nvbio::MEMFilter< device_tag, fm_index_type > Struct Template Reference

Detailed description

template< typename fm_index_type>
struct nvbio::MEMFilter< device_tag, fm_index_type >

This class implements an FM-index filter which can be used to find and filter MEMs between an arbitrary string-set and an FM-index.

The filter is designed to:

• first find and rank the suffix array ranges containing occurrences of all MEMs, expressed as a series of lists of (SA-begin, SA-end,string-id,string_begin|string-end<<16) tuples: there is one such list for each string in the set, and the entries are stored contiguously in a single vector;
• and then enumerate each individual occurrence of a MEM within the lists, as a set of (index-pos,string-id,string-begin,string-end) tuples.

Template Parameters

fm_index_type

the type of the fm-index

Definition at line 379 of file mem.h.

#include <mem.h>

Inheritance diagram for nvbio::MEMFilter< device_tag, fm_index_type >:

Public Types
typedef device_tag	system_tag
	the backend system More...
typedef fm_index_type	index_type
	the index type More...
typedef index_type::index_type	coord_type
	the coordinate type of the fm-index, uint32|uint64 More...
typedef MEMRange< coord_type >	rank_type
	rank coordinates are either uint32_4 or uint64_4 More...
typedef MEMHit< coord_type >	mem_type
	MEM coordinates are either uint32_4 or uint64_4. More...
typedef mem_type	hit_type
	MEM coordinates are either uint32_4 or uint64_4. More...

Public Methods
template<typename string_set_type >
uint64	rank (const fm_index_type &f_index, const fm_index_type &r_index, const string_set_type &string_set, const uint32 min_intv=1u, const uint32 max_intv=uint32(-1), const uint32 min_span=1u, const uint32 split_len=uint32(-1), const uint32 split_width=uint32(-1))
uint32	first_hit (const uint32 string_id) const
template<typename mems_iterator >
void	locate (const uint64 begin, const uint64 end, mems_iterator mems)
uint64	n_hits () const
uint64	n_mems () const
uint64	n_ranges () const

Public Members
uint32	m_n_queries
index_type	m_f_index
index_type	m_r_index
uint64	m_n_occurrences
DeviceVectorArray< rank_type >	m_mem_ranges
thrust::device_vector< uint64 >	m_slots
thrust::device_vector< uint8 >	d_temp_storage

Static Public Members
static const uint32	coord_dim = vector_traits<coord_type>::DIM

Member Typedef Documentation

template<typename fm_index_type >

typedef index_type::index_type nvbio::MEMFilter< device_tag, fm_index_type >::coord_type

the coordinate type of the fm-index, uint32|uint64

Definition at line 384 of file mem.h.

template<typename fm_index_type >

typedef mem_type nvbio::MEMFilter< device_tag, fm_index_type >::hit_type

MEM coordinates are either uint32_4 or uint64_4.

Definition at line 389 of file mem.h.

template<typename fm_index_type >

typedef fm_index_type nvbio::MEMFilter< device_tag, fm_index_type >::index_type

the index type

Definition at line 382 of file mem.h.

template<typename fm_index_type >

typedef MEMHit<coord_type> nvbio::MEMFilter< device_tag, fm_index_type >::mem_type

MEM coordinates are either uint32_4 or uint64_4.

Definition at line 388 of file mem.h.

template<typename fm_index_type >

typedef MEMRange<coord_type> nvbio::MEMFilter< device_tag, fm_index_type >::rank_type

rank coordinates are either uint32_4 or uint64_4

Definition at line 387 of file mem.h.

template<typename fm_index_type >

typedef device_tag nvbio::MEMFilter< device_tag, fm_index_type >::system_tag

the backend system

Definition at line 381 of file mem.h.

Member Function Documentation

template<typename fm_index_type >

uint32 nvbio::MEMFilter< device_tag, fm_index_type >::first_hit

(

const uint32

string_id)

const

find the index of the first MEM hit corresponding to a given string

Definition at line 1477 of file mem_inl.h.

template<typename fm_index_type >

template<typename mems_iterator >

void nvbio::MEMFilter< device_tag, fm_index_type >::locate	(	const uint64	begin,
		const uint64	end,
		mems_iterator	mems
	)

enumerate all mems in a given range

Template Parameters

mems_iterator

a mem_type iterator

Parameters

begin	the beginning of the mems sequence to locate, in [0,n_mems)
end	the end of the mems sequence to locate, in [0,n_mems]

Definition at line 1499 of file mem_inl.h.

template<typename fm_index_type >

uint64 nvbio::MEMFilter< device_tag, fm_index_type >::n_hits ( ) const

inline

return the number of mems from the last rank query

Definition at line 432 of file mem.h.

template<typename fm_index_type >

uint64 nvbio::MEMFilter< device_tag, fm_index_type >::n_mems ( ) const

inline

return the number of mems from the last rank query

Definition at line 436 of file mem.h.

template<typename fm_index_type >

uint64 nvbio::MEMFilter< device_tag, fm_index_type >::n_ranges ( ) const

inline

return the number of MEM ranges

Definition at line 440 of file mem.h.

template<typename fm_index_type >

template<typename string_set_type >

uint64 nvbio::MEMFilter< device_tag, fm_index_type >::rank	(	const fm_index_type &	f_index,
		const fm_index_type &	r_index,
		const string_set_type &	string_set,
		const uint32	min_intv = 1u,
		const uint32	max_intv = uint32(-1),
		const uint32	min_span = 1u,
		const uint32	split_len = uint32(-1),
		const uint32	split_width = uint32(-1)
	)

enact the filter on an FM-index and a string-set

Parameters

f_index	the forward FM-index
r_index	the reverse FM-index
string-set	the query string-set
min_intv	the minimum number of occurrences k of a k-MEM
max_intv	the maximum number of occurrences k of a k-MEM
min_span	the minimum span length on the pattern of MEM

Returns

the total number of mems

Definition at line 1312 of file mem_inl.h.

Member Data Documentation

template<typename fm_index_type >

const uint32 nvbio::MEMFilter< device_tag, fm_index_type >::coord_dim = vector_traits<coord_type>::DIM

static

Definition at line 385 of file mem.h.

template<typename fm_index_type >

thrust::device_vector<uint8> nvbio::MEMFilter< device_tag, fm_index_type >::d_temp_storage

Definition at line 448 of file mem.h.

template<typename fm_index_type >

index_type nvbio::MEMFilter< device_tag, fm_index_type >::m_f_index

Definition at line 443 of file mem.h.

template<typename fm_index_type >

DeviceVectorArray<rank_type> nvbio::MEMFilter< device_tag, fm_index_type >::m_mem_ranges

Definition at line 446 of file mem.h.

template<typename fm_index_type >

uint64 nvbio::MEMFilter< device_tag, fm_index_type >::m_n_occurrences

Definition at line 445 of file mem.h.

template<typename fm_index_type >

uint32 nvbio::MEMFilter< device_tag, fm_index_type >::m_n_queries

Definition at line 442 of file mem.h.

template<typename fm_index_type >

index_type nvbio::MEMFilter< device_tag, fm_index_type >::m_r_index

Definition at line 444 of file mem.h.

template<typename fm_index_type >

thrust::device_vector<uint64> nvbio::MEMFilter< device_tag, fm_index_type >::m_slots

Definition at line 447 of file mem.h.

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

• E:/git/nvbio/nvbio/fmindex/mem.h
• E:/git/nvbio/nvbio/fmindex/mem_inl.h