nvLighter

Detailed Description

This module contains all of nvLighter's class hierarchy. nvLighter is composed of the following important pieces:

• the BloomFilters class, containing all the per-device data needed during nvLighter's execution, i.e. the sampled and trusted kmers Bloom filters and the error correction statistics
• the InputStage, i.e. an object encapsulating an nvbio::Pipeline stage loading read batches
• the OutputStage, i.e. an object encapsulating an nvbio::Pipeline stage writing read batches
• the SampleKmersStage, i.e. an object encapsulating an nvbio::Pipeline stage performing kmer sampling
• the TrustedKmersStage, i.e. an object encapsulating an nvbio::Pipeline stage performing trusted kmer marking
• the ErrorCorrectStage, i.e. an object encapsulating an nvbio::Pipeline stage performing the actual error correction

Classes
struct	BloomFilters< system_tag >
struct	block_occupancy_functor
struct	ErrorCorrectStage
struct	InputStageData
struct	InputStage
struct	OutputStageData
struct	OutputStage
struct	SampleKmersStage
struct	TrustedKmersStage

Enumerations
enum	KmersType { SAMPLED_KMERS = 0, TRUSTED_KMERS = 1 }

Functions
void	merge (BloomFilters< host_tag > *h_bloom_filters, const uint32 device_count, BloomFilters< device_tag > *d_bloom_filters, const KmersType type)
void	merged_stats (const BloomFilters< host_tag > *h_bloom_filters, const uint32 device_count, const BloomFilters< device_tag > *d_bloom_filters, nvbio::vector< host_tag, uint64 > &stats)
template<typename system_tag >
void	compute_bloom_filter_stats (const BloomFilters< system_tag > &bloom_filters, const KmersType type, const uint32 K, float &occupancy, float &approx_size, float &fp)

Enumeration Type Documentation

enum KmersType

The kmer Bloom filter types

Enumerator
SAMPLED_KMERS
TRUSTED_KMERS

Definition at line 61 of file bloom_filters.h.

Function Documentation

template<typename system_tag >

void compute_bloom_filter_stats	(	const BloomFilters< system_tag > &	bloom_filters,
		const KmersType	type,
		const uint32	K,
		float &	occupancy,
		float &	approx_size,
		float &	fp
	)

compute Bloom filter usage statistics

Definition at line 253 of file bloom_filters.h.

void merge ( BloomFilters< host_tag > *  h_bloom_filters, const uint32  device_count, BloomFilters< device_tag > *  d_bloom_filters, const KmersType  type  )

inline

merge several Bloom filters

Definition at line 154 of file bloom_filters.h.

void merged_stats ( const BloomFilters< host_tag > *  h_bloom_filters, const uint32  device_count, const BloomFilters< device_tag > *  d_bloom_filters, nvbio::vector< host_tag, uint64 > &  stats  )

inline

merge several stats

Definition at line 208 of file bloom_filters.h.