vg
tools for working with variation graphs
Namespaces | Typedefs | Functions
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 "algorithms/dagify.hpp"
#include "algorithms/dijkstra.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.