vg
tools for working with variation graphs
Classes | Namespaces | Functions
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.