Needle
An application for fast and efficient searches of NGS data.
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Functions | Variables
main.cpp File Reference
#include <filesystem>
#include <seqan3/argument_parser/all.hpp>
#include <seqan3/core/debug_stream.hpp>
#include "estimate.hpp"
#include "ibf.hpp"
#include "shared.hpp"

Functions

void initialise_min_arguments (seqan3::argument_parser &parser, min_arguments &args)
 
void initialise_arguments_ibf (seqan3::argument_parser &parser, estimate_ibf_arguments &ibf_args, size_t &num_hash, std::vector< double > &fpr)
 
void parsing (seqan3::argument_parser &parser, min_arguments &args)
 
void initialise_arguments_minimiser (seqan3::argument_parser &parser, minimiser_arguments &minimiser_args, std::vector< uint8_t > &cutoffs)
 
void read_input_file_list (std::vector< std::filesystem::path > &sequence_files, std::filesystem::path input_file)
 
int run_needle_count (seqan3::argument_parser &parser)
 
int run_needle_count_genome (seqan3::argument_parser &parser)
 
int run_needle_estimate (seqan3::argument_parser &parser)
 
int run_needle_ibf (seqan3::argument_parser &parser)
 
int run_needle_insert (seqan3::argument_parser &parser)
 
int run_needle_ibf_min (seqan3::argument_parser &parser)
 
int run_needle_insert_min (seqan3::argument_parser &parser)
 
int run_needle_delete_bin (seqan3::argument_parser &parser)
 
int run_needle_minimiser (seqan3::argument_parser &parser)
 
int main (int argc, char const **argv)
 

Variables

uint32_t w_size
 
uint64_t shape {}
 
uint64_t se
 

Function Documentation

◆ initialise_arguments_ibf()

void initialise_arguments_ibf ( seqan3::argument_parser &  parser,
estimate_ibf_arguments ibf_args,
size_t &  num_hash,
std::vector< double > &  fpr 
)

◆ initialise_arguments_minimiser()

void initialise_arguments_minimiser ( seqan3::argument_parser &  parser,
minimiser_arguments minimiser_args,
std::vector< uint8_t > &  cutoffs 
)

◆ initialise_min_arguments()

void initialise_min_arguments ( seqan3::argument_parser &  parser,
min_arguments args 
)

◆ main()

int main ( int  argc,
char const **  argv 
)

◆ parsing()

void parsing ( seqan3::argument_parser &  parser,
min_arguments args 
)

◆ read_input_file_list()

void read_input_file_list ( std::vector< std::filesystem::path > &  sequence_files,
std::filesystem::path  input_file 
)

◆ run_needle_count()

int run_needle_count ( seqan3::argument_parser &  parser)

◆ run_needle_count_genome()

int run_needle_count_genome ( seqan3::argument_parser &  parser)

◆ run_needle_delete_bin()

int run_needle_delete_bin ( seqan3::argument_parser &  parser)

◆ run_needle_estimate()

int run_needle_estimate ( seqan3::argument_parser &  parser)

◆ run_needle_ibf()

int run_needle_ibf ( seqan3::argument_parser &  parser)

◆ run_needle_ibf_min()

int run_needle_ibf_min ( seqan3::argument_parser &  parser)

◆ run_needle_insert()

int run_needle_insert ( seqan3::argument_parser &  parser)

◆ run_needle_insert_min()

int run_needle_insert_min ( seqan3::argument_parser &  parser)

◆ run_needle_minimiser()

int run_needle_minimiser ( seqan3::argument_parser &  parser)

Variable Documentation

◆ se

uint64_t se

◆ shape

uint64_t shape {}

◆ w_size

uint32_t w_size