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Module Biocaml_wig

module Biocaml_wig: sig .. end

WIG data.

Internal representation of coordinates always assumes the first position on a chromosome is numbered 1. Also, integer ranges are always closed; the range [1, 10] is the set of integers from 1 to 10 inclusive of 1 and 10. WIG data can be in three formats---bed, variable-step, or fixed-step---and unfortunately each has different conventions as follows:

Bed format requires half-open intervals [low, high\) and numbers the first base as 0. Thus 1 is added to the low value when parsing. The line "chrI 0 10 3.14" is parsed to ("chrI", 1, 10, 3.14).
Variable-step format numbers the first position 1 and uses closed intervals. Thus no change is required. The line "1 3.14" is parsed to (1, 3.14).
Fixed-step format numbers the first position 1 and uses closed intervals. Thus no change is required. The header line "fixedStep chrom=chrI start=1 step=100 span=30" is parsed to ("chrI", 1, 100, 30).

The inverse is done for printing routines. You are freed from these details if you always use this module to parse and print.

All parsers allow columns (fields) on a line to be separated by any combination of space, tab, or carriage return characters. Printers always separate columns with a single tab. Tag-value pairs must be in the form "tag=value" with no space around the '='.

type pt = string * int * int * float

A data point is a 4-tuple (chr,lo,hi,x), where x is the value assigned to interval [lo, hi], inclusive of end-points, on chromosome chr.

type t

Type of WIG data. Can be thought of as a collection of pt's. Coordinates of data points are not allowed to overlap, for each chromosome.

type format =

| Bed

| VariableStep

| FixedStep (* The three formats in which WIG data can be specified. *)

exception Bad of string

val of_list : pt list -> t

Construct WIG data from given pt's. Raise Bad if any pt's are invalid.

val to_list : t -> pt list

Extract data as a flat list.

val iter : (pt -> unit) -> t -> unit

val fold : ('a -> pt -> 'a) -> 'a -> t -> 'a

val to_file : ?fmt:format -> t -> string -> unit

to_file ~fmt t file prints t to file. Printing is in most efficient format possible by default. Optional fmt argument forces printing in a specific format. Requesting VariableStep or FixedStep may raise Failure if given data cannot be represented in those formats.

val to_channel : ?fmt:format -> t -> Pervasives.out_channel -> unit

Like to_file but print to channel.

val of_channel : ?fmt:format ->
 ?chr_map:(string -> string) ->
 ?header:bool ->
 ?increment_lo_hi:int * int -> Pervasives.in_channel -> t

val of_file : ?fmt:format ->
 ?chr_map:(string -> string) ->
 ?header:bool -> ?increment_lo_hi:int * int -> string -> t