minimizer_mapper.cpp File Reference

#include "minimizer_mapper.hpp"
#include "annotation.hpp"
#include "path_subgraph.hpp"
#include "multipath_alignment.hpp"
#include "split_strand_graph.hpp"
#include "subgraph.hpp"
#include <bdsg/overlays/strand_split_overlay.hpp>
#include <gbwtgraph/algorithms.h>
#include <gbwtgraph/cached_gbwtgraph.h>
#include <iostream>
#include <algorithm>
#include <cmath>

Namespaces
	vg

Typedefs
typedef std::pair< uint32_t, int32_t >	vg::pareto_point

Functions
void	vg::find_pareto_frontier (std::vector< pareto_point > &v)
int32_t	vg::gap_penalty (size_t length, const Aligner *aligner)
int32_t	vg::mismatch_penalty (size_t n, const Aligner *aligner)
int32_t	vg::gap_penalty (size_t start, size_t limit, const Aligner *aligner)
int32_t	vg::flank_penalty (size_t length, const std::vector< pareto_point > &frontier, const Aligner *aligner)

Detailed Description

Defines the code for the minimizer-and-GBWT-based mapper.