import json
import re
from hail.typecheck import typecheck_method, sequenceof, dictof, oneof, \
sized_tupleof, nullable, transformed, lazy
from hail.utils.misc import wrap_to_list
from hail.utils.java import Env
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, Genome Reference Consortium Human Build 37
- GRCh38, Genome Reference Consortium Human Build 38
- GRCm38, Genome Reference Consortium Mouse Build 38
from hail.typecheck import typecheck_method, lazy, nullable, anytype
import hail as hl
interval_type = lazy()
class Interval(object):
"""
An object representing a range of values between `start` and `end`.
>>> interval2 = hl.Interval(3, 6)
Parameters
----------
start : any type
Object with type `point_type`.
end : any type
Object with type `point_type`.
includes_start : :obj:`bool`
Interval includes start.
includes_end : :obj:`bool`
Interval includes end.
Note
----
This object refers to the Python value returned by taking or collecting
Hail expressions, e.g. ``mt.interval.take(5)``. This is rare; it is much
more common to manipulate the :class:`.IntervalExpression` object, which is
constructed using the following functions:
- :func:`.interval`