gaf_sorter.hpp File Reference

#include <algorithm>
#include <cstdint>
#include <functional>
#include <iostream>
#include <limits>
#include <memory>
#include <string>
#include <string_view>
#include <vector>
#include <gbwt/utils.h>

Classes
struct	vg::GAFSorterRecord
struct	vg::GAFSorterFile
struct	vg::GAFSorterParameters

Namespaces
	vg

Functions
bool	vg::sort_gaf (const std::string &input_file, const std::string &output_file, const GAFSorterParameters &params)
void	vg::sort_gaf_lines (std::unique_ptr< std::vector< std::string >> lines, GAFSorterRecord::key_type key_type, bool stable, GAFSorterFile &output)
void	vg::merge_gaf_records (std::unique_ptr< std::vector< GAFSorterFile >> inputs, GAFSorterFile &output, size_t buffer_size)

Detailed Description

Tools for sorting GAF records.

NOTE: There is an equivalent standalone tool included with GBZ-base.

TODO: Asynchronous I/O. TODO: Option for automatic detection of merge width to guarantee <= 2 rounds. TODO: Option for giving approximate batch size in bytes.