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nvbio::bowtie2::cuda::ReduceBestApproxContext Struct Reference

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
trystrys vector
n_exttotal 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: