Detailed description

An in-RAM FM-index.

Definition at line 211 of file fmindex.h.

#include <fmindex.h>

Inheritance diagram for nvbio::io::FMIndexDataHost:

Public Methods
int	load (const char *genome_prefix, const uint32 flags=FORWARD\|REVERSE\|SA)

Public Methods inherited from nvbio::io::FMIndexData
	FMIndexData ()
	empty constructor More...

virtual	~FMIndexData ()
	virtual destructor More...

occ_type	occ_iterator () const

occ_type	rocc_iterator () const

bwt_type	bwt_iterator () const

bwt_type	rbwt_iterator () const

ssa_type	ssa_iterator () const

ssa_type	rssa_iterator () const

count_table_type	count_table_iterator () const

rank_dict_type	rank_dict () const

rank_dict_type	rrank_dict () const

fm_index_type	index () const

fm_index_type	rindex () const

partial_fm_index_type	partial_index () const

partial_fm_index_type	rpartial_index () const

Public Methods inherited from nvbio::io::FMIndexDataCore
	FMIndexDataCore ()

uint32	flags () const
	return loading flags More...

uint32	length () const
	return sequence length More...

uint32	primary () const
	return the primary key More...

uint32	rprimary () const
	return the reverse primary key More...

bool	has_ssa () const
	return whether the sampled suffix array is present More...

bool	has_rssa () const
	return whether the reverse sampled suffix array is present More...

const uint32 *	bwt_occ () const
	return the BWT stream More...

const uint32 *	rbwt_occ () const
	return the reverse BWT stream More...

const uint32 *	count_table () const
	return the count table More...

uint32	bwt_occ_words () const
	return the number of sequence words More...

uint32	sa_words () const
	return the number of SA words More...

ssa_type	ssa () const

ssa_type	rssa () const

const uint32 *	L2 () const
	return the L2 table More...

Public Members
nvbio::vector< host_tag, uint32 >	m_bwt_occ_vec
	local storage for the forward BWT/OCC More...

nvbio::vector< host_tag, uint32 >	m_rbwt_occ_vec
	local storage for the reverse BWT/OCC More...

nvbio::vector< host_tag, uint32 >	m_ssa_vec
	local storage for the forward SSA More...

nvbio::vector< host_tag, uint32 >	m_rssa_vec
	local storage for the reverse SSA More...

uint32	m_count_table_vec [256]
	local storage for the BWT counting table More...

uint32	m_L2_vec [5]
	local storage for the L2 vector More...

Additional Inherited Members
Public Types inherited from nvbio::io::FMIndexData
typedef const uint4 *	bwt_occ_type

typedef deinterleaved_iterator < 2, 0, bwt_occ_type >	bwt_type

typedef deinterleaved_iterator < 2, 1, bwt_occ_type >	occ_type

typedef const uint32 *	count_table_type

typedef SSA_index_multiple < SA_INT >	ssa_storage_type

typedef PackedStream< bwt_type, uint8, BWT_BITS, BWT_BIG_ENDIAN >	bwt_stream_type

typedef rank_dictionary < BWT_BITS, FMIndexDataCore::OCC_INT, bwt_stream_type, occ_type, count_table_type >	rank_dict_type

typedef fm_index < rank_dict_type, ssa_type >	fm_index_type

typedef fm_index < rank_dict_type, null_type >	partial_fm_index_type

Static Public Members inherited from nvbio::io::FMIndexDataCore
static const uint32	FORWARD = 0x02

static const uint32	REVERSE = 0x04

static const uint32	SA = 0x10

static const uint32	BWT_BITS = 2u

static const bool	BWT_BIG_ENDIAN = true

static const uint32	BWT_SYMBOLS_PER_WORD = (8*sizeof(uint32))/BWT_BITS

static const uint32	OCC_INT = 64

static const uint32	SA_INT = 16

Member Function Documentation

int nvbio::io::FMIndexDataHost::load	(	const char *	genome_prefix,
		const uint32	flags = `FORWARD\|REVERSE\|SA`
	)

load a genome from file

Parameters

genome_prefix	prefix file name
flags	loading flags specifying which elements to load

Member Data Documentation

nvbio::vector<host_tag,uint32> nvbio::io::FMIndexDataHost::m_bwt_occ_vec

local storage for the forward BWT/OCC

Definition at line 221 of file fmindex.h.

uint32 nvbio::io::FMIndexDataHost::m_count_table_vec[256]

local storage for the BWT counting table

Definition at line 225 of file fmindex.h.

uint32 nvbio::io::FMIndexDataHost::m_L2_vec[5]

local storage for the L2 vector

Definition at line 226 of file fmindex.h.

nvbio::vector<host_tag,uint32> nvbio::io::FMIndexDataHost::m_rbwt_occ_vec

local storage for the reverse BWT/OCC

Definition at line 222 of file fmindex.h.

nvbio::vector<host_tag,uint32> nvbio::io::FMIndexDataHost::m_rssa_vec

local storage for the reverse SSA

Definition at line 224 of file fmindex.h.

nvbio::vector<host_tag,uint32> nvbio::io::FMIndexDataHost::m_ssa_vec

local storage for the forward SSA

Definition at line 223 of file fmindex.h.

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

E:/git/nvbio/nvbio/io/fmindex/fmindex.h

Detailed description

Public Methods

Public Members

Additional Inherited Members

Member Function Documentation

Member Data Documentation