Detailed description

A staged scoring work unit, implemented inheriting from StagedAlignmentUnitBase

Definition at line 252 of file batched_stream.h.

Inheritance diagram for nvbio::aln::BandedScoreUnit< BAND_LEN, stream_type >:

Public Types
typedef ScoreStream < stream_type >::cell_type	cell_type

typedef ScoreStream < stream_type > ::checkpoint_type	checkpoint_type

typedef ScoreStream < stream_type >::column_type	column_type

Public Types inherited from nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >
typedef stream_type::context_type	context_type

typedef stream_type::strings_type	strings_type

typedef stream_type::aligner_type	aligner_type

Public Methods
template<typename pattern_string , typename qual_string , typename text_string , typename sink_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	execute (const ScoreStream< stream_type > &score_stream, const uint32 queue_slot, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score, const uint32 window_begin, const uint32 window_end, sink_type &sink)

Public Methods inherited from nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	setup (const uint32 _job_id, const uint32 _queue_slot, const stream_type &stream)

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	run (const ScoreStream< stream_type > &score_stream)

Additional Inherited Members
Public Members inherited from nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >
uint32	job_id
	the job id More...

uint32	queue_slot
	the job's execution slot More...

context_type	context
	the alignment context More...

strings_type	strings
	the strings to be aligned More...

volatile uint32	window_begin
	the beginning of the pattern window More...

volatile bool	valid
	valid flag More...

Static Public Members inherited from nvbio::aln::StagedAlignmentUnitBase< stream_type, derived_type >
static const uint32	WINDOW_SIZE = 32

Member Typedef Documentation

template<uint32 BAND_LEN, typename stream_type >

Definition at line 257 of file batched_stream.h.

template<uint32 BAND_LEN, typename stream_type >

Definition at line 258 of file batched_stream.h.

template<uint32 BAND_LEN, typename stream_type >

Definition at line 259 of file batched_stream.h.

template<uint32 BAND_LEN, typename stream_type >

template<typename pattern_string , typename qual_string , typename text_string , typename sink_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::aln::BandedScoreUnit< BAND_LEN, stream_type >::execute	(	const ScoreStream< stream_type > &	score_stream,
		const uint32	queue_slot,
		const pattern_string	pattern,
		const qual_string	quals,
		const text_string	text,
		const int32	min_score,
		const uint32	window_begin,
		const uint32	window_end,
		sink_type &	sink
	)

inline

Definition at line 268 of file batched_stream.h.

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