haplotype_indexer.cpp File Reference

#include "haplotype_indexer.hpp"
#include <iostream>
#include <mutex>
#include <vector>
#include <string>
#include <vg/io/stream.hpp>
#include <gbwtgraph/algorithms.h>
#include <gbwtgraph/path_cover.h>
#include "gbwt_helper.hpp"
#include "alignment.hpp"
#include "hash_map.hpp"
#include "path.hpp"

Namespaces
	vg

Functions
std::vector< std::pair< size_t, size_t > >	vg::present_symbols (const std::vector< std::vector< size_t >> &counts_by_job)
std::vector< std::pair< size_t, size_t > >	vg::canonical_huffman (const std::vector< std::pair< size_t, size_t >> &symbols)
std::string	vg::longest_common_prefix (const std::vector< std::vector< std::string >> &read_names)
void	vg::create_alignment_metadata (std::vector< std::vector< std::string >> &read_names, const std::string &prefix, gbwt::Metadata &metadata)

Detailed Description

: implementations of haplotype indexing with the GBWT