"""Core data models and configuration for Phaser."""

from haplophaser.core.config import PhaserConfig, load_config
from haplophaser.core.filters import (
    BiallelicFilter,
    ChromosomeFilter,
    FilterChain,
    FilterChainStats,
    FilterStats,
    InformativeFilter,
    MAFFilter,
    MaxMissingFilter,
    MinDepthFilter,
    MinGQFilter,
    MinQualityFilter,
    PassFilter,
    PolyploidGenotypeFilter,
    RegionFilter,
    SNPFilter,
    VariantFilter,
    create_default_filter_chain,
)
from haplophaser.core.frequencies import (
    AlleleFrequencies,
    AlleleFrequency,
    AlleleFrequencyCalculator,
    VariantAlleleFrequencies,
    calculate_population_frequencies,
    get_founder_frequencies,
)
from haplophaser.core.models import (
    HaplotypeBlock,
    Population,
    PopulationRole,
    Sample,
    Subgenome,
    Variant,
    Window,
)

__all__ = [
    # Models
    "Sample",
    "Subgenome",
    "Population",
    "PopulationRole",
    "Variant",
    "Window",
    "HaplotypeBlock",
    # Config
    "PhaserConfig",
    "load_config",
    # Filters
    "VariantFilter",
    "FilterChain",
    "FilterStats",
    "FilterChainStats",
    "MinQualityFilter",
    "MinDepthFilter",
    "MinGQFilter",
    "MaxMissingFilter",
    "MAFFilter",
    "BiallelicFilter",
    "SNPFilter",
    "PassFilter",
    "RegionFilter",
    "ChromosomeFilter",
    "InformativeFilter",
    "PolyploidGenotypeFilter",
    "create_default_filter_chain",
    # Frequencies
    "AlleleFrequency",
    "VariantAlleleFrequencies",
    "AlleleFrequencies",
    "AlleleFrequencyCalculator",
    "calculate_population_frequencies",
    "get_founder_frequencies",
]
