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fmindex_inl.h File Reference

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Namespaces

 nvbio
 Define a vector_view POD type and plain_view() for std::vector.
 

Functions

template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE fm_index
< TRankDictionary,
TSuffixArray, TL2 >
::index_type 
nvbio::rank (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type k, uint8 c)
 
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE fm_index
< TRankDictionary,
TSuffixArray, TL2 >
::range_type 
nvbio::rank (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type range, uint8 c)
 
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE
TRankDictionary::vec4_type 
nvbio::rank4 (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type k)
 
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 
nvbio::rank4 (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type range, typename TRankDictionary::vec4_type *outl, typename TRankDictionary::vec4_type *outh)
 
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 
nvbio::rank_all (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type k, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::vector_type *out)
 
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 
nvbio::rank_all (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type range, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::vector_type *outl, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::vector_type *outh)
 
template<typename TRankDictionary , typename TSuffixArray , typename TL2 , typename Iterator >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE fm_index
< TRankDictionary,
TSuffixArray, TL2 >
::range_type 
nvbio::match (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const Iterator pattern, const uint32 pattern_len)
 
template<typename TRankDictionary , typename TSuffixArray , typename TL2 , typename Iterator >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE fm_index
< TRankDictionary,
TSuffixArray, TL2 >
::range_type 
nvbio::match (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const Iterator pattern, const uint32 pattern_len, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type in_range)
 
template<typename TRankDictionary , typename TSuffixArray , typename TL2 , typename Iterator >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE fm_index
< TRankDictionary,
TSuffixArray, TL2 >
::range_type 
nvbio::match_reverse (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const Iterator pattern, const uint32 pattern_len)
 
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE fm_index
< TRankDictionary,
TSuffixArray, TL2 >
::index_type 
nvbio::basic_inv_psi (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type i)
 
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE fm_index
< TRankDictionary,
TSuffixArray, TL2 >
::range_type 
nvbio::inv_psi (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type i)
 
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE fm_index
< TRankDictionary,
TSuffixArray, TL2 >
::index_type 
nvbio::locate (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type i)
 
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE fm_index
< TRankDictionary,
TSuffixArray, TL2 >
::range_type 
nvbio::locate_ssa_iterator (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type i)
 
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE fm_index
< TRankDictionary,
TSuffixArray, TL2 >
::index_type 
nvbio::lookup_ssa_iterator (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type it)