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TrustedKmersStage Struct Reference

Detailed description

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

Definition at line 100 of file sample_kmers.h.

#include <sample_kmers.h>

Public Types

typedef io::SequenceDataHost argument_type

Public Methods

 TrustedKmersStage ()
 TrustedKmersStage (const int _device, const uint32 _k, const uint64 _sampled_filter_size, const uint32 *_sampled_filter_storage, const uint64 _trusted_filter_size, uint32 *_trusted_filter_storage, const uint32 *_threshold, SequenceStats *_stats)
bool process (PipelineContext &context)

Public Members

int device
uint32 k
uint64 sampled_filter_size
const uint32sampled_filter_storage
uint64 trusted_filter_size
const uint32threshold
for_each_enactor< host_taghost_for_each
for_each_enactor< device_tagdevice_for_each

Member Typedef Documentation

Definition at line 102 of file sample_kmers.h.

Constructor & Destructor Documentation

TrustedKmersStage::TrustedKmersStage ( )

default constructor

Definition at line 106 of file sample_kmers.h.

TrustedKmersStage::TrustedKmersStage ( const int  _device,
const uint32  _k,
const uint64  _sampled_filter_size,
const uint32 _sampled_filter_storage,
const uint64  _trusted_filter_size,
uint32 _trusted_filter_storage,
const uint32 _threshold,
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 115 of file sample_kmers.h.

Member Function Documentation

bool TrustedKmersStage::process ( PipelineContext context)

process the next batch

Member Data Documentation

int TrustedKmersStage::device

Definition at line 138 of file sample_kmers.h.

for_each_enactor<device_tag> TrustedKmersStage::device_for_each

Definition at line 148 of file sample_kmers.h.

for_each_enactor<host_tag> TrustedKmersStage::host_for_each

Definition at line 147 of file sample_kmers.h.

uint32 TrustedKmersStage::k

Definition at line 139 of file sample_kmers.h.

uint64 TrustedKmersStage::sampled_filter_size

Definition at line 140 of file sample_kmers.h.

const uint32* TrustedKmersStage::sampled_filter_storage

Definition at line 141 of file sample_kmers.h.

SequenceStats* TrustedKmersStage::stats

Definition at line 145 of file sample_kmers.h.

const uint32* TrustedKmersStage::threshold

Definition at line 144 of file sample_kmers.h.

uint64 TrustedKmersStage::trusted_filter_size

Definition at line 142 of file sample_kmers.h.

uint32* TrustedKmersStage::trusted_filter_storage

Definition at line 143 of file sample_kmers.h.

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