biocaml.unix
Biocaml_unix.Phred_scoreSourcePHRED 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.
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.
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 of_probability, the optional f parameter is provided to dictate this.
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.
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).