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. However, note the term
fastq-illumina is now misleading since Illumina has also switched
to using an offset of 33.

`module Biocaml_phred_score: `

`sig`

type`t = private`

`int`

type`offset =`

`[ `Offset33 | `Offset64 ]`

`val of_char : ``?offset:offset ->`

char -> t Core.Std.Or_error.t

`of_char ~offset x`

returns the PHRED score encoded by ASCII
character `x`

.`val to_char : ``?offset:offset ->`

t -> char Core.Std.Or_error.t

`to_char t`

encodes `t`

as a visible ASCII character (codes 33 -
126) if possible.`val of_int : ``int -> t Core.Std.Or_error.t`

`of_int x`

returns the PHRED score with the same value `x`

, or
returns Error if `x`

is negative.`val of_probability : ``?f:(float -> int) -> float -> t Core.Std.Or_error.t`

`of_probability ~f x`

returns `-10 * log_10(x)`

, which is the
definition of PHRED scores.
PHRED scores are integral, and it is only loosely specified that
float value returned by the above formula should be "rounded to
the closest integer". However, that statement is imprecise;
there is more than one way to do such a rounding. A reasonable
choice is made by default, but you can control the behavior by
providing `f`

.

Return Error if given probability `x`

not between 0.0 and 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.

`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 offset_of_sexp : ``Sexplib.Sexp.t -> offset`

`val __offset_of_sexp__ : ``Sexplib.Sexp.t -> offset`

`val sexp_of_offset : ``offset -> Sexplib.Sexp.t`

`of_char ~offset x`

returns the PHRED score encoded by ASCII
character `x`

.`to_char t`

encodes `t`

as a visible ASCII character (codes 33 -
126) if possible.`of_int x`

returns the PHRED score with the same value `x`

, or
returns Error if `x`

is 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 only loosely specified that
float value returned by the above formula should be "rounded to
the closest integer". However, that statement is imprecise;
there is more than one way to do such a rounding. A reasonable
choice is made by default, but you can control the behavior by
providing `f`

.

Return Error if given probability `x`

not between 0.0 and 1.0.

`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.
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.

`to_solexa_score t`

converts PHRED score `t`

to a Solexa score.
`Biocaml_phred_score.of_probability`

, the optional `f`

parameter is
provided to dictate this.

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).`end`