module Biocaml_phredScore:PHRED quality scores.`sig`

..`end`

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.

`exception Error of ``string`

`type `

t

`val of_ascii : ``?offset:[ `offset33 | `offset64 ] -> char -> t`

`of_ascii ~offset x`

returns the PHRED score encoded by ASCII
character `x`

.`Error`

if `x`

does not represent a valid score.`val to_ascii : ``?offset:[ `offset33 | `offset64 ] -> t -> char`

`to_ascii t`

encodes `t`

as an ASCII character.`Error`

if `t`

with the given `offset`

cannot be encoded as
a visible ASCII character (codes 33 - 126).`val of_int : ``int -> t`

`of_int x`

returns the PHRED score with the same value `x`

, but
assures that `x`

is non-negative.`Error`

if `x`

is negative.`val to_int : ``t -> int`

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

`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.

**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_solexaScore.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_phredScore.of_probability`

, the optional `f`

parameter is
provided to dictate this.

`val to_solexa_score : ``?f:(float -> int) -> t -> Biocaml_solexaScore.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_phredScore.of_probability`

, the optional `f`

parameter is
provided to dictate this.