"""Pre/Post-Processing Module."""

from scphylo.pp._bifiltering import bifiltering
from scphylo.pp._binary import (
    binarym_filter_clonal_mutations,
    binarym_filter_nonsense_mutations,
    binarym_filter_private_mutations,
    binarym_statistics,
    consensus_combine,
)
from scphylo.pp._readcount import (
    build_scmatrix,
    filter_mut_mutant_must_present_in_at_least,
    filter_mut_reference_must_present_in_at_least,
    filter_mut_vaf_greater_than_coverage_mutant_greater_than,
    filter_snpeff,
    group_obs_apply_func,
    keep_cell_by_list,
    keep_mut_by_list,
    mut_seperated_by_cell_group,
    remove_cell_by_list,
    remove_mut_by_list,
    remove_nonsense_cells,
    statistics,
)
from scphylo.pp._tree import collapse, sample_from_tree

__all__ = (
    bifiltering,
    binarym_filter_clonal_mutations,
    binarym_filter_nonsense_mutations,
    binarym_filter_private_mutations,
    binarym_statistics,
    consensus_combine,
    build_scmatrix,
    filter_mut_mutant_must_present_in_at_least,
    filter_mut_reference_must_present_in_at_least,
    filter_mut_vaf_greater_than_coverage_mutant_greater_than,
    filter_snpeff,
    keep_cell_by_list,
    keep_mut_by_list,
    remove_cell_by_list,
    remove_mut_by_list,
    statistics,
    collapse,
    group_obs_apply_func,
    sample_from_tree,
    mut_seperated_by_cell_group,
    remove_nonsense_cells,
)
