NVBIO
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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 uint32 * | trusted_filter_storage |
uint64 * | stats_vec |
float | max_correction |
char | bad_quality |
char | new_quality |
SequenceStats * | stats |
for_each_enactor< host_tag > | host_for_each |
for_each_enactor< device_tag > | device_for_each |
Definition at line 53 of file error_correct.h.
Definition at line 54 of file error_correct.h.
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inline |
empty constructor
Definition at line 58 of file error_correct.h.
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inline |
constructor
_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 67 of file error_correct.h.
bool ErrorCorrectStage::process | ( | PipelineContext & | context) |
process the next batch
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.
Definition at line 95 of file error_correct.h.