Constructor functions

Constructors

bool(x)

Convert to a Boolean expression.

float(x)

Convert to a 64-bit floating point expression.

float32(x)

Convert to a 32-bit floating point expression.

float64(x)

Convert to a 64-bit floating point expression.

int(x)

Convert to a 32-bit integer expression.

int32(x)

Convert to a 32-bit integer expression.

int64(x)

Convert to a 64-bit integer expression.

interval(start, end[, includes_start, ...])

Construct an interval expression.

struct(**kwargs)

Construct a struct expression.

tuple(iterable)

Construct a tuple expression.

Collection constructors

array(collection)

Construct an array expression.

empty_array(t)

Returns an empty array of elements of a type t.

set(collection)

Convert a set expression.

empty_set(t)

Returns an empty set of elements of a type t.

dict(collection)

Creates a dictionary.

empty_dict(key_type, value_type)

Returns an empty dictionary with key type key_type and value type value_type.
hail.expr.functions.bool(x)[source]

Convert to a Boolean expression.

Examples

>>> hl.eval(hl.bool('TRUE'))
True

>>> hl.eval(hl.bool(1.5))
True

Notes

Numeric expressions return True if they are non-zero, and False if they are zero.

Acceptable string values are: 'True', 'true', 'TRUE', 'False', 'false', and 'FALSE'.

Parameters:

x (NumericExpression or BooleanExpression or StringExpression)

Returns:

BooleanExpression

hail.expr.functions.float(x)[source]

Convert to a 64-bit floating point expression.

Examples

>>> hl.eval(hl.float('1.1'))
1.1

>>> hl.eval(hl.float(1))
1.0

>>> hl.eval(hl.float(True))
1.0

Note

Alias for float64().

Parameters:

x (NumericExpression or BooleanExpression or StringExpression)

Returns:

NumericExpression of type tfloat64

hail.expr.functions.float32(x)[source]

Convert to a 32-bit floating point expression.

Examples

>>> hl.eval(hl.float32('1.1'))
1.100000023841858

>>> hl.eval(hl.float32(1))
1.0

>>> hl.eval(hl.float32(True))
1.0
Parameters:

x (NumericExpression or BooleanExpression or StringExpression)

Returns:

NumericExpression of type tfloat32

hail.expr.functions.float64(x)[source]

Convert to a 64-bit floating point expression.

Examples

>>> hl.eval(hl.float64('1.1'))
1.1

>>> hl.eval(hl.float64(1))
1.0

>>> hl.eval(hl.float64(True))
1.0
Parameters:

x (NumericExpression or BooleanExpression or StringExpression)

Returns:

NumericExpression of type tfloat64

hail.expr.functions.int(x)[source]

Convert to a 32-bit integer expression.

Examples

>>> hl.eval(hl.int('1'))
1

>>> hl.eval(hl.int(1.5))
1

>>> hl.eval(hl.int(True))
1

Note

Alias for int32().

Parameters:

x (NumericExpression or BooleanExpression or StringExpression)

Returns:

NumericExpression of type tint32

hail.expr.functions.int32(x)[source]

Convert to a 32-bit integer expression.

Examples

>>> hl.eval(hl.int32('1'))
1

>>> hl.eval(hl.int32(1.5))
1

>>> hl.eval(hl.int32(True))
1
Parameters:

x (NumericExpression or BooleanExpression or StringExpression)

Returns:

NumericExpression of type tint32

hail.expr.functions.int64(x)[source]

Convert to a 64-bit integer expression.

Examples

>>> hl.eval(hl.int64('1'))
1

>>> hl.eval(hl.int64(1.5))
1

>>> hl.eval(hl.int64(True))
1
Parameters:

x (NumericExpression or BooleanExpression or StringExpression)

Returns:

NumericExpression of type tint64

hail.expr.functions.interval(start, end, includes_start=True, includes_end=False)[source]

Construct an interval expression.

Examples

>>> hl.eval(hl.interval(5, 100))
Interval(start=5, end=100, includes_start=True, includes_end=False)

>>> hl.eval(hl.interval(hl.locus("1", 100), hl.locus("1", 1000)))
    Interval(start=Locus(contig=1, position=100, reference_genome=GRCh37),
             end=Locus(contig=1, position=1000, reference_genome=GRCh37),
             includes_start=True,
             includes_end=False)

Notes

start and end must have the same type.

Parameters:
Returns:

IntervalExpression

hail.expr.functions.struct(**kwargs)[source]

Construct a struct expression.

Examples

>>> s = hl.struct(a=5, b='Foo')
>>> hl.eval(s.a)
5
Returns:

StructExpression – Keyword arguments as a struct.

hail.expr.functions.tuple(iterable)[source]

Construct a tuple expression.

Examples

>>> t = hl.tuple([1, 2, '3'])
>>> hl.eval(t)
(1, 2, '3')

>>> hl.eval(t[2])
'3'
Parameters:

iterable (an iterable of Expression) – Tuple elements.

Returns:

TupleExpression

hail.expr.functions.array(collection)[source]

Construct an array expression.

Examples

>>> s = {'Bob', 'Charlie', 'Alice'}

>>> hl.eval(hl.array(s))
['Alice', 'Bob', 'Charlie']
Parameters:

collection (ArrayExpression or SetExpression or DictExpression)

Returns:

ArrayExpression

hail.expr.functions.empty_array(t)[source]

Returns an empty array of elements of a type t.

Examples

>>> hl.eval(hl.empty_array(hl.tint32))
[]
Parameters:

t (str or HailType) – Type of the array elements.

Returns:

ArrayExpression

hail.expr.functions.set(collection)[source]

Convert a set expression.

Examples

>>> s = hl.set(['Bob', 'Charlie', 'Alice', 'Bob', 'Bob'])
>>> hl.eval(s) 
{'Alice', 'Bob', 'Charlie'}
Returns:

SetExpression – Set of all unique elements.

hail.expr.functions.empty_set(t)[source]

Returns an empty set of elements of a type t.

Examples

>>> hl.eval(hl.empty_set(hl.tstr))
set()
Parameters:

t (str or HailType) – Type of the set elements.

Returns:

SetExpression

hail.expr.functions.dict(collection)[source]

Creates a dictionary.

Examples

>>> hl.eval(hl.dict([('foo', 1), ('bar', 2), ('baz', 3)]))
{'bar': 2, 'baz': 3, 'foo': 1}

Notes

This method expects arrays or sets with elements of type ttuple with 2 fields. The first field of the tuple becomes the key, and the second field becomes the value.

Parameters:

collection (DictExpression or ArrayExpression or SetExpression)

Returns:

DictExpression

hail.expr.functions.empty_dict(key_type, value_type)[source]

Returns an empty dictionary with key type key_type and value type value_type.

Examples

>>> hl.eval(hl.empty_dict(hl.tstr, hl.tint32))
{}
Parameters:
Returns:

DictExpression