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SeqAn3
3.0.1
The Modern C++ library for sequence analysis.
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SeqAn3
3.0.1
The Modern C++ library for sequence analysis.
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Provides the various quality score types. More...
Collaboration diagram for Quality:Classes | |
| class | seqan3::phred42 |
| Quality type for traditional Sanger and modern Illumina Phred scores (typical range). More... | |
| class | seqan3::phred63 |
| Quality type for traditional Sanger and modern Illumina Phred scores (full range). More... | |
| class | seqan3::phred68legacy |
| Quality type for Solexa and deprecated Illumina formats. More... | |
| class | seqan3::qualified< sequence_alphabet_t, quality_alphabet_t > |
| Joins an arbitrary alphabet with a quality alphabet. More... | |
| interface | quality_alphabet |
| A concept that indicates whether an alphabet represents quality scores. More... | |
| class | seqan3::quality_base< derived_type, size > |
| A CRTP-base that refines seqan3::alphabet_base and is used by the quality alphabets. More... | |
| interface | writable_quality_alphabet |
| A concept that indicates whether a writable alphabet represents quality scores. More... | |
Typedefs | |
| template<typename alphabet_type > | |
| using | seqan3::alphabet_phred_t = decltype(seqan3::to_phred(std::declval< alphabet_type >())) |
The phred_type of the alphabet; defined as the return type of seqan3::to_phred. | |
Function objects (Quality) | |
| constexpr auto | seqan3::to_phred = detail::adl_only::to_phred_fn{} |
| The public getter function for the phred representation of a quality score. More... | |
| constexpr auto | seqan3::assign_phred_to = detail::adl_only::assign_phred_to_fn{} |
| Assign a phred score to a quality alphabet object. More... | |
Provides the various quality score types.
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:
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.| Format | Quality Type | Phred Score Range | Rank Range | ASCII Range | Assert |
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| Sanger, Illumina 1.8+ short | seqan3::phred42 | [0 .. 41] | [0 .. 41] | ['!' .. 'J'] | Phred score in [0 .. 61] |
| Sanger, Illumina 1.8+ long | seqan3::phred63 | [0 .. 62] | [0 .. 62] | ['!' .. '_'] | Phred score in [0 .. 62] |
| Solexa, Illumina [1.0; 1.8[ | seqan3::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 seqan3::phred42 due to its more space efficient implementation. For other formats, like Solexa and Illumina 1.0 to 1.7 the type seqan3::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.
The quality submodule defines the seqan3::writable_quality_alphabet which encompasses all the alphabets, defined in the submodule, and refines the seqan3::writable_alphabet by providing Phred score assignment and conversion operations. Additionally, this submodule defines the seqan3::quality_alphabet, which only requires readablity and not assignability.
Quality alphabets can be converted to their char and rank representation via seqan3::to_char and seqan3::to_rank respectively (like all other alphabets). Additionally they can be converted to their Phred representation via seqan3::to_phred.
Likewise, assignment happens via seqan3::assign_char_to, seqan3::assign_rank_to and seqan3::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 seqan3::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 seqan3::phred63 letter with value 60 will convert to a seqan3::phred42 letter of score 41).
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Assign a phred score to a quality alphabet object.
| your_type | The type of the target object. Must model the seqan3::quality_alphabet. |
| chr | The phred score being assigned; must be of the seqan3::alphabet_phred_t of the target object. |
alph if alph was given as lvalue, otherwise a copy.This is a function object. Invoke it with the parameter(s) specified above.
It acts as a wrapper and looks for three possible implementations (in this order):
assign_phred_to(phred_type const chr, your_type & a) of the class seqan3::custom::alphabet<your_type>.assign_phred_to(phred_type const chr, your_type & a) in the namespace of your type (or as friend).assign_phred(phred_type const chr) (not assign_phred_to).Functions are only considered for one of the above cases if they are marked noexcept (constexpr is not required, but recommended) and if the returned type is your_type &.
Every writable quality alphabet type must provide one of the above. Note that temporaries of your_type are handled by this function object and do not require an additional overload.
This is a customisation point (see Customisation). To specify the behaviour for your own alphabet type, simply provide one of the three functions specified above.
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inlineconstexpr |
The public getter function for the phred representation of a quality score.
| your_type | The type of alphabet. Must model the seqan3::quality_alphabet. |
| chr | The quality value to convert into the phred score. |
This is a function object. Invoke it with the parameter(s) specified above.
It acts as a wrapper and looks for three possible implementations (in this order):
to_phred(your_type const a) of the class seqan3::custom::alphabet<your_type>.to_phred(your_type const a) in the namespace of your type (or as friend).to_phred().Functions are only considered for one of the above cases if they are marked noexcept (constexpr is not required, but recommended) and if the returned type is convertible to size_t.
Every quality alphabet type must provide one of the above.
This is a customisation point (see Customisation). To specify the behaviour for your own alphabet type, simply provide one of the three functions specified above.
1.8.16