Index of values

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.

Low-level Alignment Parsers and Constructors

For cigar and qual, empty list indicates no value, i.e.

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

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

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

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

Returns some element in the set

Low-level Optional field Parsers and Constructors

CIGAR operations.

Closes an open file.

Closes a file opened for writing.

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

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

Cumulative distribution function.

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_of_list l returns a comparison function that defines a < b if a comes before b in l.

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.

confusion_matrix ~scores ~labels ~threshold computes a confusion matrix from the classifier scores and example labels, based on a threshold.

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}.

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

Compute the difference between two sets.

Set difference.

Releases the ressources associated to a (BGZF) channel (it can thus not be used after that call), apart from the underlying regular channel (which can be used further).

Releases the ressources associated to a (BGZF) channel (it can thus not be used after that call), apart from the underlying regular channel (which can be used further).

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.

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

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

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

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

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.

Git commit if known.

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

Low-level Header Parsers and Constructors

@HD.

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 high-level items.

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

Parse an input-channel into item values.

Parse an input-channel into item values.

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

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

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

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

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

incr_line ?n pos increments the line number of pos by n.

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

input ic buf pos len reads at most len characters in file ic, stores them in string buf at position pos, and returns the number of characters actually read.

Same as really_input but returns the result in a fresh string.

Compute the intersection of two sets.

Set intersection.

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

intersecting_elems lmap loc returns a stream of elements in lmap whose location intersects with loc.

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

intersects lset loc returns true if loc has a non-empty intersection with one of the locations in lset, 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.

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.

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.

This function converts item values to strings that can be dumped to a file, i.e.

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).

Loads a database in SQL dump format, as available at Jaspar website

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.

make lo hi returns the range {lo; hi}.

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 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.

Map the function f over the list, stopping on the first error encountered.

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.

The min and max PHRED scores when encoded as ASCII characters.

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.

Low-level Parsing

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.

Convert integer to roman numeral.

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

Make sequence from buffer.

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

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

Parse a stream of characters into a stream of lines.

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.

Uses a regular channel to read a BGZF compressed file.

of_int x returns the PHRED score with the same value x, or returns Error if x is negative.

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

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

Uses a regular channel to write a BGZF compressed file.

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.

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

Parse string as a roman numeral if possible.

of_solexa_score x converts Solexa score x to a PHRED score.

of_stream f ls builds a signal from a collection of annotated locations.

of_stream e computes a selection (i.e.

Parse tags (for now S-Expressions).

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

Convert string to strand name if possible.

Parses a string representation of a sequence range, as <seq>:<start>-<end>

Make sequence from string.

Get a stream of lines out a string

Parse tags (for now S-Expressions).

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.

Opens a BGZF file for reading.

open_out ~level fn opens the file at path fn for writing a BGZF-compressed file with compression level level (default is 6, legal values are 1 to 9).

Like open_out but will not overwrite existing file.

Low-level Optional field Parsers and Constructors

The constructor encodes the TYPE and each carries its corresponding VALUE.

output oc buf pos len writes len characters of string buf from position pos into the compressed file oc.

output_s8 oz n writes a signed representation of n, if n is between -32768 and 32767.

output_s32 oz n writes a signed representation of n.

output_s8 oz n writes a signed representation of n, if n is between -128 and 127.

output_u16 oz n writes the 16 least significant bits onto channel oz

output_u8 oz n writes the 8 least significant bits onto channel oz

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.

performance_curve ~scores ~labels returns the series of confusion matrices obtained by varying the threshold from infinity to neg_infinity.

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.

same as positive_predictive_value

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.

Low-level Header Printers

Low-level Alignment Printers

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

@PG.

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

qualities sequence line parses given qualities line in the context of a previously parsed sequence.

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.

read ic returns an error if a valid header cannot be read from ic or a pair containing a header and a stream of possibly errored alignments.

Input/Output

read0 ic returns an error if a valid header cannot be read from ic or a pair containing a header and a stream of possibly errored (partially parsed) alignments.

The run_date string will be parsed as a Date.t or Time.t, whichever is possible.

@RG.

Same as input but reads exactly len characters.

same as sensitivity

@SQ.

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.

roc_curve ~scores ~labels returns the ROC curve of the prediction, and the associated Area Under Curve (AUC)

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.

Parse a name string to a structured Illumina sequence_id.

Parse a space separated list of integers.

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.

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.

Split a name string into a sequence identifier and an optional description.

Standard deviation.

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

stream_to_out_channel xs t oc consumes a stream of 'inputs using t to transform them into strings, which are then written on the out_channel oc.

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.

Create a composite parser for UCSC GFF files.

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-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.

A tag-value pair comprising the content of header items.

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.

E.g.

Inverse of tile_of_string.

Integer representation of a roman numeral.

to_arabic s returns the canonical Arabic representation of s.

to_ascii t encodes t as an ASCII character.

Write a stream of lines to an output-channel.

to_char t encodes t as a visible ASCII character (codes 33 - 126) if possible.

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 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_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.

String representation of a roman numeral.

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

stream 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).

Serialize tags.

Return string representation of sequence.

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

Print string in a human legible format.

Serialize tags (for now S-Expressions).

transpose m transpose the given matrix m.

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 range(s) representing the union of u and v.

Position with all fields set to None.

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.

Version: "0.4-dev"

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.

with_file fn ~f opens a BAM file for reading, applies f and closes the file after that, even if f raises an exception.

with_file fn ~f opens a BAM file for reading, applies f and closes the file after that, even if f raises an exception.

with_file_in fn ~f opens a channel for reading, pass it to f, and returns the result after having closed the channel.

with_file_out ~level fn ~f opens a file for writing at compression level level (default is 6), passes the channel to f and returns the result after closing the channel.

write h xs oc writes the header h and the alignments xs to oc.

write0 h xs oc writes the header h and (partially parsed) alignments xs to oc.

Create a transform that writes compressed data.

Compress an Input Channel.

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