_null_model hypergeom. '
-                              'Set 0 (auto) to use adaptive stages ending at --omega_pvalue_niter '
-                              '(typically 100,1000,target). '
+                              '--calc_omega_pvalue refinement under all --omega_pvalue_null_model modes '
+                              '(upper-tail edge focused). '
+                              'Set 0 (auto) to use adaptive stages (100,1000). '
                               'Custom values should be comma-delimited strictly increasing integers '
                               '(e.g., 200,2000,10000).')
-    analyze.add_argument('--omega_pvalue_refine_threshold', metavar='FLOAT', default=0.05, type=float,
-                         help='default=%(default)s: Experimental feature. Target p-value threshold used by '
-                              'staged refinement under --omega_pvalue_null_model hypergeom. '
-                              'Rows whose confidence interval overlaps this threshold are refined to later stages.')
-    analyze.add_argument('--omega_pvalue_refine_ci_alpha', metavar='FLOAT', default=0.01, type=float,
-                         help='default=%(default)s: Experimental feature. Two-sided confidence level alpha used in '
-                              'staged refinement under --omega_pvalue_null_model hypergeom '
-                              '(Clopper-Pearson interval for upper-tail exceedance probability).')
+    analyze.add_argument('--omega_pvalue_refine_upper_edge_bins', metavar='INTEGER', default=2, type=int,
+                         help='default=%(default)s: Experimental feature. Number of upper-tail p-value edge bins '
+                              'used to select rows for the next refinement stage. '
+                              'Rows with exceedance rank <= this value are refined; set 0 to disable.')
     analyze.add_argument('--omega_pvalue_rounding', metavar='round|stochastic|floor|ceil', default='stochastic', type=str,
                          choices=['round', 'stochastic', 'floor', 'ceil'],
                          help='default=%(default)s: Experimental feature. How fractional branch-wise substitution masses are converted to '