Mirror vcztools view-bed options in mount-plink#10
Merged
jeromekelleher merged 1 commit intosgkit-dev:mainfrom May 7, 2026
Merged
Mirror vcztools view-bed options in mount-plink#10jeromekelleher merged 1 commit intosgkit-dev:mainfrom
jeromekelleher merged 1 commit intosgkit-dev:mainfrom
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Replaces the count-style -v/-vv with --log-level / --log-file and exposes every bcftools-view-style option that vcztools view-bed already supports (-r/-R/-s/-S/-t/-T/-i/-e/-v/-V/-m/-M plus --storage-option). The mounted PLINK view can now be filtered to a region or sample subset at mount time instead of always materialising the full dataset. Reuses vcztools' new ViewBedOptions / view_bed_options / LogConfig / log_options bundle so biofuse's CLI surface tracks view-bed automatically; new options added in vcztools propagate without changes here. The frozen ViewBedOptions and LogConfig dataclasses cross the multiprocessing.spawn boundary unchanged, replacing the previous backend_storage / int log_level positional arguments to PlinkClient.start and _server_main. Also drops --backend-storage's Click Choice constraint (now str-typed, inherited from vcztools) so biofuse accepts the same backend names vcztools does, including the deprecated --zarr-backend-storage alias.
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Reuses vcztools' new ViewBedOptions / view_bed_options / LogConfig / log_options bundle so biofuse's CLI surface tracks view-bed automatically; new options added in vcztools propagate without changes here. The frozen ViewBedOptions and LogConfig dataclasses cross the multiprocessing.spawn boundary unchanged, replacing the previous backend_storage / int log_level positional arguments to PlinkClient.start and _server_main.