AlleleType

class hail.genetics.AlleleType[source]

Bases: IntEnum

An enumeration for allele type.

Notes

The precise values of the enumeration constants are not guarenteed to be stable and must not be relied upon.

Attributes

`UNKNOWN`	Unknown Allele Type
`SNP`	Single-nucleotide Polymorphism (SNP)
`MNP`	Multi-nucleotide Polymorphism (MNP)
`INSERTION`	Insertion
`DELETION`	Deletion
`COMPLEX`	Complex Polymorphism
`STAR`	Star Allele (`alt=*`)
`SYMBOLIC`	Symbolic Allele
`TRANSITION`	Transition SNP
`TRANSVERSION`	Transversion SNP
`pretty_name`	A formatted (as opposed to uppercase) version of the member's name, to match `allele_type()`

Methods

strings

Returns the names of the allele types, for use with literal()

COMPLEX = 5: Complex Polymorphism

DELETION = 4: Deletion

INSERTION = 3: Insertion

MNP = 2: Multi-nucleotide Polymorphism (MNP)

SNP = 1: Single-nucleotide Polymorphism (SNP)

STAR = 6: Star Allele (alt=*)

SYMBOLIC = 7

Symbolic Allele

e.g. alt=<INS>

TRANSITION = 8

Transition SNP

e.g. ref=A alt=G

Note

This is only really used internally in hail.vds.sample_qc() and hail.methods.sample_qc().

TRANSVERSION = 9

Transversion SNP

e.g. ref=A alt=C

Note

This is only really used internally in hail.vds.sample_qc() and hail.methods.sample_qc().

UNKNOWN = 0: Unknown Allele Type

property pretty_name

A formatted (as opposed to uppercase) version of the member’s name, to match allele_type()

Examples

>>> AlleleType.INSERTION.pretty_name
'Insertion'
>>> at = AlleleType(hl.eval(hl.numeric_allele_type('a', 'att')))
>>> at.pretty_name == hl.eval(hl.allele_type('a', 'att'))
True

static strings()[source]: Returns the names of the allele types, for use with literal()