mem.h File Reference

#include <nvbio/fmindex/fmindex.h>
#include <nvbio/fmindex/bidir.h>
#include <nvbio/basic/types.h>
#include <nvbio/basic/numbers.h>
#include <nvbio/basic/algorithms.h>
#include <nvbio/basic/exceptions.h>
#include <nvbio/basic/vector.h>
#include <nvbio/basic/vector_array.h>
#include <nvbio/basic/cuda/sort.h>
#include <nvbio/basic/cuda/primitives.h>
#include <nvbio/strings/string.h>
#include <thrust/sort.h>
#include <thrust/scan.h>
#include <thrust/binary_search.h>
#include <thrust/iterator/constant_iterator.h>
#include <thrust/iterator/counting_iterator.h>
#include <nvbio/fmindex/mem_inl.h>

Go to the source code of this file.

Classes
struct	nvbio::MEMFilter< system_tag, fm_index_type >
struct	nvbio::MEMRange< coord_type >
struct	nvbio::MEMHit< coord_type >
struct	nvbio::MEMFilter< host_tag, fm_index_type >
struct	nvbio::MEMFilter< device_tag, fm_index_type >
struct	nvbio::MEMFilterHost< fm_index_type >
struct	nvbio::MEMFilterDevice< fm_index_type >

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

Functions
template<typename pattern_type , typename fm_index_type , typename delegate_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::find_kmems (const uint32 pattern_len, const pattern_type pattern, const uint32 x, const fm_index_type f_index, const fm_index_type r_index, delegate_type &handler, const uint32 min_intv=1u, const uint32 min_span=1u)
template<typename pattern_type , typename fm_index_type , typename delegate_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::find_threshold_kmems (const uint32 pattern_len, const pattern_type pattern, const uint32 x, const fm_index_type f_index, const fm_index_type r_index, delegate_type &handler, const uint32 min_intv=1u, const uint32 min_span=1u)
template<typename system_tag , typename fm_index_type >
uint32	nvbio::string_batch_bound (const MEMFilter< system_tag, fm_index_type > &filter, const uint32 mem_count)