def get_reference(name) -> 'hail.ReferenceGenome':
"""Returns the reference genome corresponding to `name`.
Notes
-----
Hail's built-in references are ``'GRCh37'`` and ``GRCh38'``. The contig names
and lengths come from the GATK resource bundle:
`human_g1k_v37.dict <ftp://[email protected]/bundle/b37/human_g1k_v37.dict>`__
and `Homo_sapiens_assembly38.dict <ftp://[email protected]/bundle/hg38/Homo_sapiens_assembly38.dict>`__.
If ``name='default'``, the value of :func:`.default_reference` is returned.
Parameters
----------
name : :obj:`str`
Name of a previously loaded reference genome or one of Hail's built-in
references: ``'GRCh37'``, ``'GRCh38'``, and ``'default'``.
Returns
-------
:class:`.ReferenceGenome`
"""
from hail import ReferenceGenome
if name == 'default':
return default_reference()
else:
return ReferenceGenome._references.get(
name,
ReferenceGenome._from_java(
Env.hail().variant.ReferenceGenome.getReference(name)))
def default_reference(self):
if not self._default_ref:
self._default_ref = ReferenceGenome._from_java(
Env.hail().variant.ReferenceGenome.defaultReference())
return self._default_ref
def default_reference(self):
if not self._default_ref:
self._default_ref = ReferenceGenome._from_java(Env.hail().variant.ReferenceGenome.defaultReference())
return self._default_ref