package biocaml

You can search for identifiers within the package.

in-package search v0.2.0

The OCaml Bioinformatics Library

Install

Dune Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

Maintainers

B

biocaml@googlegroups.com

Sources

v0.10.1.tar.gz

md5=4cf944bcae5d36bf47b67f6bcb2455d7

sha512=0262b5768aefd7c080f664c46c88876fce9a658cc6a87358a77b7112c49ae3042e7ab542e76be5738fbaeda853149b308b48d4897960b5c7ae3b4da71d978bd8

doc/biocaml.ez/Biocaml_ez/Phred_score/index.html

Module `Biocaml_ez.Phred_score`

include module type of struct include Biocaml_unix.Phred_score end

type t = private int

include Ppx_sexp_conv_lib.Sexpable.S with type t := t

val t_of_sexp : Sexplib0.Sexp.t -> t

val sexp_of_t : t -> Sexplib0.Sexp.t

type offset = [

| `Offset33
| `Offset64

]

val sexp_of_offset : offset -> Ppx_sexp_conv_lib.Sexp.t

val offset_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> offset

val __offset_of_sexp__ : Ppx_sexp_conv_lib.Sexp.t -> offset

val to_int : t -> int

Convert a PHRED score to an integer.

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_unix.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 of_probability, the optional f parameter is provided to dictate this.

val to_solexa_score : ?f:(float -> int) -> t -> Biocaml_unix.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 of_probability, the optional f parameter is provided to dictate this.

val min_as_char : offset -> t

The min and max PHRED scores when encoded as ASCII characters. Since PHRED scores are virtually always ASCII encoded, you are unlikely to see values outside this range. However, this module allows creating values outside this range, e.g. of_probability 1e-13 exceeds max_as_char, and of_probability 0.9 is smaller than min_as_char (for either offset).

val max_as_char : t

val of_char : ?offset:offset -> char -> t

val to_char : ?offset:offset -> t -> char

val of_int : int -> t

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