kff.hpp File Reference

#include <deque>
#include <mutex>
#include <kff_io.hpp>
#include <gbwtgraph/minimizer.h>

Classes
struct	vg::kff_recoding_t
	A mapping of character values from KFF encoding to minimizer index encoding. More...
class	vg::ParallelKFFReader

Namespaces
	vg

Functions
size_t	vg::kff_bytes (size_t k)
	Returns the number of bytes required for a kmer in KFF format. More...
bool	vg::kff_is_trivial (const uint8_t *encoding)
	Returns true if the encoding is trivial (0, 1, 2, 3). More...
std::string	vg::kff_invert (const uint8_t *encoding)
	Inverts the KFF encoding into a packed -> char table. More...
kff_recoding_t	vg::kff_recoding (const uint8_t *encoding)
	Returns a recoding for the given encoding. More...
uint64_t	vg::kff_parse (const uint8_t *data, size_t bytes)
	Parses a big-endian integer from KFF data. More...
std::vector< uint8_t >	vg::kff_encode (const std::string &kmer, const uint8_t *encoding)
std::string	vg::kff_decode (const uint8_t *kmer, size_t k, const std::string &decoding)
	Decodes a kmer in KFF format according to the given encoding. More...
std::vector< uint8_t >	vg::kff_recode (gbwtgraph::Key64::value_type kmer, size_t k, const uint8_t *encoding)
	Recodes a kmer from a minimizer index in KFF format according to the given encoding. More...
gbwtgraph::Key64::value_type	vg::kff_recode (const uint8_t *kmer, size_t k, kff_recoding_t recoding)
gbwtgraph::Key64::value_type	vg::kff_recode_trivial (const uint8_t *kmer, size_t k, size_t bytes)
std::vector< gbwtgraph::Key64::value_type >	vg::kff_recode (const uint8_t *kmers, size_t n, size_t k, kff_recoding_t recoding)
std::vector< uint8_t >	vg::kff_reverse_complement (const uint8_t *kmer, size_t k, const uint8_t *encoding)
	Returns the reverse complement of a KFF kmer. More...
gbwtgraph::Key64::value_type	vg::minimizer_reverse_complement (gbwtgraph::Key64::value_type kmer, size_t k)
	Returns the reverse complement of a minimizer index kmer. More...

Detailed Description

Tools for working with the Kmer File Format (KFF).