nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType > Struct Template Reference

Detailed description

template< typename AlignerType, typename PipelineType>
struct nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >

a container for the strings to be aligned

Definition at line 173 of file alignment_utils.h.

#include <alignment_utils.h>

Public Types
typedef PipelineType::genome_iterator	genome_iterator
typedef PipelineType::read_batch_type	read_batch_type
typedef PipelineType::scheme_type	scheme_type
typedef AlignerType	aligner_type
typedef nvbio::lmem_cache_tag < CACHE_SIZE >	lmem_cache_type
typedef ReadLoader < read_batch_type, lmem_cache_type >	pattern_loader_type
typedef pattern_loader_type::string_type	pattern_string
typedef pattern_string::qual_string_type	qual_string
typedef PackedStringLoader < typename genome_iterator::storage_iterator, genome_iterator::SYMBOL_SIZE, genome_iterator::BIG_ENDIAN, lmem_cache_type >	text_loader_type
typedef text_loader_type::iterator	text_iterator
typedef vector_view < text_iterator >	text_string

Public Methods
template<typename context_type >
NVBIO_HOST_DEVICE void	load (const PipelineType &pipeline, const context_type *context)

Public Members
pattern_loader_type	pattern_loader
text_loader_type	text_loader
pattern_string	pattern
qual_string	quals
text_string	text

Static Public Members
static const uint32	CACHE_SIZE = 64

Member Typedef Documentation

template<typename AlignerType , typename PipelineType >

typedef AlignerType nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::aligner_type

Definition at line 178 of file alignment_utils.h.

template<typename AlignerType , typename PipelineType >

typedef PipelineType::genome_iterator nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::genome_iterator

Definition at line 175 of file alignment_utils.h.

template<typename AlignerType , typename PipelineType >

typedef nvbio::lmem_cache_tag<CACHE_SIZE> nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::lmem_cache_type

Definition at line 181 of file alignment_utils.h.

template<typename AlignerType , typename PipelineType >

typedef ReadLoader<read_batch_type,lmem_cache_type > nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::pattern_loader_type

Definition at line 183 of file alignment_utils.h.

template<typename AlignerType , typename PipelineType >

typedef pattern_loader_type::string_type nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::pattern_string

Definition at line 184 of file alignment_utils.h.

template<typename AlignerType , typename PipelineType >

typedef pattern_string::qual_string_type nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::qual_string

Definition at line 185 of file alignment_utils.h.

template<typename AlignerType , typename PipelineType >

typedef PipelineType::read_batch_type nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::read_batch_type

Definition at line 176 of file alignment_utils.h.

template<typename AlignerType , typename PipelineType >

typedef PipelineType::scheme_type nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::scheme_type

Definition at line 177 of file alignment_utils.h.

template<typename AlignerType , typename PipelineType >

typedef text_loader_type::iterator nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::text_iterator

Definition at line 192 of file alignment_utils.h.

template<typename AlignerType , typename PipelineType >

typedef PackedStringLoader< typename genome_iterator::storage_iterator, genome_iterator::SYMBOL_SIZE, genome_iterator::BIG_ENDIAN, lmem_cache_type> nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::text_loader_type

Definition at line 191 of file alignment_utils.h.

template<typename AlignerType , typename PipelineType >

typedef vector_view<text_iterator> nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::text_string

Definition at line 193 of file alignment_utils.h.

Member Function Documentation

template<typename AlignerType , typename PipelineType >

template<typename context_type >

NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::load ( const PipelineType &  pipeline, const context_type *  context  )

inline

Definition at line 198 of file alignment_utils.h.

Member Data Documentation

template<typename AlignerType , typename PipelineType >

const uint32 nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::CACHE_SIZE = 64

static

Definition at line 180 of file alignment_utils.h.

template<typename AlignerType , typename PipelineType >

pattern_string nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::pattern

Definition at line 222 of file alignment_utils.h.

template<typename AlignerType , typename PipelineType >

pattern_loader_type nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::pattern_loader

Definition at line 220 of file alignment_utils.h.

template<typename AlignerType , typename PipelineType >

qual_string nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::quals

Definition at line 223 of file alignment_utils.h.

template<typename AlignerType , typename PipelineType >

text_string nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::text

Definition at line 224 of file alignment_utils.h.

template<typename AlignerType , typename PipelineType >

text_loader_type nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >::text_loader

Definition at line 221 of file alignment_utils.h.

---

The documentation for this struct was generated from the following file:

• E:/git/nvbio/nvBowtie/bowtie2/cuda/alignment_utils.h