SampleKmersStage Struct Reference

Detailed description

A small class implementing an nvbio::Pipeline sink stage building the sampled kmers filter

Definition at line 51 of file sample_kmers.h.

#include <sample_kmers.h>

Public Types
typedef io::SequenceDataHost	argument_type

Public Methods
	SampleKmersStage ()
	SampleKmersStage (const int _device, const uint32 _k, const float _alpha, const uint64 _filter_size, uint32 *_filter_storage, SequenceStats *_stats)
bool	process (PipelineContext &context)

Public Members
int	device
uint32	k
float	alpha
uint64	filter_size
uint32 *	filter_storage
SequenceStats *	stats
for_each_enactor< host_tag >	host_for_each
for_each_enactor< device_tag >	device_for_each

Member Typedef Documentation

typedef io::SequenceDataHost SampleKmersStage::argument_type

Definition at line 53 of file sample_kmers.h.

Constructor & Destructor Documentation

SampleKmersStage::SampleKmersStage ( )

inline

empty constructor

Definition at line 57 of file sample_kmers.h.

SampleKmersStage::SampleKmersStage ( const int  _device, const uint32  _k, const float  _alpha, const uint64  _filter_size, uint32 *  _filter_storage, SequenceStats *  _stats  )

inline

constructor

Parameters

_k	kmer length
_alpha	the sampling frequency
_filter_size	the kmer Bloom filter's size, in bits
_filter_storage	the kmer Bloom filter's storage

Definition at line 66 of file sample_kmers.h.

Member Function Documentation

bool SampleKmersStage::process

(

PipelineContext &

context)

process the next batch

Member Data Documentation

float SampleKmersStage::alpha

Definition at line 87 of file sample_kmers.h.

int SampleKmersStage::device

Definition at line 85 of file sample_kmers.h.

for_each_enactor<device_tag> SampleKmersStage::device_for_each

Definition at line 93 of file sample_kmers.h.

uint64 SampleKmersStage::filter_size

Definition at line 88 of file sample_kmers.h.

uint32* SampleKmersStage::filter_storage

Definition at line 89 of file sample_kmers.h.

for_each_enactor<host_tag> SampleKmersStage::host_for_each

Definition at line 92 of file sample_kmers.h.

uint32 SampleKmersStage::k

Definition at line 86 of file sample_kmers.h.

SequenceStats* SampleKmersStage::stats

Definition at line 90 of file sample_kmers.h.

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

• E:/git/nvbio/nvLighter/sample_kmers.h