vg::ParallelKFFReader Class Reference

#include <kff.hpp>

Public Types
typedef gbwtgraph::Key64::value_type	kmer_type

Public Member Functions
	ParallelKFFReader (const std::string &filename)
std::vector< std::pair< kmer_type, size_t > >	read (size_t n)

Public Attributes
Kff_reader	reader
	KFF reader. More...
std::deque< std::pair< kmer_type, size_t > >	buffer
	Buffer from unused kmers from the latest block. More...
std::mutex	mtx
	Mutex for accessing reader and buffer. More...
size_t	k
	Length of the kmers. More...
size_t	max_kmers_per_block
	Maximum number of kmers per block. More...
size_t	data_bytes
	Number of bytes reserved for each kmer count. More...
std::uint8_t	encoding [4]
	Encoding used for the kmers. More...
kff_recoding_t	recoding
	Recoding from KFF kmers to minimizer index kmers. More...

Private Member Functions
	ParallelKFFReader (const ParallelKFFReader &)=delete
ParallelKFFReader &	operator= (const ParallelKFFReader &)=delete

Detailed Description

A wrapper over Kff_reader that allows reading kmers safely from multiple threads.

Member Typedef Documentation

kmer_type

typedef gbwtgraph::Key64::value_type vg::ParallelKFFReader::kmer_type

Constructor & Destructor Documentation

ParallelKFFReader() [1/2]

vg::ParallelKFFReader::ParallelKFFReader

(

const std::string &

filename

)

Creates a new reader for the given file. Throws std::runtime_error if the file cannot be opened or the sanity checks fail.

ParallelKFFReader() [2/2]

vg::ParallelKFFReader::ParallelKFFReader ( const ParallelKFFReader &  )

privatedelete

Member Function Documentation

operator=()

ParallelKFFReader& vg::ParallelKFFReader::operator= ( const ParallelKFFReader &  )

privatedelete

read()

std::vector< std::pair< ParallelKFFReader::kmer_type, size_t > > vg::ParallelKFFReader::read

(

size_t

n

)

Reads the next n kmers and counts from the file. This can be called safely from multiple threads. If the returned vector contains fewer than n kmers this indicates that the reader has reached the end of the file.

Member Data Documentation

buffer

std::deque<std::pair<kmer_type, size_t> > vg::ParallelKFFReader::buffer

Buffer from unused kmers from the latest block.

data_bytes

size_t vg::ParallelKFFReader::data_bytes

Number of bytes reserved for each kmer count.

encoding

std::uint8_t vg::ParallelKFFReader::encoding[4]

Encoding used for the kmers.

k

size_t vg::ParallelKFFReader::k

Length of the kmers.

max_kmers_per_block

size_t vg::ParallelKFFReader::max_kmers_per_block

Maximum number of kmers per block.

mtx

std::mutex vg::ParallelKFFReader::mtx

Mutex for accessing reader and buffer.

reader

Kff_reader vg::ParallelKFFReader::reader

KFF reader.

recoding

kff_recoding_t vg::ParallelKFFReader::recoding

Recoding from KFF kmers to minimizer index kmers.

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The documentation for this class was generated from the following files:

• src/kff.hpp
• src/kff.cpp