process_file.cpp File Reference

#include <algorithm>
#include <cinttypes>
#include <filesystem>
#include <fstream>
#include <ranges>
#include <string>
#include <vector>
#include <seqan3/io/sequence_file/all.hpp>
#include <seqan3/search/views/minimiser_hash.hpp>
#include <chopper/adjust_seed.hpp>
#include "shared.hpp"

Classes
struct	dna4_traits

Typedefs
using	sequence_file_type = seqan3::sequence_file_input< dna4_traits, seqan3::fields< seqan3::field::seq >, seqan3::type_list< seqan3::format_fasta, seqan3::format_fastq > >

Functions
void	process_file (std::string const &filename, robin_hood::unordered_set< uint64_t > &current_kmer_set, std::vector< uint64_t > &current_kmers, seqan::hibf::sketch::hyperloglog &sketch, bool const fill_current_kmers, uint8_t const kmer_size, uint8_t const window_size)
void	process_file (std::string const &filename, std::vector< uint64_t > &current_kmers, uint8_t const kmer_size, uint8_t const window_size)

Typedef Documentation

sequence_file_type

using sequence_file_type = seqan3::sequence_file_input<dna4_traits, seqan3::fields<seqan3::field::seq>, seqan3::type_list<seqan3::format_fasta, seqan3::format_fastq> >

Function Documentation

process_file() [1/2]

void process_file	(	std::string const &	filename,
		robin_hood::unordered_set< uint64_t > &	current_kmer_set,
		std::vector< uint64_t > &	current_kmers,
		seqan::hibf::sketch::hyperloglog &	sketch,
		bool const	fill_current_kmers,
		uint8_t const	kmer_size,
		uint8_t const	window_size
	)

process_file() [2/2]

void process_file	(	std::string const &	filename,
		std::vector< uint64_t > &	current_kmers,
		uint8_t const	kmer_size,
		uint8_t const	window_size
	)