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scATAC-seq/src/Utility/dna_utility.hpp
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dna_utility.hpp
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#ifndef DNA_UTILITY_HPP
#define DNA_UTILITY_HPP
#include <matrices.hpp>
namespace dna
{
/*!
* \brief Contains the mapping to convert
* DNA characters to integer codes.
* Lower and capital characters are accepted.
* \param base the character of interest.
* \param rev_compl whether the reverse
* complement of the character is of interest.
* \return the corresponding DNA code.
*/
int map(char base, bool rev_compl=false) ;
/*!
* \brief Contains the mapping to convert
* DNA code to characters.
* Only capital characters are returned.
* \param base the code of interest.
* \param rev_compl whether the reverse
* complement of the code is of interest.
* \return the corresponding DNA character.
*/
char map(int base, bool rev_compl=false) ;
/*!
* \brief Converts a DNA character (A, C,
* G, T) to an integer.
* \param c the DNA character of interest.
* \return the character integer code.
* \throw std::invalid_argument if the
* given character is not a valid DNA
* character.
*/
int char_to_int(char c, bool rev_compl= false) ;
/*!
* \brief Converts a DNA character matrix (A, C,
* G, T) to an integer matrix.
* The DNA characters are converted using
* SequenceLayer::char_to_int(char).
* param file_address the address of the file to load.
* \return the corresponding int matrix.
*/
matrix2d_i char_to_int(const matrix2d_c& matrix) ;
/*!
* \brief Converts an int DNA code to
* a regular DNA character (A, C, G, T).
* This method is the reverse method of
* char_to_int(char).
* \param n the DNA code of interest.
* \return the DNA character.
* \throw std::invalid_argument if the
* given int is not a valid DNA
* code.
*/
char int_to_char(int n, bool rev_compl=false) ;
/*!
* \brief Loads the content of a fasta file and stores the
* data in a int matrix where each row contains one sequence.
* The sequence in the file should all have the same length.
* The DNA characters are converted using
* SequenceLayer::char_to_int(char) ;
* \param file_address the address of the file to load.
* \throw std::invalid_argument if the file cannot be read,
* if an invalid DNA character is detected in the sequences
* or if the sequences have variable lengths.
* \return a matrix containing the sequences on the rows and
* the characters over the columns.
*/
matrix2d_i read_fasta(const std::string& file_address) ;
}
#endif // DNA_UTILITY_HPP
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