Module Biocaml.Bpmap

module Bpmap: Biocaml_bpmap

type probe = {

`org_name : string;`	`(*`	name of organism on which probe is based	`*)`
`version : string;`	`(*`	genome build version on which probe is based	`*)`
`chr_name : string;`	`(*`	name of chromosome on which probe is based	`*)`
`start_pos : int;`	`(*`	start position of probe on given chromosome	`*)`
`sequence : Biocaml_seq.t;`	`(*`	sequence of the perfect match probe	`*)`

}
type row = {

`pmcoord : int * int;`	`(*`	x,y-coordinates of perfect match probe.	`*)`
`mmcoord : int * int;`	`(*`	x,y-coordinates of mis-match probe	`*)`
`probe : probe;`

}

Type of information on one data row.

type t

Type of a BPMAP file.

exception Bad of string

Raised when encountering ill-formed BPMAP.

val num_probes : t -> int

Number of PM/MM probe pairs in given BPMAP. The number of total probes is twice this value.

val col_names : string list

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

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

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

val to_list : t -> row list

val of_file : ?chr_map:(string -> string) -> string -> t

of_file file parses file. If given, chr_map is applied to every chromosome name. Raise Bad if there is a parse error.

val row_to_string : row -> string

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

val to_file : string -> t -> unit

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