Locus

class hail.genetics.Locus(contig, position, reference_genome='default')[source]

An object that represents a location in the genome.

Parameters:
  • contig (str or int) – chromosome identifier
  • position (int) – chromosomal position (1-indexed)
  • reference_genome (str or ReferenceGenome) – Reference genome to use.

Attributes

contig Chromosome identifier.
position Chromosomal position (1-based).
reference_genome Reference genome.

Methods

__init__ Initialize self.
parse Parses a locus object from a CHR:POS string.
contig

Chromosome identifier. :rtype: str

classmethod parse(string, reference_genome='default')[source]

Parses a locus object from a CHR:POS string.

Examples

>>> l1 = hl.Locus.parse('1:101230')
>>> l2 = hl.Locus.parse('X:4201230')
Parameters:
Return type:

Locus

position

Chromosomal position (1-based). :rtype: int

reference_genome

Reference genome.

Returns:ReferenceGenome