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fmindex.h File Reference
#include <nvbio/basic/types.h>
#include <nvbio/basic/packedstream.h>
#include <nvbio/fmindex/rank_dictionary.h>
#include <nvbio/strings/string_traits.h>
#include <nvbio/fmindex/fmindex_inl.h>

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Classes

struct  nvbio::fm_index< TRankDictionary, TSuffixArray, TL2 >
 

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 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 >
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 >::range_type i)