def __get_translated_reference_allele(
cls, call: SimpleCall, panel: Panel,
call_reference_assembly: ReferenceAssembly) -> Optional[str]:
if panel.contains_rs_id_matching_call(call, call_reference_assembly):
rs_id_info = panel.get_matching_rs_id_info(
call.start_coordinate, call.reference_allele,
call_reference_assembly)
cls.__assert_rs_id_call_matches_info(call.rs_ids,
(rs_id_info.rs_id, ))
return rs_id_info.get_reference_allele(
call_reference_assembly.opposite())
else:
# unknown variant
return None
def __fill_in_rs_ids_if_needed(
cls, call: SimpleCall, panel: Panel,
reference_assembly: ReferenceAssembly) -> SimpleCall:
rs_ids: Tuple[str, ...]
if call.rs_ids == (".", ) and panel.contains_rs_id_matching_call(
call, reference_assembly):
rs_id_info = panel.get_matching_rs_id_info(call.start_coordinate,
call.reference_allele,
reference_assembly)
rs_ids = (rs_id_info.rs_id, )
new_simple_call = SimpleCall(
call.start_coordinate,
call.reference_allele,
call.alleles,
call.gene,
rs_ids,
call.variant_annotation,
call.filter,
)
return new_simple_call
else:
return call