kmer.hpp File Reference

#include <vg/vg.pb.h>
#include <iostream>
#include <atomic>
#include "vg/io/json2pb.h"
#include "handle.hpp"
#include "position.hpp"
#include "gcsa/gcsa.h"

Classes
struct	vg::kmer_t
class	vg::SizeLimitExceededException

Namespaces
	vg

Functions
void	vg::for_each_kmer (const HandleGraph &graph, size_t k, const function< void(const kmer_t &)> &lambda, id_t head_id, id_t tail_id, atomic< int > *stop_flag)
ostream &	vg::operator<< (ostream &out, const kmer_t &kmer)
	Print a kmer_t to a stream. More...
void	vg::kmer_to_gcsa_kmers (const kmer_t &kmer, const gcsa::Alphabet &alpha, const function< void(const gcsa::KMer &)> &lambda)
	Convert the kmer_t to a set of gcsa2 binary kmers which are exposed via a callback. More...
gcsa::byte_type	vg::encode_chars (const vector< char > &chars, const gcsa::Alphabet &alpha)
	Encode the chars into the gcsa2 byte. More...
void	vg::write_gcsa_kmers (const HandleGraph &graph, int kmer_size, ostream &out, size_t &size_limit, id_t head_id, id_t tail_id)
string	vg::write_gcsa_kmers_to_tmpfile (const HandleGraph &graph, int kmer_size, size_t &size_limit, id_t head_id, id_t tail_id, const string &base_file_name)

Detailed Description

Functions for working with kmers_t's in HandleGraphs.