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 >:

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 uint32 *	m_idx
const uint32	m_buffer_offset
const uint32	m_buffer_size
io::Alignment *	m_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_len	effective band length; NOTE: this value must match the template BAND_LEN parameter used for instantiating aln::BatchedBandedAlignmentScore.
_pipeline	the pipeline object
_aligner	the 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.

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

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