resolve merge conflict

Author: jennifer-bowser

src/anyvlm/functions/get_caf.py

@@ -3,15 +3,21 @@
 from ga4gh.va_spec.base.core import CohortAlleleFrequencyStudyResult
 
 from anyvlm.anyvar.base_client import BaseAnyVarClient
+from anyvlm.utils.types import (
+    ChromosomeName,
+    GenomicSequence,
+    GrcAssemblyId,
+    UscsAssemblyBuild,
+)
 
 
 def get_caf(
     anyvar_client: BaseAnyVarClient,
-    assembly_id: str,
-    reference_name: str,
+    assembly_id: GrcAssemblyId | UscsAssemblyBuild,
+    reference_name: ChromosomeName,
     start: int,
-    reference_bases: str,
-    alternate_bases: str,
+    reference_bases: GenomicSequence,
+    alternate_bases: GenomicSequence,
 ) -> list[CohortAlleleFrequencyStudyResult]:
     """Retrieve Cohort Allele Frequency data for all known variants matching provided search params
 

src/anyvlm/restapi/vlm.py

@@ -31,12 +31,12 @@ def ingest_vcf(vcf_path: Path) -> None:
 
 
 @app.get(
-    "/vlm-query",
-    summary="Provides counts of occurrences of a single sequence variant, broken down by zygosity",
-    description="Search for a single sequence variant and receive a count of its observed occurrences broken down by zygosity, in accordance with the Variant-Level Matching protocol",
+    "/variant_counts",
+    summary="Provides allele counts of a single sequence variant, broken down by zygosity",
+    description="Search for a single sequence variant and receive allele counts by zygosity, in accordance with the Variant-Level Matching protocol",
     tags=[EndpointTag.SEARCH],
 )
-def vlm_query(
+def variant_counts(
     request: Request,
     assemblyId: Annotated[  # noqa: N803
         GrcAssemblyId | UscsAssemblyBuild,
@@ -53,7 +53,7 @@ def vlm_query(
         GenomicSequence, Query(..., description="Genomic bases ('T', 'AC', etc.)")
     ],
 ) -> VlmResponse:
-    """Accept a Variant-Level Matching network request and return a count of occurrences of a single sequence variant, broken down by zygosity.
+    """Accept a Variant-Level Matching network request and return allele counts by zygosity.
 
     :param request: FastAPI `Request` object
     :param assemblyId: The genome reference assembly. Must be a GRC assembly identifier (e.g., "GRCh38) or a USCS assembly build (e.g., "hg38")

src/anyvlm/schemas/vlm.py

@@ -85,7 +85,7 @@ class ResponseField(BaseModel):
 
 
 class VlmResponse(BaseModel):
-    """Defines response structure for the vlm-query endpoint."""
+    """Define response structure for the variant_counts endpoint."""
 
     beaconHandovers: list[BeaconHandover] = [BeaconHandover()]
     meta: Meta = Meta()

src/anyvlm/utils/types.py

@@ -68,7 +68,7 @@ def _normalize_chromosome_name(chromosome_name: str) -> str:
     if is_valid_chromosome_name(chromosome_name):
         return chromosome_name
     error_message = (
-        "Invalid chromosome. Must be 1-22, 'X,' or 'Y,' with optional 'chr' prefix."
+        "Invalid chromosome. Must be 1-22, 'X', or 'Y'; with optional 'chr' prefix."
     )
     raise ValueError(error_message)