Module Biocaml_phred_score (.ml)

module Biocaml_phred_score: sig .. end

PHRED quality scores.

A PHRED score is defined as -10*log(p) rounded to an integer, where p is a probability.

To conserve space, the integer value of a PHRED score is encoded as an ASCII character in fastq files. Unfortunately two encodings have been used, one that increments the value by 33 and the other by 64. Most fastq files use 33 and that is the default in this module.

However, Illumina used a 64 offset for a brief period of time, and you must be careful to know whether you have fastq files with this encoding. For details see The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Using an offset of 33 or 64 in this module corresponds to using the fastq-sanger or fastq-illumina encodings, respectively, defined in this paper.

exception Error of string

type t

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

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

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

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

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

to_ascii t encodes t as an ASCII character.

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

to_ascii_exn t encodes t as an ASCII character.
Raises Error if t with the given offset cannot be encoded as a visible ASCII character (codes 33 - 126).

val of_int_exn : int -> t

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

val to_int : t -> int

Convert a phred score to an integer.

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

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

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

See of_probability
Raises Error if x is not between 0.0 - 1.0.

val to_probability : t -> float

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.

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

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.

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.