package biocaml

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The OCaml Bioinformatics Library

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Dune Dependency

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Authors

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philippe.veber@gmail.com

Sources

biocaml-0.11.2.tbz

sha256=fae219e66db06f81f3fd7d9e44717ccf2d6d85701adb12004ab4ae6d3359dd2d

sha512=f6abd60dac2e02777be81ce3b5acdc0db23b3fa06731f5b2d0b32e6ecc9305fe64f407bbd95a3a9488b14d0a7ac7c41c73a7e18c329a8f18febfc8fd50eccbc6

doc/biocaml.unix/Biocaml_unix/Solexa_score/index.html

Module `Biocaml_unix.Solexa_score`Source

Solexa quality scores.

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 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.

Sourceexception Error of string

Sourcetype t = int

Sourceval 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.

Sourceval 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).

Sourceval 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.

Sourceval 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.