Module Biocaml_tags

module Biocaml_tags: sig .. end

Classification of data formats. A data format is specified by a list of tags, each of which has an attribute name and a value of some type. Currently supported tags are:

table <bool> - true means data is in Table format

bed <bool> - true means data is in Bed format

header <bool> - true means column names are provided in a header row

header_ <bool> - true means header row is followed by a row with just underscores and spaces

comment-char <char> - providing a value y means data begins with comment lines, each of which begins with character y or is all whitespace

separator <char> - value is the character separating column values within a row

The format for a list of tags is:

    x1 = y1, x2 = y2, x3 = y3, ...

where extra spaces around the equal and comma symbols are disregarded.

Not all combinations of tags are valid. In particular, some tags are 'principal' tags and none can be used with the others. The principal tags are: table, bed.

header_=true is allowed only if header=true.

bed=true disallows: header, header_, comment-char, and separator.

exception Invalid of string

Raised when an invalid tag or incompatible list of tags is encounted.

type t

Collection of tags, which classify a data format.

val of_string : string -> t

Parse given string as list of tags. Raise Invalid if any tags invalid, or if list of tags are incompatible.

val mem : string -> t -> bool

mem x t returns true if t contains a value for tag x.

val find : string -> t -> string

find x t returns the value of tag x in t. Raise Not_found if t does not contain value for x.

val tag_is : string -> string -> t -> bool

tag_is x y t returns true if x=y in t, or false if tag x assigned some other value or not found in t.