import json import re from hail.typecheck import * from hail.utils import wrap_to_list from hail.utils.java import jiterable_to_list, Env, joption from hail.typecheck import oneof, transformed import hail as hl rg_type = lazy() reference_genome_type = oneof( transformed((str, lambda x: hl.get_reference(x))), rg_type) class ReferenceGenome(object): """An object that represents a `reference genome <https://en.wikipedia.org/wiki/Reference_genome>`__. Examples -------- >>> contigs = ["1", "X", "Y", "MT"] >>> lengths = {"1": 249250621, "X": 155270560, "Y": 59373566, "MT": 16569} >>> par = [("X", 60001, 2699521)] >>> my_ref = hl.ReferenceGenome("my_ref", contigs, lengths, "X", "Y", "MT", par) Notes ----- Hail comes with predefined reference genomes (case sensitive!): - GRCh37 - GRCh38 - GRCm38
raise NotImplementedError @abc.abstractmethod def clear(self): raise NotImplementedError def _get_context(self): return _empty_context def get_context(self): if self._context is None: self._context = self._get_context() return self._context hail_type = oneof(HailType, transformed((str, dtype))) class _tvoid(HailType): def __init__(self): super(_tvoid, self).__init__() def __str__(self): return "void" def _eq(self, other): return isinstance(other, _tvoid) def _parsable_string(self): return "Void"
import json import re from hail.typecheck import * from hail.utils import wrap_to_list from hail.utils.java import jiterable_to_list, Env, joption from hail.typecheck import oneof, transformed import hail as hl rg_type = lazy() reference_genome_type = oneof(transformed((str, lambda x: hl.get_reference(x))), rg_type) class ReferenceGenome(object): """An object that represents a `reference genome <https://en.wikipedia.org/wiki/Reference_genome>`__. Examples -------- >>> contigs = ["1", "X", "Y", "MT"] >>> lengths = {"1": 249250621, "X": 155270560, "Y": 59373566, "MT": 16569} >>> par = [("X", 60001, 2699521)] >>> my_ref = hl.ReferenceGenome("my_ref", contigs, lengths, "X", "Y", "MT", par) Notes ----- Hail comes with predefined reference genomes (case sensitive!): - GRCh37 - GRCh38 - GRCm38
y_contigs, mt_contigs, par)) def _init_from_java(self, jrep): self._jrep = jrep @classmethod def _from_java(cls, jrep): gr = ReferenceGenome.__new__(cls) gr._init_from_java(jrep) gr._name = None gr._contigs = None gr._lengths = None gr._x_contigs = None gr._y_contigs = None gr._mt_contigs = None gr._par = None gr._par_tuple = None super(ReferenceGenome, gr).__init__() ReferenceGenome._references[gr.name] = gr return gr def _check_locus(self, l_jrep): self._jrep.checkLocus(l_jrep) def _check_interval(self, interval_jrep): self._jrep.checkInterval(interval_jrep) reference_genome_type = oneof( transformed((str, lambda x: hl.get_reference(x))), ReferenceGenome)