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Module Biocaml.Wig (.ml)

module Wig: Biocaml_wig

Basic Types


type comment = [ `comment of string ] 
type variable_step = [ `variable_step_state_change of string * int option
       | `variable_step_value of int * float ] 
type fixed_step = [ `fixed_step_state_change of string * int * int * int option
       | `fixed_step_value of float ] 
type bed_graph_value = string * int * int * float

Parsing and Printing


type t = [ `bed_graph_value of bed_graph_value
       | `comment of string
       | `fixed_step_state_change of string * int * int * int option
       | `fixed_step_value of float
       | `variable_step_state_change of string * int option
       | `variable_step_value of int * float ]
The most general type that the default parser outputs.
type parse_error = [ `cannot_parse_key_values of Biocaml_pos.t * string
       | `empty_line of Biocaml_pos.t
       | `incomplete_input of Biocaml_pos.t * string list * string option
       | `missing_chrom_value of Biocaml_pos.t * string
       | `missing_start_value of Biocaml_pos.t * string
       | `missing_step_value of Biocaml_pos.t * string
       | `unrecognizable_line of Biocaml_pos.t * string list
       | `wrong_bed_graph_value of Biocaml_pos.t * string
       | `wrong_fixed_step_value of Biocaml_pos.t * string
       | `wrong_span_value of Biocaml_pos.t * string
       | `wrong_start_value of Biocaml_pos.t * string
       | `wrong_step_value of Biocaml_pos.t * string
       | `wrong_variable_step_value of Biocaml_pos.t * string ]
The parsing errors.
val parse_error_to_string : parse_error -> string
Convert a parse_error to a string.
type tag = [ `pedantic | `sharp_comments ] 
val default_tags : tag list
module Transform: sig .. end
val comment_of_sexp : Sexplib.Sexp.t -> comment
val comment_of_sexp__ : Sexplib.Sexp.t -> comment
val sexp_of_comment : comment -> Sexplib.Sexp.t
val variable_step_of_sexp : Sexplib.Sexp.t -> variable_step
val variable_step_of_sexp__ : Sexplib.Sexp.t -> variable_step
val sexp_of_variable_step : variable_step -> Sexplib.Sexp.t
val fixed_step_of_sexp : Sexplib.Sexp.t -> fixed_step
val fixed_step_of_sexp__ : Sexplib.Sexp.t -> fixed_step
val sexp_of_fixed_step : fixed_step -> Sexplib.Sexp.t
val bed_graph_value_of_sexp : Sexplib.Sexp.t -> bed_graph_value
val sexp_of_bed_graph_value : bed_graph_value -> Sexplib.Sexp.t

Parsing and Printing


val t_of_sexp : Sexplib.Sexp.t -> t
val t_of_sexp__ : Sexplib.Sexp.t -> t
val sexp_of_t : t -> Sexplib.Sexp.t
The most general type that the default parser outputs.
val parse_error_of_sexp : Sexplib.Sexp.t -> parse_error
val parse_error_of_sexp__ : Sexplib.Sexp.t -> parse_error
val sexp_of_parse_error : parse_error -> Sexplib.Sexp.t
The parsing errors.

Convert a parse_error to a string.
val tag_of_sexp : Sexplib.Sexp.t -> tag
val tag_of_sexp__ : Sexplib.Sexp.t -> tag
val sexp_of_tag : tag -> Sexplib.Sexp.t

Create the parsing Biocaml_transform.t. The parser is "best-effort" and stateless (i.e. a line containing "1000 42." will parsed succesfully as a `variable_step_value (1000, 42.) even if no "variableStep" was line present before).

Create the transform that prints t values to strings.

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