mapper.hpp File Reference

#include <iostream>
#include <map>
#include <chrono>
#include <ctime>
#include "omp.h"
#include "vg.hpp"
#include "bdsg/hash_graph.hpp"
#include <gcsa/gcsa.h>
#include <gcsa/lcp.h>
#include <gbwt/gbwt.h>
#include "position.hpp"
#include "vg/io/json2pb.h"
#include "aligner.hpp"
#include "mem.hpp"
#include "mem_accelerator.hpp"
#include "cluster.hpp"
#include "haplotypes.hpp"

Classes
class	vg::AlignmentChainModelVertex
class	vg::AlignmentChainModel
class	vg::FragmentLengthDistribution
class	vg::PairedEndMapper
class	vg::BaseMapper
class	vg::FragmentLengthStatistics
class	vg::Mapper

Namespaces
	vg

Enumerations
enum	vg::MappingQualityMethod { vg::Approx, vg::Exact, vg::Adaptive, vg::None }

Functions
const vector< string >	vg::balanced_kmers (const string &seq, const int kmer_size, const int stride)
set< pos_t >	vg::gcsa_nodes_to_positions (const vector< gcsa::node_type > &nodes)
int	vg::sub_overlaps_of_first_aln (const vector< Alignment > &alns, float overlap_fraction)