Quality

Provides the various quality score types. More...

Collaboration diagram for Quality:

Classes
class	bio::alphabet::phred42
	Quality type for traditional Sanger and modern Illumina Phred scores (typical range).. More...
class	bio::alphabet::phred63
	Quality type for traditional Sanger and modern Illumina Phred scores (full range).. More...
class	bio::alphabet::phred68legacy
	Quality type for Solexa and deprecated Illumina formats.. More...
class	bio::alphabet::qualified< sequence_alphabet_t, quality_alphabet_t >
	Joins an arbitrary alphabet with a quality alphabet. More...
class	bio::alphabet::quality_base< derived_type, size >
	A CRTP-base that refines bio::alphabet::base and is used by the quality alphabets. More...

Concepts
concept	bio::alphabet::quality
	A concept that indicates whether an alphabet represents quality scores.
concept	bio::alphabet::writable_quality
	A concept that indicates whether a writable alphabet represents quality scores.

Typedefs
template<typename alphabet_type >
using	bio::alphabet::phred_t = decltype(bio::alphabet::to_phred(std::declval< alphabet_type >()))
	The phred_type of the alphabet; defined as the return type of bio::alphabet::to_phred.

Function objects (Quality)
constexpr auto	bio::alphabet::to_phred
	The public getter function for the phred representation of a quality score.
constexpr auto	bio::alphabet::assign_phred_to
	Assign a phred score to a quality alphabet object.

Detailed Description

Provides the various quality score types.

Introduction

Quality score sequences are usually output together with the DNA (or RNA) sequence by sequencing machines like the Illumina Genome Analyzer. The quality score of a nucleotide is also known as Phred score and is an integer score being inversely proportional to the propability that a base call is incorrect. Which roughly means that the higher a Phred score is, the higher is the probabality that the corresponding nucleotide is correct for that position. There exists two common variants of its computation:

• Salinger format with
• Solexa format with Thus, despite implicit conversion between different quality types is supported, for very low quality levels the scores vary significantly and need to be corrected by an offset before being compared. The Phred score range does not fit into one digit, and is therefore mapped to ASCII characters. Depending on the format and the analyzer machine generation, the mappings can differ. Output files storing DNA sequences and their quality scores are usually stored in the FASTQ format indicated by the file endings fastq or fq. This sub-module provides multiple quality alphabets that can be used in combination with regular containers and ranges.

Encoding Schemes

Format	Quality Type	Phred Score Range	Rank Range	ASCII Range	Assert
Sanger, Illumina 1.8+ short	bio::alphabet::phred42	[0 .. 41]	[0 .. 41]	['!' .. 'J']	Phred score in [0 .. 61]
Sanger, Illumina 1.8+ long	bio::alphabet::phred63	[0 .. 62]	[0 .. 62]	['!' .. '_']	Phred score in [0 .. 62]
Solexa, Illumina [1.0; 1.8[	bio::alphabet::phred68legacy	[-5 .. 62]	[0 .. 67]	[';' .. '~']	Phred score in [-5 .. 62]

The most distributed format is the Sanger or Illumina 1.8+ format. Despite typical Phred scores for Illumina machines range from 0 to maximal 41, it is possible that processed reads reach higher scores. If you don't intend to handle Phred scores larger than 41, we recommend to use bio::alphabet::phred42 due to its more space efficient implementation. For other formats, like Solexa and Illumina 1.0 to 1.7 the type bio::alphabet::phred68legacy is provided. To cover also the Solexa format, the Phred score is stored as a signed integer starting at -5. An overview of all the score formats and their encodings can be found here: https://en.wikipedia.org/wiki/FASTQ_format#Encoding.

Concept

The quality submodule defines the bio::alphabet::writable_quality which encompasses all the alphabets, defined in the submodule, and refines the bio::alphabet::writable_alphabet by providing Phred score assignment and conversion operations. Additionally, this submodule defines the bio::alphabet::quality, which only requires readablity and not assignability.

Assignment and Conversion

Quality alphabets can be converted to their char and rank representation via bio::alphabet::to_char and bio::alphabet::to_rank respectively (like all other alphabets). Additionally they can be converted to their Phred representation via bio::alphabet::to_phred.

Likewise, assignment happens via bio::alphabet::assign_char_to, bio::alphabet::assign_rank_to and bio::alphabet::assign_phred_to. Phred values outside the representable range, but inside the legal range, are converted to the closest Phred score, e.g. assigning 60 to a bio::alphabet::phred42 will result in a Phred score of 41. Assigning Phred values outside the legal range results in undefined behaviour.

All quality alphabets are explicitly convertible to each other via their Phred representation. Values not present in one alphabet are mapped to the closest value in the target alphabet (e.g. a bio::alphabet::phred63 letter with value 60 will convert to a bio::alphabet::phred42 letter of score 41).

Variable Documentation

assign_phred_to

constexpr auto bio::alphabet::assign_phred_to

inlineconstexpr

Assign a phred score to a quality alphabet object.

Template Parameters

alph_type

The type of the target object. Must model the bio::alphabet::quality.

Parameters

phr	The phred score being assigned; must be of the bio::alphabet::phred_t of the target object.

Returns

Reference to alph if alph was given as lvalue, otherwise a copy.

This is a function object. Invoke it with the parameter(s) specified above.

It is defined for all quality alphabets in BioC++.

Customisation point

This is a customisation point (see Customisation). If you don't want to create your own alphabet, everything below is irrelevant to you!

This object acts as a wrapper and looks for an implementation with the following signature:

constexpr alph_type & tag_invoke(bio::alphabet::assign_phred_to, phred_type const phr, alph_type & alph) noexcept

Functions are found via ADL and considered only if they are marked noexcept (constexpr is not required, but recommended) and if the returned type is exactly alph_type &.

To specify the behaviour for your own alphabet type, simply provide the above function as a friend or free function.

Note that temporaries of alph_type are handled by this function object and do not require an additional overload.

to_phred

constexpr auto bio::alphabet::to_phred

inlineconstexpr

The public getter function for the phred representation of a quality score.

Template Parameters

your_type

The type of alphabet. Must model the bio::alphabet::quality.

Parameters

chr	The quality value to convert into the phred score.

Returns

the phred representation of a quality score.

This is a function object. Invoke it with the parameter(s) specified above.

It is defined for all quality alphabets in BioC++.

Customisation point

This is a customisation point (see Customisation). If you don't want to create your own alphabet, everything below is irrelevant to you!

This object acts as a wrapper and looks for an implementation with the following signature:

constexpr phred_type tag_invoke(bio::alphabet::custom::to_phred, alph_type const alph) noexcept
{}

Functions are found via ADL and considered only if they are marked noexcept (constexpr is not required, but recommended) and if the returned type models std::integral.

To specify the behaviour for your own alphabet type, simply provide the above function as a friend or free function.