Detailed description

A context class for the score_reduce_kernel to be used in best-approx pipeline.

Implements the basic extension bail-out mechanisms of Bowtie2, namely stopping when a given number of extensions of a read failed in a row. This is done keeping a vector of per-read extension 'trys' counters, which start from the maximum allowed number, and get decremented towards zero upon each failure, or reset upon successful extensions.

Definition at line 63 of file reduce.h.

#include <reduce.h>

Public Methods
	ReduceBestApproxContext (uint32 *trys, const uint32 n_ext)

NVBIO_FORCEINLINE NVBIO_DEVICE void	best_score (const uint32 read_id, const ParamsPOD &params) const

NVBIO_FORCEINLINE NVBIO_DEVICE void	second_score (const uint32 read_id, const ParamsPOD &params) const

NVBIO_FORCEINLINE NVBIO_DEVICE bool	failure (const uint32 idx, const uint32 read_id, const uint32 top_flag, const ParamsPOD &params) const

Constructor & Destructor Documentation

nvbio::bowtie2::cuda::ReduceBestApproxContext::ReduceBestApproxContext	(	uint32 *	trys,
		const uint32	n_ext
	)

inline

constructor

Parameters

trys	trys vector
n_ext	total number of extensions (i.e. extension loops) already performed

Definition at line 70 of file reduce.h.

Member Function Documentation

NVBIO_FORCEINLINE NVBIO_DEVICE void nvbio::bowtie2::cuda::ReduceBestApproxContext::best_score	(	const uint32	read_id,
		const ParamsPOD &	params
	)		const

inline

this method is called from score_reduce_kernel to report updates to the best score.

Definition at line 75 of file reduce.h.

NVBIO_FORCEINLINE NVBIO_DEVICE bool nvbio::bowtie2::cuda::ReduceBestApproxContext::failure	(	const uint32	idx,
		const uint32	read_id,
		const uint32	top_flag,
		const ParamsPOD &	params
	)		const

inline

this method is called from score_reduce_kernel to report extension failures.

Definition at line 91 of file reduce.h.

NVBIO_FORCEINLINE NVBIO_DEVICE void nvbio::bowtie2::cuda::ReduceBestApproxContext::second_score	(	const uint32	read_id,
		const ParamsPOD &	params
	)		const

inline

this method is called from score_reduce_kernel to report updates to the second best score.

Definition at line 83 of file reduce.h.

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

E:/git/nvbio/nvBowtie/bowtie2/cuda/reduce.h

Detailed description

Public Methods

Constructor & Destructor Documentation

Member Function Documentation