nvbio::io::SequenceDataMMAPServer Struct Reference

Detailed description

A system mapped memory server for sequence data

Definition at line 49 of file sequence_mmap.h.

#include <sequence_mmap.h>

Public Methods
bool	load (const Alphabet alphabet, const char *file_name, const char *mapped_name, const SequenceFlags load_flags=io::SequenceFlags(io::SEQUENCE_DATA|io::SEQUENCE_QUALS|io::SEQUENCE_NAMES), const QualityEncoding qualities=Phred33)

Static Public Methods
static std::string	info_file_name (const char *name)
static std::string	sequence_file_name (const char *name)
static std::string	sequence_index_file_name (const char *name)
static std::string	qual_file_name (const char *name)
static std::string	name_file_name (const char *name)
static std::string	name_index_file_name (const char *name)

Public Members
ServerMappedFile	m_info_file
	internal memory-mapped info object server More...
ServerMappedFile	m_sequence_file
	internal memory-mapped genome object server More...
ServerMappedFile	m_sequence_index_file
	internal memory-mapped forward occurrence table object server More...
ServerMappedFile	m_qual_file
	internal memory-mapped reverse occurrence table object server More...
ServerMappedFile	m_name_file
	internal memory-mapped forward BWT object server More...
ServerMappedFile	m_name_index_file
	internal memory-mapped reverse BWT object server More...

Member Function Documentation

std::string nvbio::io::SequenceDataMMAPServer::info_file_name ( const char *  name)

static

Definition at line 56 of file sequence_mmap.cpp.

bool nvbio::io::SequenceDataMMAPServer::load	(	const Alphabet	alphabet,
		const char *	file_name,
		const char *	mapped_name,
		const SequenceFlags	load_flags = io::SequenceFlags( io::SEQUENCE_DATA | io::SEQUENCE_QUALS | io::SEQUENCE_NAMES ),
		const QualityEncoding	qualities = Phred33
	)

load a sequence from file

Parameters

alphabet	the alphabet to use for encoding
file_name	file name
mapped_name	memory mapped object name

Definition at line 40 of file sequence_mmap.cpp.

std::string nvbio::io::SequenceDataMMAPServer::name_file_name ( const char *  name)

static

Definition at line 60 of file sequence_mmap.cpp.

std::string nvbio::io::SequenceDataMMAPServer::name_index_file_name ( const char *  name)

static

Definition at line 61 of file sequence_mmap.cpp.

std::string nvbio::io::SequenceDataMMAPServer::qual_file_name ( const char *  name)

static

Definition at line 59 of file sequence_mmap.cpp.

std::string nvbio::io::SequenceDataMMAPServer::sequence_file_name ( const char *  name)

static

Definition at line 57 of file sequence_mmap.cpp.

std::string nvbio::io::SequenceDataMMAPServer::sequence_index_file_name ( const char *  name)

static

Definition at line 58 of file sequence_mmap.cpp.

Member Data Documentation

ServerMappedFile nvbio::io::SequenceDataMMAPServer::m_info_file

internal memory-mapped info object server

Definition at line 70 of file sequence_mmap.h.

ServerMappedFile nvbio::io::SequenceDataMMAPServer::m_name_file

internal memory-mapped forward BWT object server

Definition at line 74 of file sequence_mmap.h.

ServerMappedFile nvbio::io::SequenceDataMMAPServer::m_name_index_file

internal memory-mapped reverse BWT object server

Definition at line 75 of file sequence_mmap.h.

ServerMappedFile nvbio::io::SequenceDataMMAPServer::m_qual_file

internal memory-mapped reverse occurrence table object server

Definition at line 73 of file sequence_mmap.h.

ServerMappedFile nvbio::io::SequenceDataMMAPServer::m_sequence_file

internal memory-mapped genome object server

Definition at line 71 of file sequence_mmap.h.

ServerMappedFile nvbio::io::SequenceDataMMAPServer::m_sequence_index_file

internal memory-mapped forward occurrence table object server

Definition at line 72 of file sequence_mmap.h.

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

• E:/git/nvbio/nvbio/io/sequence/sequence_mmap.h
• E:/git/nvbio/nvbio/io/sequence/sequence_mmap.cpp