def __get_translated_filter_and_variant_annotation(
cls,
call: SimpleCall,
panel: Panel,
call_reference_assembly: ReferenceAssembly,
translated_reference_allele: Optional[str],
) -> Tuple[FullCallFilter, str]:
annotated_alleles = cls.__get_annotated_alleles(
call, call_reference_assembly, translated_reference_allele)
if panel.has_ref_seq_difference_annotation(call.gene,
call.start_coordinate,
call.reference_allele,
call_reference_assembly):
annotate_as_ref = all(
cls.
__is_ref_allele_to_opposite_assembly_due_to_ref_sequence_difference(
annotated_allele, call_reference_assembly)
for annotated_allele in annotated_alleles)
all_variants_are_ref_to_a_reference_assembly = all(
cls.__allele_is_ref_to_a_reference_assembly(
annotated_allele, call_reference_assembly)
for annotated_allele in annotated_alleles)
if annotate_as_ref:
translated_variant_annotation = REF_CALL_ANNOTATION_STRING
translated_filter = FullCallFilter.PASS
elif all_variants_are_ref_to_a_reference_assembly:
translated_variant_annotation = panel.get_ref_seq_difference_annotation(
call.gene, call.start_coordinate, call.reference_allele,
call_reference_assembly)
if call.is_pass():
translated_filter = FullCallFilter.PASS
else:
translated_filter = FullCallFilter.INFERRED_PASS
else:
translated_variant_annotation = call.variant_annotation + "?"
translated_filter = FullCallFilter.UNKNOWN
logging.warning(
f"Unexpected allele in ref seq difference location. Check whether annotation is correct: "
f"found alleles=({annotated_alleles[0]}, {annotated_alleles[1]}), "
f"annotation={translated_variant_annotation}")
elif panel.contains_rs_id_matching_call(call, call_reference_assembly):
# known variant and no ref seq differences involved
translated_variant_annotation = call.variant_annotation
if call.is_pass():
translated_filter = FullCallFilter.PASS
else:
translated_filter = FullCallFilter.NO_CALL
else:
# unknown variant, no ref seq difference involved
translated_variant_annotation = call.variant_annotation + "?"
translated_filter = FullCallFilter.UNKNOWN
logging.warning(
f"Unknown variant. Check whether annotation is correct: "
f"found alleles=({annotated_alleles[0]}, {annotated_alleles[1]}), "
f"annotation={translated_variant_annotation}")
return translated_filter, translated_variant_annotation
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