NVBIO
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fm_index_type | the type of the fm-index |
#include <filter.h>
Public Types | |
typedef FMIndexFilter < host_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< host_tag, fm_index_type > | |
typedef host_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< host_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< host_tag, fm_index_type > | |
uint32 | m_n_queries |
index_type | m_index |
uint64 | m_n_occurrences |
thrust::host_vector< range_type > | m_ranges |
thrust::host_vector< uint64 > | m_slots |
Static Public Members inherited from nvbio::FMIndexFilter< host_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... | |
typedef core_type::coord_type nvbio::FMIndexFilterHost< fm_index_type >::coord_type |
typedef FMIndexFilter<host_tag, fm_index_type> nvbio::FMIndexFilterHost< fm_index_type >::core_type |
typedef core_type::hit_type nvbio::FMIndexFilterHost< fm_index_type >::hit_type |
typedef core_type::index_type nvbio::FMIndexFilterHost< fm_index_type >::index_type |
typedef core_type::range_type nvbio::FMIndexFilterHost< fm_index_type >::range_type |
typedef core_type::system_tag nvbio::FMIndexFilterHost< fm_index_type >::system_tag |