gbwt_extender.cpp File Reference

#include "gbwt_extender.hpp"
#include "hash_map.hpp"
#include <algorithm>
#include <array>
#include <cstring>
#include <queue>
#include <set>
#include <structures/immutable_list.hpp>

Classes
struct	vg::state_hash
struct	vg::MatchPos
struct	vg::MatchPos::PathList
struct	vg::WFAPoint
struct	vg::WFANode
class	vg::WFATree
struct	vg::WFATree::ScoreProperties

Namespaces
	vg
	std
	Hash functor to hash NodeSides using std::hash.

Functions
template<class Element >
void	vg::in_place_subvector (std::vector< Element > &vec, size_t head, size_t tail)
void	vg::set_score (GaplessExtension &extension, const Aligner *aligner)
void	vg::match_initial (GaplessExtension &match, const std::string &seq, gbwtgraph::view_type target)
size_t	vg::match_forward (GaplessExtension &match, const std::string &seq, gbwtgraph::view_type target, uint32_t mismatch_limit)
void	vg::match_backward (GaplessExtension &match, const std::string &seq, gbwtgraph::view_type target, uint32_t mismatch_limit)
void	vg::handle_full_length (const HandleGraph &graph, std::vector< GaplessExtension > &result, double overlap_threshold)
void	vg::remove_duplicates (std::vector< GaplessExtension > &result)
void	vg::find_mismatches (const std::string &seq, const gbwtgraph::CachedGBWTGraph &graph, std::vector< GaplessExtension > &result)
size_t	vg::interval_length (std::pair< size_t, size_t > interval)
std::vector< handle_t >	vg::get_path (const std::vector< handle_t > &first, handle_t second)
std::vector< handle_t >	vg::get_path (handle_t first, const std::vector< handle_t > &second)
std::vector< handle_t >	vg::get_path (const std::vector< handle_t > &first, gbwt::node_type second)
std::vector< handle_t >	vg::get_path (gbwt::node_type reverse_first, const std::vector< handle_t > &second)
bool	vg::trim_mismatches (GaplessExtension &extension, const gbwtgraph::CachedGBWTGraph &graph, const Aligner &aligner)
std::ostream &	vg::operator<< (std::ostream &out, const WFAAlignment::Edit &edit)
	Allow printing an Edit. More...
std::string	std::to_string (const vg::WFAAlignment::Edit &edit)
	Convert a WFAAlignment Edit operation to a string. More...