aligner.hpp File Reference

#include <algorithm>
#include <utility>
#include <vector>
#include <set>
#include <string>
#include <unordered_map>
#include <unordered_set>
#include <vg/vg.pb.h>
#include "gssw.h"
#include "Variant.h"
#include "Fasta.h"
#include "handle.hpp"
#include "path.hpp"
#include "dozeu_interface.hpp"
#include "deletion_aligner.hpp"

Classes
class	vg::BaseAligner
class	vg::GSSWAligner
class	vg::Aligner
class	vg::QualAdjAligner
class	vg::AlignerClient

Namespaces
	vg

Functions
int32_t	vg::score_gap (size_t gap_length, int32_t gap_open, int32_t gap_extension)
	Score a gap with the given open and extension scores. More...