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Module Biocaml_phred_score (.ml)

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.

module Biocaml_phred_score:
sig
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.

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.

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
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.

include Core.Sexpable.S
end