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nvbio::io::FMIndexDataHost Struct Reference

Detailed description

An in-RAM FM-index.

Definition at line 211 of file fmindex.h.

#include <fmindex.h>

Inheritance diagram for nvbio::io::FMIndexDataHost:
nvbio::io::FMIndexData nvbio::io::FMIndexDataCore

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 uint32bwt_occ () const
 return the BWT stream More...
const uint32rbwt_occ () const
 return the reverse BWT stream More...
const uint32count_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 uint32L2 () const
 return the L2 table More...

Public Members

nvbio::vector< host_tag, uint32m_bwt_occ_vec
 local storage for the forward BWT/OCC More...
nvbio::vector< host_tag, uint32m_rbwt_occ_vec
 local storage for the reverse BWT/OCC More...
nvbio::vector< host_tag, uint32m_ssa_vec
 local storage for the forward SSA More...
nvbio::vector< host_tag, uint32m_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
typedef deinterleaved_iterator
< 2, 1, bwt_occ_type
typedef const uint32count_table_type
typedef SSA_index_multiple
typedef PackedStream< bwt_type,
uint8, BWT_BITS,
typedef rank_dictionary
bwt_stream_type, occ_type,
typedef fm_index
< rank_dict_type, ssa_type
typedef fm_index
< rank_dict_type, null_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

genome_prefixprefix file name
flagsloading 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: