minimizer_mapper.cpp File Reference

#include "minimizer_mapper.hpp"
#include "crash.hpp"
#include "annotation.hpp"
#include "path_subgraph.hpp"
#include "multipath_alignment.hpp"
#include "split_strand_graph.hpp"
#include "subgraph.hpp"
#include "statistics.hpp"
#include "algorithms/alignment_path_offsets.hpp"
#include "algorithms/count_covered.hpp"
#include "algorithms/intersect_path_offsets.hpp"
#include "algorithms/extract_containing_graph.hpp"
#include "algorithms/extract_connecting_graph.hpp"
#include "algorithms/chain_items.hpp"
#include "algorithms/sample_minimal.hpp"
#include "algorithms/pad_band.hpp"
#include <bdsg/overlays/strand_split_overlay.hpp>
#include <gbwtgraph/algorithms.h>
#include <gbwtgraph/cached_gbwtgraph.h>
#include <iostream>
#include <algorithm>
#include <cmath>
#include <cfloat>

Classes
struct	vg::read_alignment_index_t
	Type to point to an alignment of a known read. More...
struct	vg::alignment_index_t

Namespaces
	vg

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

Variables
const read_alignment_index_t	vg::NO_READ_INDEX = {std::numeric_limits<size_t>::infinity(), std::numeric_limits<size_t>::infinity()}
	Represents an unset index. More...
const alignment_index_t	vg::NO_INDEX {std::numeric_limits<size_t>::max(), std::numeric_limits<size_t>::max(), std::numeric_limits<bool>::max()}
	Represents an unset index. More...

Detailed Description

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