fastq_to_fasta
A template for creation of SeqAn3 apps, with a FASTQ to FASTA example app.
Public Member Functions | Public Attributes | List of all members
raptor::search_arguments Struct Reference

#include <raptor/argument_parsing/search_arguments.hpp>

Public Member Functions

raptor::threshold::threshold_parameters make_threshold_parameters () const noexcept
 

Public Attributes

uint32_t window_size {20u}
 
seqan3::shape shape {seqan3::ungapped{20u}}
 
uint8_t shape_size {shape.size()}
 
uint8_t shape_weight {shape.count()}
 
uint8_t threads {1u}
 
uint8_t parts {1u}
 
double tau {0.9999}
 
double threshold {std::numeric_limits<double>::quiet_NaN()}
 
double p_max {0.15}
 
double fpr {0.05}
 
uint64_t pattern_size {}
 
raptor::pattern_size pattern_size_strong {}
 
uint8_t errors {0}
 
std::filesystem::path index_file {}
 
bool compressed {false}
 
std::vector< std::vector< std::string > > bin_path {}
 
std::filesystem::path query_file {}
 
std::filesystem::path out_file {"search.out"}
 
bool write_time {false}
 
bool is_socks {false}
 
bool is_hibf {false}
 
bool cache_thresholds {false}
 

Member Function Documentation

◆ make_threshold_parameters()

raptor::threshold::threshold_parameters raptor::search_arguments::make_threshold_parameters ( ) const
inlinenoexcept

Member Data Documentation

◆ bin_path

std::vector<std::vector<std::string> > raptor::search_arguments::bin_path {}

◆ cache_thresholds

bool raptor::search_arguments::cache_thresholds {false}

◆ compressed

bool raptor::search_arguments::compressed {false}

◆ errors

uint8_t raptor::search_arguments::errors {0}

◆ fpr

double raptor::search_arguments::fpr {0.05}

◆ index_file

std::filesystem::path raptor::search_arguments::index_file {}

◆ is_hibf

bool raptor::search_arguments::is_hibf {false}

◆ is_socks

bool raptor::search_arguments::is_socks {false}

◆ out_file

std::filesystem::path raptor::search_arguments::out_file {"search.out"}

◆ p_max

double raptor::search_arguments::p_max {0.15}

◆ parts

uint8_t raptor::search_arguments::parts {1u}

◆ pattern_size

uint64_t raptor::search_arguments::pattern_size {}

◆ pattern_size_strong

raptor::pattern_size raptor::search_arguments::pattern_size_strong {}

◆ query_file

std::filesystem::path raptor::search_arguments::query_file {}

◆ shape

seqan3::shape raptor::search_arguments::shape {seqan3::ungapped{20u}}

◆ shape_size

uint8_t raptor::search_arguments::shape_size {shape.size()}

◆ shape_weight

uint8_t raptor::search_arguments::shape_weight {shape.count()}

◆ tau

double raptor::search_arguments::tau {0.9999}

◆ threads

uint8_t raptor::search_arguments::threads {1u}

◆ threshold

double raptor::search_arguments::threshold {std::numeric_limits<double>::quiet_NaN()}

◆ window_size

uint32_t raptor::search_arguments::window_size {20u}

◆ write_time

bool raptor::search_arguments::write_time {false}

The documentation for this struct was generated from the following file: