Module Biocaml.Phred_score (.ml)

module Phred_score: Biocaml_phred_score

---

exception Error of string

type t 

val of_ascii  : ?offset:[ `offset33 | `offset64 ] -> char -> t option

val of_ascii_exn  : ?offset:[ `offset33 | `offset64 ] -> char -> t 

val to_ascii  : ?offset:[ `offset33 | `offset64 ] -> t -> char option

val to_ascii_exn  : ?offset:[ `offset33 | `offset64 ] -> t -> char

val of_int_exn  : int -> t 

val to_int  : t -> int

val of_probability  : ?f:(float -> int) -> float -> t option

val of_probability_exn  : ?f:(float -> int) -> float -> t 

val to_probability  : t -> float

val of_solexa_score  : ?f:(float -> int) -> Biocaml_solexa_score.t -> t 

val to_solexa_score  : ?f:(float -> int) -> t -> Biocaml_solexa_score.t 

val t_of_sexp  : Sexplib.Sexp.t -> t 

val sexp_of_t  : t -> Sexplib.Sexp.t

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

Like of_ascii but may raise Error _ if x does not represent a valid score.

to_ascii t encodes t as an ASCII character.

to_ascii_exn t encodes t as an ASCII character.

of_int_exn x returns the PHRED score with the same value x, but assures that x is non-negative.

Convert a phred score to an integer.

of_probability ~f x returns -10 * log_10(x), which is the definition of PHRED scores.

PHRED scores are integral, and it is unclear what convention is used to convert the resulting float value to an integer. Thus, the optional f is provided to dictate this. The default is to round the computed score to the closest integer.

See of_probability

to_probablity x converts x to a probablity score. Note this is not the inverse of of_probability due to the rounding done by the latter.

of_solexa_score x converts Solexa score x to a PHRED score.

The conversion produces a float, and it is unclear what convention is used to convert the resulting float value to an integer. As in Biocaml_phred_score.of_probability, the optional f parameter is provided to dictate this.

to_solexa_score t converts PHRED score t to a Solexa score.

The conversion produces a float, and it is unclear what convention is used to convert the resulting float value to an integer. As in Biocaml_phred_score.of_probability, the optional f parameter is provided to dictate this.