Detailed description

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

: The filter will return an ordered set of (index-pos,string-id) pairs, where string-id is the index into the string-set and index-pos is an index into the FM-index.

Template Parameters

fm_index_type the type of the fm-index

Definition at line 240 of file filter.h.

#include <filter.h>

Inheritance diagram for nvbio::FMIndexFilterDevice< fm_index_type >:

Public Types
typedef FMIndexFilter < device_tag, fm_index_type >	core_type
	the base class More...

typedef core_type::system_tag	system_tag
	the backend system More...

typedef core_type::index_type	index_type
	the index type More...

typedef core_type::coord_type	coord_type
	the coordinate type of the fm-index, uint32\|uint2 More...

typedef core_type::range_type	range_type
	the coordinate type of the filtered ranges More...

typedef core_type::hit_type	hit_type
	hits are either uint2 or uint4 More...

Public Types inherited from nvbio::FMIndexFilter< device_tag, fm_index_type >
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\|uint32_2\|uint64_2 More...

typedef vector_type < coord_type, 2 >::type	range_type
	ranges are either uint32_2 or uint64_2; More...

typedef vector_type < coord_type, hit_dim >::type	hit_type
	hits are either uint2 or uint4 More...

Additional Inherited Members
Public Methods inherited from nvbio::FMIndexFilter< device_tag, fm_index_type >
template<typename string_set_type >
uint64	rank (const fm_index_type &index, const string_set_type &string_set)

template<typename hits_iterator >
void	locate (const uint64 begin, const uint64 end, hits_iterator hits)

uint64	n_hits () const

const range_type *	ranges () const

const uint64 *	ranks () const

Public Members inherited from nvbio::FMIndexFilter< device_tag, fm_index_type >
uint32	m_n_queries

index_type	m_index

uint64	m_n_occurrences

thrust::device_vector< range_type >	m_ranges

thrust::device_vector< uint64 >	m_slots

thrust::device_vector< hit_type >	m_hits

thrust::device_vector< uint8 >	d_temp_storage

Static Public Members inherited from nvbio::FMIndexFilter< device_tag, fm_index_type >
static const uint32	coord_dim = vector_traits<coord_type>::DIM

static const uint32	hit_dim = coord_dim*2
	hits are either uint2 or uint4 More...