update a few names, types, and comments for clairity

Author: jennifer-bowser

src/anyvlm/restapi/vlm.py

@@ -27,12 +27,12 @@ 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,
@@ -49,7 +49,7 @@ 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

@@ -4,6 +4,6 @@
 
 
 class VlmResponse(BaseModel):
-    """Define response structure for the vlm-query endpoint."""
+    """Define response structure for the variant_counts endpoint."""
 
     # TODO: Fill this in. See Issue #13

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)