Needle
An application for fast and efficient searches of NGS data.
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#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 | add_parser_meta (seqan3::argument_parser &parser) |
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 |
void add_parser_meta | ( | seqan3::argument_parser & | parser | ) |
void initialise_arguments_ibf | ( | seqan3::argument_parser & | parser, |
estimate_ibf_arguments & | ibf_args, | ||
size_t & | num_hash, | ||
std::vector< double > & | fpr | ||
) |
void initialise_arguments_minimiser | ( | seqan3::argument_parser & | parser, |
minimiser_arguments & | minimiser_args, | ||
std::vector< uint8_t > & | cutoffs | ||
) |
void initialise_min_arguments | ( | seqan3::argument_parser & | parser, |
min_arguments & | args | ||
) |
int main | ( | int | argc, |
char const ** | argv | ||
) |
void parsing | ( | seqan3::argument_parser & | parser, |
min_arguments & | args | ||
) |
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_delete_bin | ( | seqan3::argument_parser & | parser | ) |
int run_needle_estimate | ( | seqan3::argument_parser & | parser | ) |
int run_needle_ibf | ( | seqan3::argument_parser & | parser | ) |
int run_needle_ibf_min | ( | seqan3::argument_parser & | parser | ) |
int run_needle_insert | ( | seqan3::argument_parser & | parser | ) |
int run_needle_insert_min | ( | seqan3::argument_parser & | parser | ) |
int run_needle_minimiser | ( | seqan3::argument_parser & | parser | ) |
uint64_t se |
uint64_t shape {} |
uint32_t w_size |