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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
for_each_enactor< host_taghost_for_each
for_each_enactor< device_tagdevice_for_each

Member Typedef Documentation

Definition at line 53 of file sample_kmers.h.

Constructor & Destructor Documentation

SampleKmersStage::SampleKmersStage ( )

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 


_kkmer length
_alphathe sampling frequency
_filter_sizethe kmer Bloom filter's size, in bits
_filter_storagethe 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.

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