traceback.h File Reference

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

Go to the source code of this file.

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)