Index of values

As range, without the label.

As --, but accepts enumerations in reverse order.

(a, step) --. b) creates a float enumeration from a to b with an increment of step between elements.

As (--) but without the right endpoint

s // f is equivalent to filter f s

s //@ f is equivalent to filter_map f s

s /@ f is equivalent to map f s

Add the given int to the set, returning a new set

add lo hi v t adds the interval (lo, hi) labeled with value v to the contents of t.

add accu x y updates the value in accu for the bin of x by an increment y

add_child t x inserts x as the right-most child of t.

add_range t lo hi adds the range of integers lo, hi (including both endpoints) to the given set, returning a new set

after ~n t returns the portion of t in the range n+1, max_int

after u v is equivalent to before v u.

Name of algorithm used to generate scores.

Version number of algorithm used.

Return true if all pairs of given ranges are positionally comparable.

Return true if any pair of given ranges overlap each other.

arabic s returns the canonical Arabic representation of s.

auc e computes the area above the X-axis and under the piecewise linear curve passing through the points in e.

background_of_sequence seq pc estimates the base frequency in seq using pc as pseudo-counts.

Create a printer for track files containing Bed(Graph) lines.

before x t returns the portion of t in the range min_int, n-1

before u v is true if strict_before u v || equal u v.

best_hit mat seq returns the position and score of the best alignment found in seq for the motif mat.

bin hist i returns the ith bin of hist.

bin hist i returns the ith bin of hist.

Create a string communicating an error, warning, or bug.

Returns the number of elements in the set

Cut a stream of char_seq items into a stream of char_seq raw_items, where lines are cut at items_per_line characters (default 80).

Aggregate a stream of FASTA char_seq raw_items into char_seq items.

Print char_seq items.

Used for debugging purpose, should be removed in the long run

Returns some element in the set

closest loc lmap returns the location in lmap that is the closest to loc, along with its annotation and the actual (minimal) distance.

closest loc lset returns the location in lset that is the closest to loc, along with the actual (minimal) distance.

Cumulative distribution function.

Return the file name, line number, or column number.

Names of columns in BPMAP file, in the order required by specification.

column m i extracts the ith column of matrix m.

combine transforms a pair of streams into a stream of pairs of corresponding elements.

Compare two sets.

compare_containment u v returns -1 if u is a strict subset of v, 0 if u is equal to v, +1 if u is a strict superset of v, and returns None otherwise.

Compare by ranges' hi bounds, ignoring lo bounds.

Compare by ranges' lo bounds, ignoring hi bounds.

Return order between lo bounds unless they are equal, in which case return order between hi bounds.

compare_positional u v returns -1 if u is strictly before v, 0 if u is equal to v, +1 if u is strictly after v, and returns None otherwise.

Create the complement of the given set - i.e.

compose t u composes t and u.

Like Biocaml_transform.compose_results but only the first transform returns Result.ts.

compose_results t u is like Biocaml_transform.compose but for transforms returning Result.ts.

Like Biocaml_transform.compose_results but with a pre-specified on_error function.

Return any remaining lines and the unfinished string, without removing them from the buffer.

Return any remaining lines and the unfinished string, without removing them from the buffer.

Probe coordinate convention used.

Copy histogram.

Return number of elements discarded from given stream.

count hist i returns the count the ith bin.

count hist i returns the count the ith bin.

create ~n e f op creates an accumulator, which maps instances to bins with f, uses e as a neutral element (that is the value associated to a bin before any value has been added to it) and updates the value of a bin with op.

Get the current position in the stream.

Get the current position in the stream.

data bpmap cels returns a list associating probes with pairs of (PM,MM) idata in each of the given cel files (in the same order of course).

Return the type of data, either "signal" or "p-value".

Compute the difference between two sets.

Set difference.

drop xs ~n is equivalent to calling n times junk on xs.

Similar to drop: drop_while xs ~f removes elements from xs and stops when f evals to false on the head element.

Construction of efetch URLs.

Returns a list of all elements in the set

The empty set

Empty the buffer.

The empty stream.

The empty set.

Empty the buffer.

the empty tree

epsilon f init fin applies f n fin to all numbers from init to fin and adds them up.

Test whether two sets are equal.

Parse a string potentially escaped with OCaml string conventions, or stop at stop_before character if it is not escaped.

Convert non-alphanumeric characters to their "%HX" URL-escaping format.

Parses an answer of esearch under XML format

Construction of esearch URLs.

Construction of esummary URLs

function evaluation at some point in the genome

True if given integer is even.

Test whether some element of a set satisfies a predicate

exists s ~f returns true if there is some x in s such that f x is true.

exp_assoc_list dat returns a list associating each integer i with the list of values associated with all ranges overlapping i in dat.

Self-explanatory.

Identical to scan but directly implemented in C

Enqueue something in the printer.

feed t i stores i into the buffered transform.

Feed the parser with a line.

Feed the parser with a line.

Feed the parser with an arbitrary string buffer.

Feed the parser with an arbitrary string buffer.

Builds the subset of those elements that satisfy the predicate

filter_compose t u ~destruct ~reconstruct produces a transform that feeds a filtered subset of ts outputs to u.

Create an interval tree with the elements which overlap with [low, high].

find e ~f returns either Some x where x is the first element of e such that f x returns true, consuming the stream up to and including the found element, or None if no such element exists in the stream, consuming the whole stream in the search.

find_bin_index hist x returns the index of the bin in hist containing x.

find_closest lo hi t returns the interval in t which is at minimal distance of the interval [lo;hi].

Same as find except that it raises an exception Not_found instead of returning None.

find_intersecting_elem a b t is equivalent to Stream.filter ~f:(fun (x,y,_) -> intersects x y t) (stream t) but is more efficient.

Similar to find

find_min_range v pred i finds the minimum sized range within v centered around i that satisfies pred.

find_min_window a pred i finds the minimum sized window within a centered around index i that satisfies pred.

TO DO: fill in this documentation.

find_regions ~max_gap pred a returns an array of (first,last) index pairs denoting boundaries (inclusive) of regions found in a.

Uniform distribution over A, C, G, T

Methods for creating a position.

Get the current transformed content.

fold f t x0 returns the final result of merging each element of t into x0 using merge function f

fold xs ~init ~f returns f (...(f (f init x0) x1)...) xn, that is for the stream a0; a1; ...; an does the following calculations:

fold guaranteed on increasing order keywise, and for each key

folds on constant intervals of the function, in increasing order

Like fold but operates on two streams.

Like fold2 except streams required to be of equal length.

see String.fold_left.

String.fold_lefti

As fold, but operates on contiguous ranges

Tests whether a predicate applies to all elements of the set

for_all s ~f returns true if f x is true for every x in s.

from ~n t returns the portion of t in the range n, max_int

from f returns a stream whose nth element is determined by calling f n, which should return Some x to indicate value x or None to indicate the end of the stream.

fsum xs returns the sum of the floats contained in xs

gap u v returns the size of the gap between u and v.

File path of bpmap file used to generate scores.

get accu x returns the value associated to b in accu.

Create a printer for track files containing GFF lines.

group xs f applies f to the elements of xs and distribute them according to the return value of f.

Return a transform that converts a stream of lines to a stream of pairs of lines.

Same as group but with a comparison function instead of a mapping.

Return histogram of values using cmp (default = Pervasives.compare) for comparison.

identity () returns a transform that simply returns its inputs as outputs without modification.

idxsort cmp a is like Array.sort but a is unaltered, and instead an array of the indices in sorted order is returned.

ifold f a t folds over data rows in intensity section of t.

iiter f t iterates over the rows in intensity section of t.

in_channel_strings_to_stream ic t returns a stream of 'outputs given a transform t that knows how to produce 'outputs from strings.

Returns a stream of char_seq items.

Returns a stream of int_seq items.

in_range hist x is true if x greater than or equal to minimum hist and strictly less than maximum hist.

Returns an sb_model read from input stream

increment delt hist x increments the count of the bin containing x by delt (default is 1.0).

incrl pos k increments the line number of pos by k.

init n f returns the stream f 0; f 1; ... f (n-1).

Cut a stream of int_seq items into a stream of int_seq raw_items, where lines are cut at items_per_line integers (default 27).

Aggregate a stream of FASTA int_seq raw_items into int_seq items.

Print int_seq items.

Compute the intersection of two sets.

Set intersection.

intersect u v returns the range representing the intersection of u and v.

intersecting_elems loc lmap returns an enumeration of elements in lmap whose location intersects with loc.

intersecting_elems loc lset returns an enumeration of all locations in lset that intersect loc.

intersects a b t returns true if one interval in t intersects with the interval [a;b].

intersects loc lmap returns true if loc has a non-empty intersection with one of the locations in lmap, and returns false otherwise

intersects loc lmap returns true if loc has a non-empty intersection with one of the locations in lmap, and returns false otherwise

intersects loc sel returns true if loc has a non-empty intersection with sel, and false otherwise.

Test whether a set is empty, returns true if the set is empty.

Check if the printer-queue is empty.

Tell if the parser's buffers are empty or not.

True if the stream is empty, else false.

Return true if given set is empty.

Tell if the parser's buffers are empty or not.

True if given character represents one of the allowed nucleic acid codes, case-insensitive.

Basic parsing of a single line.

Basic “printing” of one single item.

Create a printer for a given version.

Create a full stoppable Biocaml_transform.t from item values to strings.

Create a Biocaml_transform.t which “prints” BED data (reminder: includes ends-of-line).

iter f t calls f once for each element of t

iter xs ~f calls in turn f x0, f x1, ...

Like iter but operates on two streams.

Like iter2 except streams required to be of equal length.

iter_range ~f t calls f once for each contiguous range of t.

Indexed variants of the previous higher-order functions.

Discard first element of given stream or do nothing if the stream is empty.

Length of sequence.

Return a transform that converts a stream of arbitrary strings to a stream of lines.

Logarithm.

Base 10 logarithm.

Base 2 logarithm.

Lower tail quantile for standard normal distribution function.

Median absolute deviation (MAD).

Create a printer-queue with a to_string function.

Build a stoppable line-oriented parsing_buffer.

make ~feed ~next () creates a transform that can be fed with feed and read from with next.

Given an enum pos (resp.

make l u returns the range from l to u.

Builds a PWM from a count_matrix and a background

Build a stoppable line-oriented parsing_buffer.

Make a new empty buffer.

make cmp bins returns a new histogram from the given bins, all initialized to a count of 0.0.

The most general way to make a transform.

Do like make but merge `incomplete_input _ with the errors of ~next (which must be polymorphic variants).

Do like make but merge `incomplete_input _ with the errors of ~next (which must be polymorphic variants).

Like make but returns None instead of raising exception.

Like Biocaml_transform.make but the output is a Result.t.

make_uniform min max n returns a histogram with n bins uniformly dividing up the range from min to max.

mass p return the mass of the precursor p without charge.

Returns a string with sb_math converted into a S-expression

Return maximum value in given array.

String explaining OCaml's array length limitation on 32-bit machines.

Returns the maximum element in the set

Return maximum gap between adjacent pairs of given ranges.

Upper limit of the maximum bin.

Mean.

Median.

test whether a given int is a member of the set

member t k returns true if t contains k.

merge test (a, b) merge the elements from a and b into a single stream.

Return minimum value in given array.

Returns the minimum element in the set

Lower limit of the minimum bin.

Return "-" or "+".

mix t u f returns a transform that takes as input a pair of the inputs expected by t and u, and outputs a single value that is the result of applying f to the outputs of t and u.

Similar to Biocaml_cel.data but the data returned are the MM mean intensity values in cels.

name t returns the name of t.

next t returns an output value if possible, `not_ready if t needs to be fed with more input before it can produce an output, or `end_of_stream if t has been stopped and has no more data.

Return first element in given stream if any and remove it from the stream.

Return first element in given stream and remove it from the stream.

Get the next line.

Get the next line.

Get the next line, but throw No_next_line if there is no line to return.

Get the next line, but throw No_next_line if there is no line to return.

npeek s n returns a list of the first n elements in stream s, or all of its remaining elements if less than n elements are available.

nth t i returns the ith nucleic acid in sequence t.

Number of bins.

Number of PM/MM probe pairs in given BPMAP.

True if given integer is odd.

of_ascii x returns the PHRED score encoded by ASCII character x.

of_ascii ~offset x returns the PHRED score encoded by ASCII character x.

Like of_ascii but may raise Error _ if x does not represent a valid score.

Make sequence from buffer.

Return a stream of characters by reading from the input channel.

of_file fname returns the spectra contained in the file fname.

Parse given file if possible.

of_file file parses file.

Parse file.

Parse given file if possible.

Convert integer to roman numeral if possible.

Like of_int but raise Bad if unable to convert integer.

of_int_exn x returns the PHRED score with the same value x, but assures that x is non-negative.

Parse a Line.t into a row while specifying a format.

Build a ISet.t out of a list or enum of ranges

Return a stream of elements as occurring in the given list.

of_probability ~f x returns -10 * log_10(x/(1-x)), which is the definition of Solexa scores.

of_probability ~f x returns -10 * log_10(x), which is the definition of PHRED scores.

See of_probability

Construct the set of integers representing the union of integers in all given ranges.

of_solexa_score x converts Solexa score x to a PHRED score.

Return a data structure containing all elements in given stream, fully consuming the stream.

of_stream e computes a selection as the union of the locations contained in e

Return a stream characters as occurring in the given string.

Convert string to chromosome name if possible.

Make sequence from string.

Parse string as a roman numeral if possible.

Like of_string but raise Bad if conversion not possible.

Like of_string but raise Bad if unable to parse string.

Make a sequence from given buffer or string.

Return the given string without checking that it is a line.

Like on_output but on the erroneous part of the output.

on_input f t returns a transform that converts its inputs with f and feeds the results to t.

Like on_output but on the successful part of the output.

on_output t f returns a transform that behaves like t except the outputs are first converted by f.

Like open_out but will not overwrite existing file.

overlap u v returns amount of overlap between two ranges.

Convert a parse_error to a string.

Create a "parser"; the optional filename is used only to create error locations.

partitions the input set into two sets with elements that satisfy the predicate and those that don't

partition e ~f splits e into two streams, where the first stream have all the elements satisfying f, the second stream is opposite.

pearson arr1 arr2 computes the Pearson product-moment correlation coefficient of two float arrays.

Return first element of given stream without removing it from the stream, or None if the stream is empty.

Similar to Biocaml_cel.data but the data returned are the PM mean intensity values in cels.

Similar to Biocaml_cel.data but the data returned are the PM-MM mean intensity values in cels.

prediction_values tp tn fp fn takes 4 arguments: the number of true-positives tp, true-negatives tn, false-positives fp, and false-negatives fn.

Used for debugging purpose, should be removed in the long run

Print an error, warning, or bug.

product filter f l1 l2 computes an histogram of values returned by f when it is applied for all combinations of elements in l1 and l2 such that the predicate filter is true

Pseudomedian is the median of all pairwise averages of values in given array (not including self-pairs).

a constant interval of an LMap lm is a range intersecting lm and that do not contain any start or end of a range from lm.

Input matrix m should be arranged such that m.(i).(j) is the ith measurement in experiment j.

Get the number of lines ready-to-use in the buffer/queue.

Get the number of lines ready-to-use in the buffer/queue.

range xs is the stream of all valid indices in xs

range p until:q creates a stream of integers [p, p+1, ..., q].

range step first last returns array [|first; first +.

Returns a list of all contiguous ranges in the set

rank arr returns an array of ranked values, where ties are given the mean of what the rank would otherwise be.

Create a printing "stoppable" transform.

reduce xs ~f returns f (...(f (f x1 x2) x3)...) xn

Remove an element from the given set, returning a new set

remove_range lo hi t removes a range of elements from the given set, returning a new set

Return histogram with same bins but all counts reset to 0.0.

Convert exception-less stream to exception-ful stream.

Return "rev" or "fwd".

Reverse complement of a PWM

Root mean square.

roman s returns the canonical Roman representation of s.

row m i returns the ith row of matrix m.

String representation of row in same format as required by specification.

Return scale data is reported in, e.g.

scan is similar to scanl but without the init value: if s contains x0, x1, x2 ..., scan s ~f contains

scan mat seq tol returns the list of positions (with corresponding scores) such that the alignment score of mat is superior to tol

Like fold but all intermediate values are returned, not just the final value.

section t name returns the section named name.

sectioni t i returns the i'th section.

Return all sections in t.

Set the file name, line number, or column number.

Type row elements (or “cells”).

Type of FASTQ items.

The type of BED data stream items.

Definition of the type of a cell.

The parsing errors.

The possible parsing errors.

The specification of how to parse the remaining columns.

The contents of an alignment line.

The "items" of a parsed SAM file stream.

The possible errors one can get while parsing SAM files.

The most general type that the default parser outputs.

A single row.

Definition of the type of a row.

The possible unzipping errors.

shuffle arr takes an array and randomly shuffles it.

Return the singleton set containing only the given element

singleton x returns a stream containing the single value x.

Number of elements in set.

size v returns the number of integers in v, i.e.

Similar to drop but returns a fresh stream obtained after discarding the n first elements.

Similar to skip: skip_while xs ~f removes elements from xs and stops when f evals to false on the head element.

slice first last t returns the sub-sequence, or slice, of t starting from index first to last (inclusive).

span test e produces two streams (hd, tl), such that hd is the same as take_while test e and tl is the same as skip_while test e.

spearman arr1 arr2 computes the Spearman rank correlation coefficient of two float arrays.

split_and_merge t u ~split ~merge returns a transform whose input is split using split, passing the result either to t or u, and then the outputs of t and u are combined using merge.

Standard deviation.

stop t declares t to be stopped, which means subsequent calls to:

strict_after u v is equivalent to strict_before v u.

strict_before u v is true if u.lo < v.lo && u.hi < v.hi.

strict_subset u v is true if u is a strict subset of v.

strict_superset u v is true if u is a strict superset of v.

Create a printer for track files containing `content line lines.

Create a composite parser for UCSC Bed(Graph) files.

Parse a stream of strings as a char_seq FASTA file.

Create a composite parser for UCSC GFF files.

Parse a stream of strings as an int_seq FASTA file.

Return a transform that converts a stream of arbitrary strings to a stream of lines.

Create a parsing Biocaml_transform.t for a given version.

Create a full stoppable Biocaml_transform.t from arbitrary strings to item values.

Create a Biocaml_transform.t-based parser, while providing the format of the additional columns (default `strings).

string_to_lines s splits s on newline characters, returning the resuling list of lines.

Create a parsing "stoppable" transform.

Create a parser that gets the "track", comment, and "browser" lines and puts the other lines in `content _.

Create the parsing Biocaml_transform.t.

Create a composite parser for UCSC WIG files.

Return a stream of strings from the input.

subset t u returns true if t is a subset of u

subset s t returns true if s is a subset of t.

subset u v is true if u is a subset of v.

sum xs returns the sum of the integers contained in xs

superset u v is true if u is a superset of v.

Create a transform which converts `variable_step_value _ and `fixed_step_value _ values to `bed_graph_value _ values, using the current state.

Create the transform that prints t values to strings.

take xs ~n builds a fresh stream from xs containing the d first elements of xs where d = min n l and l is the length of xs.

Same as take but takes elements from the input enum as long as f evaluates to true.

Indexed variants of the previous prefix/suffix constructors

tandem orientation spacer cm1 cm2 bg builds a PWM by constructing a composite motif: it builds mat1 the PWM from cm1 under background bg (resp.

to_ascii t encodes t as an ASCII character.

to_ascii t encodes t as an ASCII character.

to_ascii_exn t encodes t as an ASCII character.

Outer list will be in ascending order by chr, and inner lists will be in ascending order by coord.

Items will be printed in ascending order by (chr,coord).

to_file file t prints t to file in format required by specification.

Convert roman numeral to integer.

Convert a phred score to an integer.

Items will be returned in ascending order by (chr,coord).

Return set of integers as a list.

to_list v returns the set of integers contained in v, in ascending order.

Return a list of all bin/count pairs.

Return the data as a list of triplets (chr,pos,v) representing the chromosome name, probe position, and value.

to_pair t returns the int * int pair.

to_probablity x converts x to a probablity score.

to_probablity x converts x to a probablity score.

Return set of integers as a minimal list of non-overlapping ranges in ascending order by their coordinates.

Enumerates all contiguous ranges in the set

Return a stream containing all elements of given data structure.

enumeration over all constant intervals of the function, in increasing order

to_stream_fun t returns a function f that behaves like t but the inputs and outputs are on standard OCaml streams.

String representation of a strand.

Return string representation of sequence.

String representation of a roman numeral.

String representation of an range, intended only for human legibility.

transpose m transpose the given matrix m.

Create a full stoppable Biocaml_transform.t that trims FASTQ items.

try_finally_exn fend f a will run x = f a, then run fend a, and finally return x.

uncombine is the opposite of combine

Convert a string containing "%HX" escaped characters to a normal string.

unfold a0 f returns the stream b0; b1; ...; bn, where

Indexed variant of unfold

Compute the union of two sets.

Set union.

union u v returns the ranges representing the union of u and v.

uniq e returns a duplicate of e with repeated values omitted.

Represents an unknown position.

until ~n t returns the portion of t in the range min_int, n

Create a transform that uncompresses a stream.

Variance.

Map the function f on the list until the first error is met.

Create a printer for track files containing WIG lines.

wilcoxon_rank_sum ~alpha=(float) arr1 arr2 performs the Wilcoxon rank sum test on two arrays with an optional argument alpha, set to 0.05 by default.

Performs the wilcoxon rank sum on two float arrays and returns the p-value.

As below, except returns a z value.