Biocaml 0.4-dev : Biocaml_solexa

A Solexa score is defined as -10*log(p/(1-p)) rounded to an integer, where p is a probability. Phred scores are far more widely used, and the Biocaml_phred_score module supports converting Solexa scores to Phred scores.

For details see The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. This module supports what is called the fastq-solexa format in this paper, with one exception. We are more permissive here in allowing conversions from/to the entire range of visible ASCII characters (codes 33 - 126) instead of restricting to codes 59 - 126 as specified in this paper. The smaller range is apparently based on the original Solexa software returning minimum scores of -5, but there is no reason for this minimum based on the general definition of Solexa scores.

exception Error of string

type t = int

val of_ascii : char -> t

of_ascii x returns the PHRED score encoded by ASCII character x.
Raises Error if x's ASCII code is not between 33 - 126.

val to_ascii : t -> char

to_ascii t encodes t as an ASCII character.
Raises Error if t cannot be encoded as a visible ASCII character (codes 33 - 126).

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

of_probability ~f x returns -10 * log_10(x/(1-x)), which is the definition of Solexa scores.

Solexa 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.
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.

Module Biocaml_solexa_score (.ml)