#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 | |
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) |
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) |
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_ |