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

Detailed description

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

A scoring stream, fetching the input hits to score from the hit queue indexed by the input sorting order, and assigning them their score and sink attributes.

Definition at line 303 of file traceback_inl.h.

#include <traceback_inl.h>

Inheritance diagram for nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >:
nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TRACEBACK_STREAM, AlignerType, PipelineType >

Public Types

typedef AlignmentStreamBase
< TRACEBACK_STREAM,
AlignerType, PipelineType > 
base_type
 
typedef base_type::context_type context_type
 
typedef base_type::scheme_type scheme_type
 
- Public Types inherited from nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TRACEBACK_STREAM, AlignerType, PipelineType >
typedef AlignmentStrings
< AlignerType, PipelineType > 
strings_type
 
typedef PipelineType::scheme_type scheme_type
 
typedef AlignerType aligner_type
 

Public Methods

 AllTracebackStream (const uint32 _count, const uint32 *_idx, const uint32 _buffer_offset, const uint32 _buffer_size, io::Alignment *_alignments, const uint32 _band_len, const PipelineType _pipeline, const AlignerType _aligner, const ParamsPOD _params)
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 
max_pattern_length () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 
max_text_length () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE MateType 
mate_type () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 
size () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
init_context (const uint32 i, context_type *context) const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 
output (const uint32 i, const context_type *context)
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 
finish (const uint32 i, const context_type *context, const uint32 ed, const int32 score)
 
- Public Methods inherited from nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TRACEBACK_STREAM, AlignerType, PipelineType >
 AlignmentStreamBase (const PipelineType _pipeline, const aligner_type _aligner, const ParamsPOD _params)
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE const
aligner_type
aligner () const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 
pattern_length (const uint32 i, const context_type *context) const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE uint32 
text_length (const uint32 i, const context_type *context) const
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 
load_strings (const uint32 i, const uint32 window_begin, const uint32 window_end, const context_type *context, strings_type *strings) const
 

Public Members

const MateType m_mate_type
 
const uint32 m_count
 
const uint32m_idx
 
const uint32 m_buffer_offset
 
const uint32 m_buffer_size
 
io::Alignmentm_alignments
 
const uint32 m_band_len
 
- Public Members inherited from nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TRACEBACK_STREAM, AlignerType, PipelineType >
PipelineType m_pipeline
 the pipeline object More...
 
aligner_type m_aligner
 the aligner More...
 
ParamsPOD m_params
 global parameters More...
 

Member Typedef Documentation

template<typename AlignerType , typename PipelineType >
typedef AlignmentStreamBase<TRACEBACK_STREAM,AlignerType,PipelineType> nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::base_type

Definition at line 305 of file traceback_inl.h.

template<typename AlignerType , typename PipelineType >
typedef base_type::context_type nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::context_type

Definition at line 306 of file traceback_inl.h.

template<typename AlignerType , typename PipelineType >
typedef base_type::scheme_type nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::scheme_type

Definition at line 307 of file traceback_inl.h.

Constructor & Destructor Documentation

template<typename AlignerType , typename PipelineType >
nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::AllTracebackStream ( const uint32  _count,
const uint32 _idx,
const uint32  _buffer_offset,
const uint32  _buffer_size,
io::Alignment _alignments,
const uint32  _band_len,
const PipelineType  _pipeline,
const AlignerType  _aligner,
const ParamsPOD  _params 
)
inline

constructor

Parameters
_band_leneffective band length; NOTE: this value must match the template BAND_LEN parameter used for instantiating aln::BatchedBandedAlignmentScore.
_pipelinethe pipeline object
_alignerthe aligner object

Definition at line 319 of file traceback_inl.h.

Member Function Documentation

template<typename AlignerType , typename PipelineType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::finish ( const uint32  i,
const context_type context,
const uint32  ed,
const int32  score 
)
inline

handle the output

Definition at line 426 of file traceback_inl.h.

template<typename AlignerType , typename PipelineType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::init_context ( const uint32  i,
context_type context 
) const
inline

initialize the i-th context

Definition at line 361 of file traceback_inl.h.

template<typename AlignerType , typename PipelineType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE MateType nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::mate_type ( ) const
inline

return the mate type

Definition at line 351 of file traceback_inl.h.

template<typename AlignerType , typename PipelineType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::max_pattern_length ( ) const
inline

return the maximum pattern length

Definition at line 341 of file traceback_inl.h.

template<typename AlignerType , typename PipelineType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::max_text_length ( ) const
inline

return the maximum text length

Definition at line 346 of file traceback_inl.h.

template<typename AlignerType , typename PipelineType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::output ( const uint32  i,
const context_type context 
)
inline

handle the output

Definition at line 390 of file traceback_inl.h.

template<typename AlignerType , typename PipelineType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::size ( void  ) const
inline

return the stream size

Definition at line 356 of file traceback_inl.h.

Member Data Documentation

template<typename AlignerType , typename PipelineType >
io::Alignment* nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::m_alignments

Definition at line 453 of file traceback_inl.h.

template<typename AlignerType , typename PipelineType >
const uint32 nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::m_band_len

Definition at line 454 of file traceback_inl.h.

template<typename AlignerType , typename PipelineType >
const uint32 nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::m_buffer_offset

Definition at line 451 of file traceback_inl.h.

template<typename AlignerType , typename PipelineType >
const uint32 nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::m_buffer_size

Definition at line 452 of file traceback_inl.h.

template<typename AlignerType , typename PipelineType >
const uint32 nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::m_count

Definition at line 449 of file traceback_inl.h.

template<typename AlignerType , typename PipelineType >
const uint32* nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::m_idx

Definition at line 450 of file traceback_inl.h.

template<typename AlignerType , typename PipelineType >
const MateType nvbio::bowtie2::cuda::detail::AllTracebackStream< AlignerType, PipelineType >::m_mate_type

Definition at line 448 of file traceback_inl.h.


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