Functions

These functions are exposed at the top level of the module, e.g. hl.case.

• Core language functions
  • literal()
  • cond()
  • if_else()
  • switch()
  • case()
  • bind()
  • rbind()
  • missing()
  • null()
  • str()
  • is_missing()
  • is_defined()
  • coalesce()
  • or_else()
  • or_missing()
  • range()
  • query_table()
  • CaseBuilder
  • SwitchBuilder
• Constructor functions
  • bool()
  • float()
  • float32()
  • float64()
  • int()
  • int32()
  • int64()
  • interval()
  • struct()
  • tuple()
  • array()
  • empty_array()
  • set()
  • empty_set()
  • dict()
  • empty_dict()
• Collection functions
  • len()
  • map()
  • flatmap()
  • starmap()
  • zip()
  • enumerate()
  • zip_with_index()
  • flatten()
  • any()
  • all()
  • filter()
  • sorted()
  • find()
  • group_by()
  • fold()
  • array_scan()
  • reversed()
  • keyed_intersection()
  • keyed_union()
• Numeric functions
  • abs()
  • approx_equal()
  • bit_and()
  • bit_or()
  • bit_xor()
  • bit_lshift()
  • bit_rshift()
  • bit_not()
  • bit_count()
  • exp()
  • expit()
  • is_nan()
  • is_finite()
  • is_infinite()
  • log()
  • log10()
  • logit()
  • floor()
  • ceil()
  • sqrt()
  • sign()
  • min()
  • nanmin()
  • max()
  • nanmax()
  • mean()
  • median()
  • product()
  • sum()
  • cumulative_sum()
  • argmin()
  • argmax()
  • corr()
  • uniroot()
  • binary_search()
• String functions
  • format()
  • json()
  • parse_json()
  • hamming()
  • delimit()
  • entropy()
  • parse_int()
  • parse_int32()
  • parse_int64()
  • parse_float()
  • parse_float32()
  • parse_float64()
• Statistical functions
  • chi_squared_test()
  • fisher_exact_test()
  • contingency_table_test()
  • cochran_mantel_haenszel_test()
  • dbeta()
  • dchisq()
  • dnorm()
  • dpois()
  • hardy_weinberg_test()
  • binom_test()
  • pchisqtail()
  • pgenchisq()
  • pnorm()
  • pT()
  • pF()
  • ppois()
  • qchisqtail()
  • qnorm()
  • qpois()
• Random functions
  • Setting a seed
  • Reproducibility across sessions
• Genetics functions
  • locus()
  • locus_from_global_position()
  • locus_interval()
  • parse_locus()
  • parse_variant()
  • parse_locus_interval()
  • variant_str()
  • call()
  • unphased_diploid_gt_index_call()
  • parse_call()
  • downcode()
  • triangle()
  • is_snp()
  • is_mnp()
  • is_transition()
  • is_transversion()
  • is_insertion()
  • is_deletion()
  • is_indel()
  • is_star()
  • is_complex()
  • is_strand_ambiguous()
  • is_valid_contig()
  • is_valid_locus()
  • contig_length()
  • allele_type()
  • numeric_allele_type()
  • pl_dosage()
  • gp_dosage()
  • get_sequence()
  • mendel_error_code()
  • liftover()
  • min_rep()
  • reverse_complement()

Core language functions

literal(x[, dtype])	Captures and broadcasts a Python variable or object as an expression.
cond(condition, consequent, alternate[, ...])	Deprecated in favor of if_else().
if_else(condition, consequent, alternate[, ...])	Expression for an if/else statement; tests a condition and returns one of two options based on the result.
switch(expr)	Build a conditional tree on the value of an expression.
case([missing_false])	Chain multiple if-else statements with a CaseBuilder.
bind(f, *exprs[, _ctx])	Bind a temporary variable and use it in a function.
rbind(*exprs[, _ctx])	Bind a temporary variable and use it in a function.
null(t)	Deprecated in favor of missing().
is_missing(expression)	Returns True if the argument is missing.
is_defined(expression)	Returns True if the argument is not missing.
coalesce(*args)	Returns the first non-missing value of args.
or_else(a, b)	If a is missing, return b.
or_missing(predicate, value)	Returns value if predicate is True, otherwise returns missing.
range(start[, stop, step])	Returns an array of integers from start to stop by step.
query_table(path, point_or_interval)	Query records from a table corresponding to a given point or range of keys.

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.
str(x)	Returns the string representation of x.
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.

Collection functions

len(x)	Returns the size of a collection or string.
map(f, *collections)	Transform each element of a collection.
flatmap(f, collection)	Map each element of the collection to a new collection, and flatten the results.
zip(*arrays[, fill_missing])	Zip together arrays into a single array.
enumerate(a[, start, index_first])	Returns an array of (index, element) tuples.
zip_with_index(a[, index_first])	Deprecated in favor of enumerate().
flatten(collection)	Flatten a nested collection by concatenating sub-collections.
any(*args)	Check for any True in boolean expressions or collections of booleans.
all(*args)	Check for all True in boolean expressions or collections of booleans.
filter(f, collection)	Returns a new collection containing elements where f returns True.
sorted(collection[, key, reverse])	Returns a sorted array.
find(f, collection)	Returns the first element where f returns True.
group_by(f, collection)	Group collection elements into a dict according to a lambda function.
fold(f, zero, collection)	Reduces a collection with the given function f, provided the initial value zero.
array_scan(f, zero, a)	Map each element of a to cumulative value of function f, with initial value zero.
reversed(x)	Reverses the elements of a collection.
keyed_intersection(*arrays, key)	Compute the intersection of sorted arrays on a given key.
keyed_union(*arrays, key)	Compute the distinct union of sorted arrays on a given key.

Numeric functions

abs(x)	Take the absolute value of a numeric value, array or ndarray.
approx_equal(x, y[, tolerance, absolute, ...])	Tests whether two numbers are approximately equal.
bit_and(x, y)	Bitwise and x and y.
bit_or(x, y)	Bitwise or x and y.
bit_xor(x, y)	Bitwise exclusive-or x and y.
bit_lshift(x, y)	Bitwise left-shift x by y.
bit_rshift(x, y[, logical])	Bitwise right-shift x by y.
bit_not(x)	Bitwise invert x.
bit_count(x)	Count the number of 1s in the in the two's complement binary representation of x.
exp(x)
expit(x)
is_nan(x)
is_finite(x)
is_infinite(x)
log(x[, base])	Take the logarithm of the x with base base.
log10(x)
logit(x)
sign(x)	Returns the sign of a numeric value, array or ndarray.
sqrt(x)
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.
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.
floor(x)
ceil(x)
uniroot(f, min, max, *[, max_iter, epsilon, ...])	Finds a root of the function f within the interval [min, max].

Numeric collection functions

min(*exprs[, filter_missing])	Returns the minimum element of a collection or of given numeric expressions.
nanmin(*exprs[, filter_missing])	Returns the minimum value of a collection or of given arguments, excluding NaN.
max(*exprs[, filter_missing])	Returns the maximum element of a collection or of given numeric expressions.
nanmax(*exprs[, filter_missing])	Returns the maximum value of a collection or of given arguments, excluding NaN.
mean(collection[, filter_missing])	Returns the mean of all values in the collection.
median(collection)	Returns the median value in the collection.
product(collection[, filter_missing])	Returns the product of values in the collection.
sum(collection[, filter_missing])	Returns the sum of values in the collection.
cumulative_sum(a[, filter_missing])	Returns an array of the cumulative sum of values in the array.
argmin(array[, unique])	Return the index of the minimum value in the array.
argmax(array[, unique])	Return the index of the maximum value in the array.
corr(x, y)	Compute the Pearson correlation coefficient between x and y.
binary_search(array, elem)	Binary search array for the insertion point of elem.

String functions

format(f, *args)	Returns a formatted string using a specified format string and arguments.
json(x)	Convert an expression to a JSON string expression.
parse_json(x, dtype)	Convert a JSON string to a structured expression.
hamming(s1, s2)	Returns the Hamming distance between the two strings.
delimit(collection[, delimiter])	Joins elements of collection into single string delimited by delimiter.
entropy(s)	Returns the Shannon entropy of the character distribution defined by the string.
parse_int(x)	Parse a string as a 32-bit integer.
parse_int32(x)	Parse a string as a 32-bit integer.
parse_int64(x)	Parse a string as a 64-bit integer.
parse_float(x)	Parse a string as a 64-bit floating point number.
parse_float32(x)	Parse a string as a 32-bit floating point number.
parse_float64(x)	Parse a string as a 64-bit floating point number.

Statistical functions

chi_squared_test(c1, c2, c3, c4)	Performs chi-squared test of independence on a 2x2 contingency table.
fisher_exact_test(c1, c2, c3, c4)	Calculates the p-value, odds ratio, and 95% confidence interval using Fisher's exact test for a 2x2 table.
contingency_table_test(c1, c2, c3, c4, ...)	Performs chi-squared or Fisher's exact test of independence on a 2x2 contingency table.
cochran_mantel_haenszel_test(a, b, c, d)	Perform the Cochran-Mantel-Haenszel test for association.
dbeta(x, a, b)	Returns the probability density at x of a beta distribution with parameters a (alpha) and b (beta).
dpois(x, lamb[, log_p])	Compute the (log) probability density at x of a Poisson distribution with rate parameter lamb.
hardy_weinberg_test(n_hom_ref, n_het, n_hom_var)	Performs test of Hardy-Weinberg equilibrium.
pchisqtail(x, df[, ncp, lower_tail, log_p])	Returns the probability under the right-tail starting at x for a chi-squared distribution with df degrees of freedom.
pnorm(x[, mu, sigma, lower_tail, log_p])	The cumulative probability function of a normal distribution with mean mu and standard deviation sigma.
ppois(x, lamb[, lower_tail, log_p])	The cumulative probability function of a Poisson distribution.
qchisqtail(p, df[, ncp, lower_tail, log_p])	The quantile function of a chi-squared distribution with df degrees of freedom, inverts pchisqtail().
qnorm(p[, mu, sigma, lower_tail, log_p])	The quantile function of a normal distribution with mean mu and standard deviation sigma, inverts pnorm().
qpois(p, lamb[, lower_tail, log_p])	The quantile function of a Poisson distribution with rate parameter lamb, inverts ppois().

Randomness

rand_bool(p[, seed])	Returns True with probability p.
rand_beta(a, b[, lower, upper, seed])	Samples from a beta distribution with parameters a (alpha) and b (beta).
rand_cat(prob[, seed])	Samples from a categorical distribution.
rand_dirichlet(a[, seed])	Samples from a Dirichlet distribution.
rand_gamma(shape, scale[, seed])	Samples from a gamma distribution with parameters shape and scale.
rand_norm([mean, sd, seed, size])	Samples from a normal distribution with mean mean and standard deviation sd.
rand_pois(lamb[, seed])	Samples from a Poisson distribution with rate parameter lamb.
rand_unif([lower, upper, seed, size])	Samples from a uniform distribution within the interval [lower, upper].
rand_int32(a[, b, seed])	Samples from a uniform distribution of 32-bit integers.
rand_int64([a, b, seed])	Samples from a uniform distribution of 64-bit integers.
shuffle(a[, seed])	Randomly permute an array

Genetics functions

locus(contig, pos[, reference_genome])	Construct a locus expression from a chromosome and position.
locus_from_global_position(global_pos[, ...])	Constructs a locus expression from a global position and a reference genome.
locus_interval(contig, start, end[, ...])	Construct a locus interval expression.
parse_locus(s[, reference_genome])	Construct a locus expression by parsing a string or string expression.
parse_variant(s[, reference_genome])	Construct a struct with a locus and alleles by parsing a string.
parse_locus_interval(s[, reference_genome, ...])	Construct a locus interval expression by parsing a string or string expression.
variant_str(*args)	Create a variant colon-delimited string.
call(*alleles[, phased])	Construct a call expression.
unphased_diploid_gt_index_call(gt_index)	Construct an unphased, diploid call from a genotype index.
parse_call(s)	Construct a call expression by parsing a string or string expression.
downcode(c, i)	Create a new call by setting all alleles other than i to ref
triangle(n)	Returns the triangle number of n.
is_snp(ref, alt)	Returns True if the alleles constitute a single nucleotide polymorphism.
is_mnp(ref, alt)	Returns True if the alleles constitute a multiple nucleotide polymorphism.
is_transition(ref, alt)	Returns True if the alleles constitute a transition.
is_transversion(ref, alt)	Returns True if the alleles constitute a transversion.
is_insertion(ref, alt)	Returns True if the alleles constitute an insertion.
is_deletion(ref, alt)	Returns True if the alleles constitute a deletion.
is_indel(ref, alt)	Returns True if the alleles constitute an insertion or deletion.
is_star(ref, alt)	Returns True if the alleles constitute an upstream deletion.
is_complex(ref, alt)	Returns True if the alleles constitute a complex polymorphism.
is_valid_contig(contig[, reference_genome])	Returns True if contig is a valid contig name in reference_genome.
is_valid_locus(contig, position[, ...])	Returns True if contig and position is a valid site in reference_genome.
contig_length(contig[, reference_genome])	Returns the length of contig in reference_genome.
allele_type(ref, alt)	Returns the type of the polymorphism as a string.
pl_dosage(pl)	Return expected genotype dosage from array of Phred-scaled genotype likelihoods with uniform prior.
gp_dosage(gp)	Return expected genotype dosage from array of genotype probabilities.
get_sequence(contig, position[, before, ...])	Return the reference sequence at a given locus.
mendel_error_code(locus, is_female, father, ...)	Compute a Mendelian violation code for genotypes.
liftover(x, dest_reference_genome[, ...])	Lift over coordinates to a different reference genome.
min_rep(locus, alleles)	Computes the minimal representation of a (locus, alleles) polymorphism.
reverse_complement(s[, rna])	Reverses the string and translates base pairs into their complements .