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traceback.h File Reference
#include <nvBowtie/bowtie2/cuda/defs.h>
#include <nvBowtie/bowtie2/cuda/scoring.h>

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Classes

struct  nvbio::bowtie2::cuda::TracebackPipelineState< ScoringScheme >
 
struct  nvbio::bowtie2::cuda::AllMappingPipelineState< ScoringScheme >
 

Namespaces

 nvbio
 Define a vector_view POD type and plain_view() for std::vector.
 
 nvbio::io
 
 nvbio::bowtie2
 
 nvbio::bowtie2::cuda
 

Functions

void nvbio::bowtie2::cuda::banded_traceback_best (const uint32 aln_idx, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const TracebackPipelineState< EditDistanceScoringScheme > &pipeline, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::banded_traceback_best (const uint32 aln_idx, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const TracebackPipelineState< SmithWatermanScoringScheme<> > &pipeline, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::opposite_traceback_best (const uint32 aln_idx, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const TracebackPipelineState< EditDistanceScoringScheme > &pipeline, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::opposite_traceback_best (const uint32 aln_idx, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const TracebackPipelineState< SmithWatermanScoringScheme<> > &pipeline, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::banded_traceback_all (const uint32 count, const uint32 *idx, const uint32 buffer_offset, const uint32 buffer_size, io::Alignment *alignments, const uint32 band_len, const AllMappingPipelineState< EditDistanceScoringScheme > &pipeline, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::banded_traceback_all (const uint32 count, const uint32 *idx, const uint32 buffer_offset, const uint32 buffer_size, io::Alignment *alignments, const uint32 band_len, const AllMappingPipelineState< SmithWatermanScoringScheme<> > &pipeline, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::finish_alignment_best (const uint32 aln_idx, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const TracebackPipelineState< EditDistanceScoringScheme > &pipeline, const SmithWatermanScoringScheme<> scoring_scheme, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::finish_alignment_best (const uint32 aln_idx, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const TracebackPipelineState< SmithWatermanScoringScheme<> > &pipeline, const SmithWatermanScoringScheme<> scoring_scheme, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::finish_opposite_alignment_best (const uint32 aln_idx, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const TracebackPipelineState< EditDistanceScoringScheme > &pipeline, const SmithWatermanScoringScheme<> scoring_scheme, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::finish_opposite_alignment_best (const uint32 aln_idx, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const TracebackPipelineState< SmithWatermanScoringScheme<> > &pipeline, const SmithWatermanScoringScheme<> scoring_scheme, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::finish_alignment_all (const uint32 count, const uint32 *idx, const uint32 buffer_offset, const uint32 buffer_size, io::Alignment *alignments, const uint32 band_len, const AllMappingPipelineState< EditDistanceScoringScheme > &pipeline, const SmithWatermanScoringScheme<> scoring_scheme, const ParamsPOD &params)
 
void nvbio::bowtie2::cuda::finish_alignment_all (const uint32 count, const uint32 *idx, const uint32 buffer_offset, const uint32 buffer_size, io::Alignment *alignments, const uint32 band_len, const AllMappingPipelineState< SmithWatermanScoringScheme<> > &pipeline, const SmithWatermanScoringScheme<> scoring_scheme, const ParamsPOD &params)