Initial commit

tests/test_store.py

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+from genomic_consultant.store.query import GenomicStore
+from genomic_consultant.utils.models import FilterConfig, Variant
+
+
+def test_filter_by_gene_and_af():
+    store = GenomicStore(
+        variants=[
+            Variant(chrom="1", pos=1, ref="A", alt="T", gene="GENE1", allele_frequency=0.02),
+            Variant(chrom="1", pos=2, ref="G", alt="C", gene="GENE2", allele_frequency=0.0001),
+        ]
+    )
+    res = store.get_variants_by_gene("ind", ["GENE2"], filters=FilterConfig(max_af=0.001))
+    assert len(res) == 1
+    assert res[0].gene == "GENE2"
+
+
+def test_consequence_include_exclude():
+    store = GenomicStore(
+        variants=[
+            Variant(chrom="1", pos=1, ref="A", alt="T", gene="GENE1", consequence="missense_variant"),
+            Variant(chrom="1", pos=2, ref="G", alt="C", gene="GENE1", consequence="synonymous_variant"),
+        ]
+    )
+    res = store.get_variants_by_gene(
+        "ind", ["GENE1"], filters=FilterConfig(consequence_includes=["missense"], consequence_excludes=["synonymous"])
+    )
+    assert len(res) == 1
+    assert res[0].consequence == "missense_variant"