aligner_inst.h File Reference

#include <nvBowtie/bowtie2/cuda/aligner.h>
#include <nvBowtie/bowtie2/cuda/fmindex_def.h>
#include <nvBowtie/bowtie2/cuda/scoring.h>

Go to the source code of this file.

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

Functions
void	nvbio::bowtie2::cuda::all_ed (Aligner &aligner, const Params &params, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, const UberScoringScheme &scoring_scheme, const io::SequenceDataDevice &reference_data, const io::FMIndexDataDevice &driver_data, io::SequenceDataDevice &read_data, io::HostOutputBatchSE &cpu_batch, Stats &stats)
void	nvbio::bowtie2::cuda::all_sw (Aligner &aligner, const Params &params, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, const UberScoringScheme &scoring_scheme, const io::SequenceDataDevice &reference_data, const io::FMIndexDataDevice &driver_data, io::SequenceDataDevice &read_data, io::HostOutputBatchSE &cpu_batch, Stats &stats)
void	nvbio::bowtie2::cuda::best_approx_ed (Aligner &aligner, const Params &params, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, const UberScoringScheme &scoring_scheme, const io::SequenceDataDevice &reference_data, const io::FMIndexDataDevice &driver_data, io::SequenceDataDevice &read_data, io::HostOutputBatchSE &cpu_batch, Stats &stats)
void	nvbio::bowtie2::cuda::best_approx_sw (Aligner &aligner, const Params &params, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, const UberScoringScheme &scoring_scheme, const io::SequenceDataDevice &reference_data, const io::FMIndexDataDevice &driver_data, io::SequenceDataDevice &read_data, io::HostOutputBatchSE &cpu_batch, Stats &stats)
void	nvbio::bowtie2::cuda::best_approx_ed (Aligner &aligner, const Params &params, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, const UberScoringScheme &scoring_scheme, const io::SequenceDataDevice &reference_data, const io::FMIndexDataDevice &driver_data, io::SequenceDataDevice &read_data1, io::SequenceDataDevice &read_data2, io::HostOutputBatchPE &cpu_batch, Stats &stats)
void	nvbio::bowtie2::cuda::best_approx_sw (Aligner &aligner, const Params &params, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, const UberScoringScheme &scoring_scheme, const io::SequenceDataDevice &reference_data, const io::FMIndexDataDevice &driver_data, io::SequenceDataDevice &read_data1, io::SequenceDataDevice &read_data2, io::HostOutputBatchPE &cpu_batch, Stats &stats)