fastq_to_fasta
A template for creation of SeqAn3 apps, with a FASTQ to FASTA example app.
|
Classes | |
struct | forward_strand_minimiser |
class | threshold |
struct | threshold_parameters |
Functions | |
std::vector< double > | multiple_error_model (size_t const number_of_minimisers, size_t const errors, std::vector< double > const &affected_by_one_error_prob) |
std::vector< double > | one_error_model (size_t const kmer_size, double const p_mean, std::vector< double > const &affected_by_one_error_indirectly_prob) |
std::vector< double > | one_indirect_error_model (size_t const pattern_size, size_t const window_size, seqan3::shape const shape) |
std::vector< double > | pascal_row (size_t const n) |
std::vector< size_t > | precompute_correction (threshold_parameters const &arguments) |
std::vector< size_t > | precompute_threshold (threshold_parameters const &arguments) |
void | impl (size_t const minimisers_to_affect, std::vector< double > const &affected_by_one_error_prob, std::vector< size_t > affected_by_error, size_t const current_error, double &result) |
std::string const | correction_filename (threshold_parameters const &arguments) |
void | write_correction (std::vector< size_t > const &vec, threshold_parameters const &arguments) |
bool | read_correction (std::vector< size_t > &vec, threshold_parameters const &arguments) |
std::string const | threshold_filename (threshold_parameters const &arguments) |
void | write_thresholds (std::vector< size_t > const &vec, threshold_parameters const &arguments) |
bool | read_thresholds (std::vector< size_t > &vec, threshold_parameters const &arguments) |
std::string const raptor::threshold::correction_filename | ( | threshold_parameters const & | arguments | ) |
void raptor::threshold::impl | ( | size_t const | minimisers_to_affect, |
std::vector< double > const & | affected_by_one_error_prob, | ||
std::vector< size_t > | affected_by_error, | ||
size_t const | current_error, | ||
double & | result | ||
) |
std::vector< double > raptor::threshold::multiple_error_model | ( | size_t const | number_of_minimisers, |
size_t const | errors, | ||
std::vector< double > const & | affected_by_one_error_prob | ||
) |
std::vector< double > raptor::threshold::one_error_model | ( | size_t const | kmer_size, |
double const | p_mean, | ||
std::vector< double > const & | affected_by_one_error_indirectly_prob | ||
) |
std::vector< double > raptor::threshold::one_indirect_error_model | ( | size_t const | pattern_size, |
size_t const | window_size, | ||
seqan3::shape const | shape | ||
) |
std::vector< double > raptor::threshold::pascal_row | ( | size_t const | n | ) |
std::vector< size_t > raptor::threshold::precompute_correction | ( | threshold_parameters const & | arguments | ) |
std::vector< size_t > raptor::threshold::precompute_threshold | ( | threshold_parameters const & | arguments | ) |
bool raptor::threshold::read_correction | ( | std::vector< size_t > & | vec, |
threshold_parameters const & | arguments | ||
) |
bool raptor::threshold::read_thresholds | ( | std::vector< size_t > & | vec, |
threshold_parameters const & | arguments | ||
) |
std::string const raptor::threshold::threshold_filename | ( | threshold_parameters const & | arguments | ) |
void raptor::threshold::write_correction | ( | std::vector< size_t > const & | vec, |
threshold_parameters const & | arguments | ||
) |
void raptor::threshold::write_thresholds | ( | std::vector< size_t > const & | vec, |
threshold_parameters const & | arguments | ||
) |