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 uint32 *	sampled_filter_storage
uint64	trusted_filter_size
uint32 *	trusted_filter_storage
const uint32 *	threshold
SequenceStats *	stats
for_each_enactor< host_tag >	host_for_each
for_each_enactor< device_tag >	device_for_each

Member Typedef Documentation

typedef io::SequenceDataHost TrustedKmersStage::argument_type

Definition at line 102 of file sample_kmers.h.

Constructor & Destructor Documentation

TrustedKmersStage::TrustedKmersStage ( )

inline

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  )

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 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.

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

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