Detailed description

A device-side FM-index - which can take a host memory FM-index and map it to device memory.

Definition at line 294 of file fmindex.h.

#include <fmindex.h>

Inheritance diagram for nvbio::io::FMIndexDataDevice:

Public Types
typedef cuda::ldg_pointer< 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 cuda::ldg_pointer< uint32 >	count_table_type

typedef cuda::ldg_pointer< uint32 >	ssa_ldg_type

typedef SSA_index_multiple_device < SA_INT >	ssa_storage_type

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

typedef SSA_index_multiple_context < FMIndexDataCore::SA_INT, ssa_ldg_type >	ssa_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

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

Public Types inherited from nvbio::io::FMIndexDataCore
typedef const uint32 *	bwt_occ_type

typedef const uint32 *	count_table_type

typedef SSA_index_multiple_context < SA_INT, const uint32 * >	ssa_type

Public Methods
	FMIndexDataDevice (const FMIndexData &host_data, const uint32 flags=FORWARD\|REVERSE)

uint64	allocated () const
	return the amount of allocated device memory 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::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...

Static Public Members
static const uint32	FORWARD = 0x02

static const uint32	REVERSE = 0x04

static const uint32	SA = 0x10

Additional Inherited Members
Public Members inherited from nvbio::io::FMIndexDataCore
uint32	m_flags

uint32	m_seq_length

uint32	m_bwt_occ_words

uint32	m_sa_words

uint32	m_primary

uint32	m_rprimary

uint32 *	m_L2

uint32 *	m_bwt_occ

uint32 *	m_rbwt_occ

uint32 *	m_count_table

ssa_type	m_ssa

ssa_type	m_rssa

Member Typedef Documentation

typedef cuda::ldg_pointer<uint4> nvbio::io::FMIndexDataDevice::bwt_occ_type

Definition at line 302 of file fmindex.h.

typedef PackedStream<bwt_type,uint8,BWT_BITS,BWT_BIG_ENDIAN> nvbio::io::FMIndexDataDevice::bwt_stream_type

Definition at line 308 of file fmindex.h.

typedef deinterleaved_iterator<2,0,bwt_occ_type> nvbio::io::FMIndexDataDevice::bwt_type

Definition at line 303 of file fmindex.h.

typedef cuda::ldg_pointer<uint32> nvbio::io::FMIndexDataDevice::count_table_type

Definition at line 305 of file fmindex.h.

typedef fm_index<rank_dict_type,ssa_type> nvbio::io::FMIndexDataDevice::fm_index_type

Definition at line 321 of file fmindex.h.

typedef deinterleaved_iterator<2,1,bwt_occ_type> nvbio::io::FMIndexDataDevice::occ_type

Definition at line 304 of file fmindex.h.

typedef fm_index<rank_dict_type,null_type> nvbio::io::FMIndexDataDevice::partial_fm_index_type

Definition at line 322 of file fmindex.h.

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

Definition at line 319 of file fmindex.h.

typedef cuda::ldg_pointer<uint32> nvbio::io::FMIndexDataDevice::ssa_ldg_type

Definition at line 306 of file fmindex.h.

typedef SSA_index_multiple_device<SA_INT> nvbio::io::FMIndexDataDevice::ssa_storage_type

Definition at line 307 of file fmindex.h.

typedef SSA_index_multiple_context< FMIndexDataCore::SA_INT, ssa_ldg_type> nvbio::io::FMIndexDataDevice::ssa_type

Definition at line 312 of file fmindex.h.

Constructor & Destructor Documentation

nvbio::io::FMIndexDataDevice::FMIndexDataDevice	(	const FMIndexData &	host_data,
		const uint32	flags = `FORWARD\|REVERSE`
	)

load a host-memory FM-index in device memory

Parameters

host_data	host-memory FM-index to load
flags	specify which parts of the FM-index to load

Member Function Documentation

uint64 nvbio::io::FMIndexDataDevice::allocated ( ) const

inline

return the amount of allocated device memory

Definition at line 330 of file fmindex.h.

bwt_type nvbio::io::FMIndexDataDevice::bwt_iterator ( ) const

inline

Definition at line 337 of file fmindex.h.

count_table_type nvbio::io::FMIndexDataDevice::count_table_iterator ( ) const

inline

Definition at line 343 of file fmindex.h.

fm_index_type nvbio::io::FMIndexDataDevice::index ( ) const

inline

Definition at line 348 of file fmindex.h.

occ_type nvbio::io::FMIndexDataDevice::occ_iterator ( ) const

inline

iterators access

Definition at line 334 of file fmindex.h.

partial_fm_index_type nvbio::io::FMIndexDataDevice::partial_index ( ) const

inline

Definition at line 351 of file fmindex.h.

rank_dict_type nvbio::io::FMIndexDataDevice::rank_dict ( ) const

inline

Definition at line 345 of file fmindex.h.

bwt_type nvbio::io::FMIndexDataDevice::rbwt_iterator ( ) const

inline

Definition at line 338 of file fmindex.h.

fm_index_type nvbio::io::FMIndexDataDevice::rindex ( ) const

inline

Definition at line 349 of file fmindex.h.

occ_type nvbio::io::FMIndexDataDevice::rocc_iterator ( ) const

inline

Definition at line 335 of file fmindex.h.

partial_fm_index_type nvbio::io::FMIndexDataDevice::rpartial_index ( ) const

inline

Definition at line 352 of file fmindex.h.

rank_dict_type nvbio::io::FMIndexDataDevice::rrank_dict ( ) const

inline

Definition at line 346 of file fmindex.h.

ssa_type nvbio::io::FMIndexDataDevice::rssa_iterator ( ) const

inline

Definition at line 341 of file fmindex.h.

ssa_type nvbio::io::FMIndexDataDevice::ssa_iterator ( ) const

inline

Definition at line 340 of file fmindex.h.

Member Data Documentation

const uint32 nvbio::io::FMIndexDataDevice::FORWARD = 0x02

static

Definition at line 296 of file fmindex.h.

const uint32 nvbio::io::FMIndexDataDevice::REVERSE = 0x04

static

Definition at line 297 of file fmindex.h.

const uint32 nvbio::io::FMIndexDataDevice::SA = 0x10

static

Definition at line 298 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 Types

Public Methods

Static Public Members

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation