quality.hpp File Reference

#include <array>
#include <iosfwd>
#include <memory>
#include <stdexcept>
#include <string>
#include <vector>

Go to the source code of this file.

Namespaces
	genesis
	Container namespace for all symbols of genesis in order to keep them separate when used as a library.
	genesis::sequence
	genesis::utils

Enumerations
enum	QualityEncoding {   kSanger, kSolexa, kIllumina13, kIllumina15,   kIllumina18 }
	List of quality encodings for which we support decoding. More...

Functions
bool	compatible_quality_encodings (QualityEncoding lhs, QualityEncoding rhs)
	Return whether two quality encodings are compatible with each other. More...
unsigned char	error_probability_to_phred_score (double error_probability)
std::vector< unsigned char >	error_probability_to_phred_score (std::vector< double > error_probability)
signed char	error_probability_to_solexa_score (double error_probability)
std::vector< signed char >	error_probability_to_solexa_score (std::vector< double > error_probability)
QualityEncoding	guess_fastq_quality_encoding (std::shared_ptr< utils::BaseInputSource > source, size_t max_lines=0, size_t max_chars=0)
	Guess the quality score encoding for a fastq input, based on counts of how often each char appeared in the quality string (of the input fastq file for example). More...
QualityEncoding	guess_quality_encoding (std::array< size_t, 128 > const &char_counts)
	Guess the quality score encoding, based on counts of how often each char appeared in the quality string (of a fastq file for example). More...
QualityEncoding	guess_quality_encoding_from_name (std::string const &name)
	Guess the QualityEncoding type, given its description name. More...
std::vector< double >	phred_score_to_error_probability (std::vector< unsigned char > phred_score)
double	phred_score_to_error_probability (unsigned char phred_score)
std::vector< signed char >	phred_score_to_solexa_score (std::vector< unsigned char > phred_score)
signed char	phred_score_to_solexa_score (unsigned char phred_score)
unsigned char	quality_decode_to_phred_score (char quality_code, QualityEncoding encoding=QualityEncoding::kSanger)
	Decode a single quality score char (for example coming from a fastq file) to a phred score. More...
std::vector< unsigned char >	quality_decode_to_phred_score (std::string const &quality_codes, QualityEncoding encoding=QualityEncoding::kSanger)
	Decode a string of quality scores (for example coming from a fastq file) to phred scores. More...
std::string	quality_encode_from_phred_score (std::vector< unsigned char > const &phred_scores, bool clamp=true)
	Encode phred scores into quality chars, using the Sanger convention. More...
char	quality_encode_from_phred_score (unsigned char phred_score, bool clamp=true)
	Encode a phred score into a quality char, using the Sanger convention. More...
std::string	quality_encoding_name (QualityEncoding encoding, bool with_offset=false)
	Return a readable name for each of the encoding types. More...
double	solexa_score_to_error_probability (signed char solexa_score)
std::vector< double >	solexa_score_to_error_probability (std::vector< signed char > solexa_score)
unsigned char	solexa_score_to_phred_score (signed char solexa_score)
std::vector< unsigned char >	solexa_score_to_phred_score (std::vector< signed char > solexa_score)