quality.cpp File Reference

#include "genesis/sequence/functions/quality.hpp"
#include "genesis/sequence/formats/fastq_reader.hpp"
#include "genesis/sequence/sequence.hpp"
#include "genesis/utils/io/input_source.hpp"
#include "genesis/utils/io/input_stream.hpp"
#include "genesis/utils/text/char.hpp"
#include "genesis/utils/text/string.hpp"
#include <algorithm>
#include <array>
#include <cassert>
#include <cmath>
#include <cstdint>
#include <stdexcept>

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

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_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)
void	throw_invalid_quality_code_ (char quality_code, QualityEncoding encoding)
	Local helper function to throw if any invalid fastq quality chars are being used. More...

Variables
static const std::array< double, 256 >	phred_score_to_error_probability_lookup_