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ErrorCorrectStage Struct Reference

Detailed description

A small class implementing an nvbio::Pipeline stage performing the actual error correction work

Definition at line 51 of file error_correct.h.

#include <error_correct.h>

Public Types

typedef io::SequenceDataHost argument_type
typedef io::SequenceDataHost return_type

Public Methods

 ErrorCorrectStage ()
 ErrorCorrectStage (const int _device, const uint32 _k, const uint64 _trusted_filter_size, const uint32 *_trusted_filter_storage, uint64 *_stats_vec, const float _max_correction, const char _bad_quality, const char _new_quality, SequenceStats *_stats)
bool process (PipelineContext &context)

Public Members

int device
uint32 k
uint64 trusted_filter_size
const uint32trusted_filter_storage
float max_correction
char bad_quality
char new_quality
for_each_enactor< host_taghost_for_each
for_each_enactor< device_tagdevice_for_each

Member Typedef Documentation

Definition at line 53 of file error_correct.h.

Definition at line 54 of file error_correct.h.

Constructor & Destructor Documentation

ErrorCorrectStage::ErrorCorrectStage ( )

empty constructor

Definition at line 58 of file error_correct.h.

ErrorCorrectStage::ErrorCorrectStage ( const int  _device,
const uint32  _k,
const uint64  _trusted_filter_size,
const uint32 _trusted_filter_storage,
uint64 _stats_vec,
const float  _max_correction,
const char  _bad_quality,
const char  _new_quality,
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 67 of file error_correct.h.

Member Function Documentation

bool ErrorCorrectStage::process ( PipelineContext context)

process the next batch

Member Data Documentation

char ErrorCorrectStage::bad_quality

Definition at line 98 of file error_correct.h.

int ErrorCorrectStage::device

Definition at line 92 of file error_correct.h.

for_each_enactor<device_tag> ErrorCorrectStage::device_for_each

Definition at line 103 of file error_correct.h.

for_each_enactor<host_tag> ErrorCorrectStage::host_for_each

Definition at line 102 of file error_correct.h.

uint32 ErrorCorrectStage::k

Definition at line 93 of file error_correct.h.

float ErrorCorrectStage::max_correction

Definition at line 97 of file error_correct.h.

char ErrorCorrectStage::new_quality

Definition at line 99 of file error_correct.h.

SequenceStats* ErrorCorrectStage::stats

Definition at line 100 of file error_correct.h.

uint64* ErrorCorrectStage::stats_vec

Definition at line 96 of file error_correct.h.

uint64 ErrorCorrectStage::trusted_filter_size

Definition at line 94 of file error_correct.h.

const uint32* ErrorCorrectStage::trusted_filter_storage

Definition at line 95 of file error_correct.h.

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