sufsort_inl.h File Reference

#include <nvbio/sufsort/sufsort_priv.h>
#include <nvbio/sufsort/sufsort_bucketing.h>
#include <nvbio/sufsort/sufsort_utils.h>
#include <nvbio/sufsort/compression_sort.h>
#include <nvbio/sufsort/prefix_doubling_sufsort.h>
#include <nvbio/sufsort/blockwise_sufsort.h>
#include <nvbio/sufsort/dcs.h>
#include <nvbio/strings/string_set.h>
#include <nvbio/basic/omp.h>
#include <nvbio/basic/thrust_view.h>
#include <nvbio/basic/cuda/sort.h>
#include <nvbio/basic/timer.h>
#include <thrust/device_vector.h>
#include <thrust/transform_scan.h>
#include <thrust/binary_search.h>
#include <thrust/iterator/constant_iterator.h>
#include <thrust/iterator/counting_iterator.h>
#include <thrust/sort.h>
#include <mgpuhost.cuh>
#include <moderngpu.cuh>

Go to the source code of this file.

Classes
struct	nvbio::cuda::HostBWTConfigGPUBucketer< BUCKETING_BITS_T, SYMBOL_SIZE, BIG_ENDIAN, storage_type >
struct	nvbio::cuda::HostBWTConfigCPUBucketer< BUCKETING_BITS_T, SYMBOL_SIZE, BIG_ENDIAN, storage_type >
struct	nvbio::cuda::DeviceBWTConfig< BUCKETING_BITS_T, SYMBOL_SIZE, BIG_ENDIAN, storage_type >
struct	nvbio::cuda::LargeBWTStatus
struct	nvbio::cuda::LargeBWTSkeleton< ConfigType, SYMBOL_SIZE, BIG_ENDIAN, storage_type >

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_set_type , typename output_handler >
void	nvbio::cuda::suffix_sort (const string_set_type &string_set, output_handler &output, BWTParams *params=NULL)
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<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)