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nvbio::io::FMIndexDataMMAPServer Struct Reference

Detailed description

A memory-mapped FM-index server, which can load an FM-index from disk and map it to a shared memory arena.

Definition at line 243 of file fmindex.h.

#include <fmindex.h>

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

Public Types

typedef FMIndexDataMMAPInfo Info
 
- 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 uint32count_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 uint32bwt_occ_type
 
typedef const uint32count_table_type
 
typedef
SSA_index_multiple_context
< SA_INT, const uint32 * > 
ssa_type
 

Public Methods

int load (const char *genome_prefix, const char *mapped_name)
 
- 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...
 

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
 
uint32m_L2
 
uint32m_bwt_occ
 
uint32m_rbwt_occ
 
uint32m_count_table
 
ssa_type m_ssa
 
ssa_type m_rssa
 
- 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 Typedef Documentation

Definition at line 245 of file fmindex.h.

Member Function Documentation

int nvbio::io::FMIndexDataMMAPServer::load ( const char *  genome_prefix,
const char *  mapped_name 
)

load a genome from file

Parameters
genome_prefixprefix file name
mapped_namememory mapped object name

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