from genomic_consultant.acmg.tagger import ACMGConfig, tag_variant
from genomic_consultant.utils.models import Variant


def test_ba1_trumps():
    cfg = ACMGConfig(ba1_af=0.05, bs1_af=0.01, pm2_af=0.0005, lof_genes=set())
    v = Variant(chrom="1", pos=1, ref="A", alt="T", allele_frequency=0.2)
    result = tag_variant(v, cfg)
    assert result.suggested_class == "Benign"
    assert any(e.tag == "BA1" for e in result.evidence)


def test_pvs1_pm2_likely_pathogenic():
    cfg = ACMGConfig(lof_genes={"GENE1"}, pm2_af=0.0005, ba1_af=0.05, bs1_af=0.01)
    v = Variant(
        chrom="1",
        pos=1,
        ref="A",
        alt="T",
        gene="GENE1",
        consequence="stop_gained",
        allele_frequency=0.0001,
    )
    result = tag_variant(v, cfg)
    assert result.suggested_class == "Likely pathogenic"
    tags = {e.tag for e in result.evidence}
    assert {"PVS1", "PM2"} <= tags


def test_bp7_supporting():
    cfg = ACMGConfig(bp7_splice_ai_max=0.1)
    v = Variant(
        chrom="1",
        pos=1,
        ref="A",
        alt="T",
        consequence="synonymous_variant",
        annotations={"splice_ai_delta_score": 0.05},
    )
    result = tag_variant(v, cfg)
    assert any(e.tag == "BP7" for e in result.evidence)