def __init__(
self,
header_fields, # type: vcf_header_parser.HeaderFields
split_alternate_allele_info_fields=True, # type: bool
annotation_fields=None, # type: List[str]
use_allele_num=False, # type: bool
minimal_match=False, # type: bool
counter_factory=None # type: metrics_util.CounterFactoryInterface
):
"""Sets the internal state of the factory class.
Args:
header_fields: Header information used for parsing and splitting INFO
fields of thei variant.
split_alternate_allele_info_fields: If True, splits fields with
field_count='A' (i.e., one value for each alternate) among alternates.
annotation_fields: If provided, this is the list of INFO field names that
store variant annotations. The format of how annotations are stored and
their names are extracted from header_fields.
use_allele_num: If set, then "ALLELE_NUM" annotation is used to determine
the index of the ALT that corresponds to an annotation set.
minimal_match: If set, then the --minimal mode of VEP is simulated for
annotation ALT matching.
"""
self._header_fields = header_fields
self._split_alternate_allele_info_fields = (
split_alternate_allele_info_fields)
self._annotation_field_set = set(annotation_fields or [])
cfactory = counter_factory or metrics_util.NoOpCounterFactory()
self._variant_counter = cfactory.create_counter(
_CounterEnum.VARIANT.value)
self._annotation_processor = _AnnotationProcessor(
annotation_fields, self._header_fields, cfactory, use_allele_num,
minimal_match)
self._minimal_match = minimal_match
def __init__(
self,
header_fields, # type: vcf_header_io.VcfHeader
split_alternate_allele_info_fields=True, # type: bool
allow_alternate_allele_info_mismatch=False, # type: bool
annotation_fields=None, # type: List[str]
use_allele_num=False, # type: bool
minimal_match=False, # type: bool
infer_annotation_types=False, # type: bool
counter_factory=None # type: metrics_util.CounterFactoryInterface
):
# type: (...) -> None
"""Sets the internal state of the factory class.
Args:
header_fields: Header information used for parsing and splitting INFO
fields of the variant.
split_alternate_allele_info_fields: If True, splits fields with
`field_count='A'` (i.e., one value for each alternate) among alternates.
allow_alternate_allele_info_mismatch: By default (when False), an error
will be raised for INFO fields with `field_count='A'` (i.e. one value
for each alternate base) that do not have the same cardinality as
alternate bases. If True, an error will not be raised and excess values
will be dropped or insufficient values will be set to null. Only
applicable if `split_alternate_allele_info_fields` is True.
annotation_fields: If provided, this is the list of INFO field names that
store variant annotations. The format of how annotations are stored and
their names are extracted from header_fields.
use_allele_num: If True, then "ALLELE_NUM" annotation is used to determine
the index of the ALT that corresponds to an annotation set.
minimal_match: If True, then the --minimal mode of VEP is simulated for
annotation ALT matching.
infer_annotation_types: If True, then warnings will be provided if header
fields fail to contain Info type lines for annotation fields
counter_factory: If provided, it will be used to record counters (e.g. the
number of variants processed).
"""
self._header_fields = header_fields
self._split_alternate_allele_info_fields = (
split_alternate_allele_info_fields)
self._allow_alternate_allele_info_mismatch = (
allow_alternate_allele_info_mismatch)
self._annotation_field_set = set(annotation_fields or [])
cfactory = counter_factory or metrics_util.NoOpCounterFactory()
self._variant_counter = cfactory.create_counter(
_CounterEnum.VARIANT.value)
self._alternate_allele_info_mismatche_counter = cfactory.create_counter(
_CounterEnum.ALTERNATE_ALLELE_INFO_MISMATCH.value)
self._annotation_processor = _AnnotationProcessor(
annotation_fields, self._header_fields, cfactory, use_allele_num,
minimal_match, infer_annotation_types)
self._minimal_match = minimal_match
self._infer_annotation_types = infer_annotation_types
