NVBIO
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DeviceStagedThreadScheduler specialization of BatchedBandedAlignmentScore.
stream_type | the stream of alignment jobs |
Definition at line 171 of file batched_banded_inl.h.
#include <batched_banded_inl.h>
Public Types | |
typedef stream_type::aligner_type | aligner_type |
typedef checkpoint_storage_type < aligner_type >::type | cell_type |
Public Methods | |
void | enact (stream_type stream, uint64 temp_size=0u, uint8 *temp=NULL) |
Static Public Methods | |
static uint32 | column_storage (const uint32 max_pattern_len, const uint32 max_text_len) |
static uint64 | min_temp_storage (const uint32 max_pattern_len, const uint32 max_text_len, const uint32 stream_size) |
static uint64 | max_temp_storage (const uint32 max_pattern_len, const uint32 max_text_len, const uint32 stream_size) |
Static Public Members | |
static const uint32 | BLOCKDIM = 128 |
typedef stream_type::aligner_type nvbio::aln::BatchedBandedAlignmentScore< BAND_LEN, stream_type, DeviceStagedThreadScheduler >::aligner_type |
Definition at line 175 of file batched_banded_inl.h.
typedef checkpoint_storage_type<aligner_type>::type nvbio::aln::BatchedBandedAlignmentScore< BAND_LEN, stream_type, DeviceStagedThreadScheduler >::cell_type |
Definition at line 176 of file batched_banded_inl.h.
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inlinestatic |
return the per-element column storage size
Definition at line 180 of file batched_banded_inl.h.
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inline |
enact the batch execution
Definition at line 203 of file batched_banded_inl.h.
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inlinestatic |
return the maximum number of bytes required by the algorithm
Definition at line 196 of file batched_banded_inl.h.
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inlinestatic |
return the minimum number of bytes required by the algorithm
Definition at line 189 of file batched_banded_inl.h.
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static |
Definition at line 173 of file batched_banded_inl.h.