NVBIO
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A small class implementing an nvbio::Pipeline sink stage building the sampled kmers filter
Definition at line 51 of file sample_kmers.h.
#include <sample_kmers.h>
Public Types | |
typedef io::SequenceDataHost | argument_type |
Public Methods | |
SampleKmersStage () | |
SampleKmersStage (const int _device, const uint32 _k, const float _alpha, const uint64 _filter_size, uint32 *_filter_storage, SequenceStats *_stats) | |
bool | process (PipelineContext &context) |
Public Members | |
int | device |
uint32 | k |
float | alpha |
uint64 | filter_size |
uint32 * | filter_storage |
SequenceStats * | stats |
for_each_enactor< host_tag > | host_for_each |
for_each_enactor< device_tag > | device_for_each |
Definition at line 53 of file sample_kmers.h.
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inline |
empty constructor
Definition at line 57 of file sample_kmers.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 66 of file sample_kmers.h.
bool SampleKmersStage::process | ( | PipelineContext & | context) |
process the next batch
float SampleKmersStage::alpha |
Definition at line 87 of file sample_kmers.h.
int SampleKmersStage::device |
Definition at line 85 of file sample_kmers.h.
for_each_enactor<device_tag> SampleKmersStage::device_for_each |
Definition at line 93 of file sample_kmers.h.
uint64 SampleKmersStage::filter_size |
Definition at line 88 of file sample_kmers.h.
uint32* SampleKmersStage::filter_storage |
Definition at line 89 of file sample_kmers.h.
for_each_enactor<host_tag> SampleKmersStage::host_for_each |
Definition at line 92 of file sample_kmers.h.
uint32 SampleKmersStage::k |
Definition at line 86 of file sample_kmers.h.
SequenceStats* SampleKmersStage::stats |
Definition at line 90 of file sample_kmers.h.