Alphabets

The following alphabets are available

Nucleotide based	Amino acid based	Quality based
ivs::dna2	ivs::aa27	ivs::pthred42
ivs::dna4	ivs::aa20	ivs::pthred63
ivs::dna5	ivs::aa10li	ivs::pthred68solexa
ivs::rna4	ivs::aa10murphy	ivs::pthred94
ivs::rna5
ivs::iupac
ivs::dna3bs
ivs::d_dna4
ivs::d_dna5
ivs::d_rna4
ivs::d_rna5
ivs::d_iupac
ivs::d_dna3bs

Common functionality

• All functions are guaranteed to not throw.
• Alphabets starting with d_ are alphabets with a additional delimiter $ as rank 0.

• static size_t size()

  Returns the number of elements of the alphabet.

• static uint8_t char_to_rank(char c)

  Converts ASCII symbol c to an ranked uint8_t representation (0 ≤ r < size()). Invalid ASCII symbols will return value 255.

• static char rank_to_char(uint8_t r)

  Converts the ranked value r to its ACSII corresponding value. Value r must be fulfill (0 ≤ r < size()).

• static char normalize_char(char c)

  Normalizes the ASCII value c. Normalizing depends on the alphabet. Typically this includes representing the value in captial letter.

Nucleotide based

Additionall functionality for Nucleotide based values:

• static char complement_char(char c)

  Computes the complement of the ASCII value c. Example given: the complement of dna4 for 'A' is 'T'.

• static uint8_t complement_rank(uint8_t)

  Computes the complement in rank space. Example given: the complement of dna4 of rank value 0 is 3. (A -> T).

Ambigous bases

Some alphabets have ambiguous bases. Like in dna5 the letter 'N' can stand for 'A', 'C', 'G' or 'T'. For this we provide a sepecial functionality:

• static auto ambigous_bases() -> std::array<uint8_t, /*alphabet dependent*/>

  Returns an array of bases that are ambiguous.

• static auto base_alternatives(uint8_t base) -> std::vector<uint8_t>

  Returns a list of values that base could stand for.