Index of values

p1/p2 is equivalent to concat p1 p2.

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.

For a given tags value and a list of file-base-names add extensions to the files, and return also the base-names not touched.

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.

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 (where items_per_line is defined with the `max_items_per_line _ tag, if not specified the default is 80).

Aggregate a stream of FASTA char_seq raw_items into char_seq items.

Print char_seq items.

Convert a raw_item to a string (ignore comments).

The default tags (for char_seq).

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.

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.

Probe coordinate convention used.

Copy histogram.

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.

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".

Default tags ({allow_empty_lines = false; sharp_comments = true}).

The default tags define a loose TSV format.

Default tags for a random Gff file: {version = `three; allow_empty_lines = false; sharp_comments = true}.

Get a filename extension for a given format.

Give a file extension ("tsv", "csv", or "table").

Do like default_extension but for potentially multiple file-formats.

Compute the difference between two sets.

Set difference.

Construction of efetch URLs.

Returns a list of all elements in the set

The empty set

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

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

Parse a header line into a more detailed type.

Self-explanatory.

Identical to scan but directly implemented in C

Create a transform that builds item records thanks to sequences from Fasta.(char_seq item) values and qualities converted from Fasta.(int_seq item) values.

Create a transform that split a FASTQ item into to FASTA items (i.e.

feed t i stores i into the buffered transform.

Feed the parser with a line.

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_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].

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.

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.

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

fold guaranteed on increasing order keywise, and for each key

folds on constant intervals of the function, in increasing order

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

Get the defined format if any.

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

Create an Input_transform.t from tags describing the format.

Guess the Output_transform.t from file tags.

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.

Get the first Tags.t in the specification, if any.

Create a printer for track files containing GFF lines.

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

Get a tag as precise as possible for a given filename.

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

identity () returns a transform that simply returns its inputs as outputs without modification (it can be seen as a simple Queue.t).

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.

Get a stream of bed_graph_value values out of a WIG-file input-channel.

Do like in_channel_to_bed_graph but each call to Stream.next may throw an exception.

Parse an input-channel into a stream of char_seq item results.

Returns a stream of char_seq items.

Parse an input-channel into a stream of char_seq raw_item results.

Returns a stream of char_seq raw_items.

Parse an input-channel into a stream of int_seq item results.

Returns a stream of int_seq items.

Parse an input-channel into a stream of int_seq raw_item results.

Returns a stream of int_seq raw_items.

Get a stream of item values out of an input-channel.

Parse an input-channel into a stream of high-level items.

Parse an input-channel into item values.

Parse an input-channel into a stream of item results.

Parse an input-channel into item values.

Create a stream of full Sam.item results from an input-channel.

Do like in_channel_to_item_stream but each call to Stream.next may throw an exception.

Like in_channel_to_item_stream but each call to Stream.next may raise Error _

Like in_channel_to_item_stream but use exceptions for errors (raised within Stream.next).

Returns a stream of items.

Like in_channel_to_item_stream but use exceptions for errors (raised within Stream.next).

Create a stream of Sam.items from an input-channel (any call to Stream.next may throw an Error _ exception).

Parse an input-channel into a stream of low-level (“raw”) items.

Create a stream of raw_item results from an input-channel.

Like in_channel_to_raw_item_stream but each call to Stream.next may raise Error _

Create a stream of raw_items from an input-channel (any call to Stream.next may throw an Error _ exception).

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.

Cut a stream of int_seq items into a stream of int_seq raw_items, the default line-cutting threshold is 27 (c.f.

Aggregate a stream of FASTA int_seq raw_items into int_seq items.

Print int_seq items.

Convert a raw_item to a string (ignore comments).

The default tags (for int_seq).

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 the value of t.sequence.

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

Return true if given set is empty.

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

Test the value of t.sequence.

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

Basic parsing of a single line.

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

Create a Biocaml_transform.t that converts rows to lines using the first separator in the tags or '\t' if none (default tags: Biocaml_table.Row.Tags.default).

Basic “printing” of one single item.

Create a transform that downgrades items to raw_items

Create a transform that downgrades Sam.items to raw_items.

Create the transform that prints item values to strings.

Convert an item to a string (including new line characters).

Return a transform that output Line.items to strings (in other words a buffer with the lines plus their end-of-line character).

Create a printer for a given version.

Convert an item to a string.

Create a Biocaml_transform.t from item values to strings.

Convert a item to a string.

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

Length of sequence.

The default compression level used in Transform.zip.

Create a Biocaml_transform.t that converts lines to table-rows according to the tags (default: Biocaml_table.Row.Tags.default).

Load a motif list from a given path (reading file path ^ "/matrix_list.txt").

Logarithm.

Base 10 logarithm.

Base 2 logarithm.

Lower tail quantile for standard normal distribution function.

Median absolute deviation (MAD).

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).

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.

Return minimum value in given array.

Returns the minimum element in the set

Lower limit of the minimum bin.

Return "-" or "+".

mix t u returns a transform that takes as input a pair of the inputs expected by t and u, and outputs either both outputs, or, when one transform has reach the end of its stream, the output of the remaining one (as `left _ or `right _).

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

name t returns the name of t.

Get a string describing and input transform (for debug/display purposes).

Get a string naming the transform (for debug/error messages).

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.

Get the next line.

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

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.

Get a stream of lines out of an input-channel.

Parse a stream of characters into a stream of lines.writing the

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.

of_function f is like identity () but the transform outputs are passed to the function f.

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

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.

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

Parse tags (for now S-Expressions).

Parse a tag specification (the format is, for now, based on S-Expressions, but this will change).

Parse the description of the tags (for now S-Expressions).

Convert string to chromosome name if possible.

Make sequence from string.

Parse string as a roman numeral if possible.

Parse tags (for now S-Expressions).

Parse tags (for now S-Expressions).

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.

Parse CIGAR operations from a string (c.f.

Parse CIGAR operations from a string.

Parse a header line form a string.

Parse optional content from a string (c.f.

Parse optional content from a “tokenized” string.

Convert a parsing error to a string.

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

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

Peek at the next line, without removing it from the buffer.

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.

range xs is the stream of all valid indices in xs

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 transform that lifts raw_items to items

Create a transform that lifts raw_items to the higher-level representation defined in the Biocaml_sam module.

Create a printing "stoppable" transform.

Create a transform that “prints” raw_items in the BAM format.

Create a reference sequence.

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.

Return "rev" or "fwd".

Reverse complement of a PWM

Root mean square.

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

section t name returns the section named name.

sectioni t i returns the i'th section.

Return all sections in t.

Get the list of separators defined in t.

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

shuffle arr takes an array and randomly shuffles it.

Return the singleton set containing only the given element

Number of elements in set.

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

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

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

Parse a specification from a string.

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.

Tell whether one should be strict about the types of the cells (defined with `format _).

Tell whether one should be strict about the minimal number of cells per row (defined with `format _).

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.

Create the parsing Biocaml_transform.t.

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 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 transform that parses a BAM file.

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

Create a composite parser for UCSC WIG files.

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.

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

Transform error to a human-readable string.

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_arabic s returns the canonical Arabic representation of s.

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.

Write a stream of lines to an output-channel.

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.

Write the row to a Line.t.

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.

to_roman s returns the canonical Roman representation of s.

to_solexa_score t converts PHRED score t to a Solexa score.

Enumerates all contiguous ranges in the set

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.

Serialize tags (for now S-Expressions).

Convert a tag to its string specification.

Serialize tags.

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.

String representation of a position.

Serialize tags (for now S-Expressions).

Serialize tags (for now S-Expressions).

Do a practical coercion.

transpose m transpose the given matrix m.

Create a 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.

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

Compute the union of two sets.

Set union.

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

Create a transformation that generates random char_seq raw_item values according to the specification.

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.

Decompress an Input Channel.

Like unzip_in_channel but calls to Stream.next may raise Error e exceptions.

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.

Create a transform that writes compressed data.

Compress an Input Channel.

The default size of the internal buffer used by the ZLib library.