nucleus.util.vcf_constants -- Constants related to the VCF variant specification.
Source code: nucleus/util/vcf_constants.py
Documentation index: doc_index.md
See the full specification at https://samtools.github.io/hts-specs/VCFv4.3.pdf for details.
Functions overview
| Name | Description |
|---|---|
create_get_fn(value_type, number) |
Returns a callable that extracts the typed information from a ListValue. |
reserved_filter_field(field_id) |
Returns the reserved FILTER field with the given ID. |
reserved_format_field(field_id) |
Returns the reserved FORMAT field with the given ID. |
reserved_format_field_get_fn(field_name) |
Returns the callable that gets the proper field for the given field_name. |
reserved_format_field_set_fn(field_name) |
Returns the callable that sets the proper field for the given field_name. |
reserved_info_field(field_id) |
Returns the reserved INFO field with the given ID. |
reserved_info_field_get_fn(field_name) |
Returns the callable that gets the proper field for the given field_name. |
reserved_info_field_set_fn(field_name) |
Returns the callable that sets the proper field for the given field_name. |
Functions
create_get_fn(value_type, number)
Returns a callable that extracts the typed information from a ListValue.
Args:
value_type: str. The value type stored as defined in the VCF 4.3 spec.
number: str. The number of entries of this value as defined in the VCF spec.
Returns:
A callable that takes two inputs: A Map(str --> ListValue) and a string
field name and returns the associated typed value(s). The return value is
a list of typed values or a single typed value, depending on the expected
number of values returned.
reserved_filter_field(field_id)
Returns the reserved FILTER field with the given ID.
reserved_format_field(field_id)
Returns the reserved FORMAT field with the given ID.
reserved_format_field_get_fn(field_name)
Returns the callable that gets the proper field for the given field_name.
Args:
field_name: str. The field name of the reserved FORMAT field (e.g. 'AD').
Returns:
The callable that takes in a Map(str --> ListValue), and field name and
returns the associated typed value(s).
Raises:
ValueError: The field_name is not a known reserved FORMAT field.
reserved_format_field_set_fn(field_name)
Returns the callable that sets the proper field for the given field_name.
Args:
field_name: str. The field name of the reserved FORMAT field (e.g. 'AD').
Returns:
The callable that takes in a Map(str --> ListValue), field name, and value
and modifies the map to populate the field_name entry with the given value.
Raises:
ValueError: The field_name is not a known reserved FORMAT field.
reserved_info_field(field_id)
Returns the reserved INFO field with the given ID.
reserved_info_field_get_fn(field_name)
Returns the callable that gets the proper field for the given field_name.
Args:
field_name: str. The field name of the reserved INFO field (e.g. 'MQ').
Returns:
The callable that takes in a Map(str --> ListValue), and field name and
returns the associated typed value(s).
Raises:
ValueError: The field_name is not a known reserved INFO field.
reserved_info_field_set_fn(field_name)
Returns the callable that sets the proper field for the given field_name.
Args:
field_name: str. The field name of the reserved INFO field (e.g. 'MQ').
Returns:
The callable that takes in a Map(str --> ListValue), field name, and value
and modifies the map to populate the field_name entry with the given value.
Raises:
ValueError: The field_name is not a known reserved INFO field.