fix: pass rerooting argument to ARG initialization
@@ -489,13 +489,15 @@ def arg_time_trees(params):
fill_overhangs=not params.keep_overhangs)
dates = utils.parse_dates(params.dates, date_col=params.date_column, name_col=params.name_column)
+ root = None if params.keep_root else params.reroot
+
for i,(tree,mask) in enumerate(zip(arg_params['trees'], arg_params['masks'])):
outdir = get_outdir(params, f'_ARG-treetime')
gtr = create_gtr(params)
tt = setup_arg(tree, arg_params['alignment'], arg_params['combined_mask'], mask, dates, arg_params['MCCs'],
gtr=gtr, verbose=params.verbose, fill_overhangs=not params.keep_overhangs,
- fixed_clock_rate = params.clock_rate)
+ fixed_clock_rate = params.clock_rate, reroot=root)
run_timetree(tt, params, outdir, tree_suffix=f"_{i+1}", prune_short=False, method_anc=params.method_anc)
