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