NVBIO
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
Classes | Namespaces | Functions
sufsort.h File Reference
#include <nvbio/strings/string_set.h>
#include <nvbio/basic/thrust_view.h>
#include <nvbio/basic/cuda/sort.h>
#include <thrust/device_vector.h>
#include <thrust/transform_scan.h>
#include <thrust/sort.h>
#include <nvbio/sufsort/sufsort_inl.h>

Go to the source code of this file.

Classes

struct  nvbio::BWTParams
 

Namespaces

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

Functions

template<typename string_type >
string_type::index_type nvbio::cuda::find_primary (const typename string_type::index_type string_len, const string_type string)
 
template<typename string_type , typename output_iterator >
void nvbio::cuda::suffix_sort (const typename stream_traits< string_type >::index_type string_len, const string_type string, output_iterator output, BWTParams *params)
 
template<typename string_type , typename output_handler >
void nvbio::cuda::blockwise_suffix_sort (const typename string_type::index_type string_len, string_type string, output_handler &output, BWTParams *params)
 
template<typename string_type , typename output_iterator >
string_type::index_type nvbio::cuda::bwt (const typename string_type::index_type string_len, string_type string, output_iterator output, BWTParams *params)
 
template<typename string_set_type , typename output_handler >
void nvbio::cuda::suffix_sort (const string_set_type &string_set, output_handler &output, BWTParams *params=NULL)
 
template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type , typename output_handler >
void nvbio::cuda::bwt (const ConcatenatedStringSet< PackedStream< storage_type, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 >, uint64 * > string_set, output_handler &output, BWTParams *params=NULL)
 
template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type , typename output_handler >
void nvbio::large_bwt (const ConcatenatedStringSet< PackedStream< storage_type, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 >, uint64 * > string_set, output_handler &output, BWTParams *params=NULL)