locate.h File Reference

#include <nvBowtie/bowtie2/cuda/defs.h>
#include <nvBowtie/bowtie2/cuda/params.h>
#include <nvbio/io/alignments.h>
#include <nvBowtie/bowtie2/cuda/locate_inl.h>

Go to the source code of this file.

Classes
struct	nvbio::bowtie2::cuda::BaseScoringPipelineState< ScoringScheme >
struct	nvbio::bowtie2::cuda::BestApproxScoringPipelineState< ScoringScheme >

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

Functions
template<typename BatchType , typename FMType , typename rFMType >
void	nvbio::bowtie2::cuda::locate (const BatchType read_batch, const FMType fmi, const rFMType rfmi, const uint32 in_count, const uint32 *idx_queue, HitQueuesDeviceView hits, const ParamsPOD params)
template<typename BatchType , typename FMType , typename rFMType >
void	nvbio::bowtie2::cuda::locate_init (const BatchType read_batch, const FMType fmi, const rFMType rfmi, const uint32 in_count, const uint32 *idx_queue, HitQueuesDeviceView hits, const ParamsPOD params)
template<typename BatchType , typename FMType , typename rFMType >
void	nvbio::bowtie2::cuda::locate_lookup (const BatchType read_batch, const FMType fmi, const rFMType rfmi, const uint32 in_count, const uint32 *idx_queue, HitQueuesDeviceView hits, const ParamsPOD params)
template<typename ScoringScheme >
void	nvbio::bowtie2::cuda::locate_init (const BaseScoringPipelineState< ScoringScheme > &pipeline, const ParamsPOD params)
template<typename ScoringScheme >
void	nvbio::bowtie2::cuda::locate_lookup (const BaseScoringPipelineState< ScoringScheme > &pipeline, const ParamsPOD params)
template<typename index_iterator , typename flags_iterator >
void	nvbio::bowtie2::cuda::mark_straddling (const uint32 in_count, const uint32 *idx_queue, const uint32 reference_count, const index_iterator reference_index, HitQueuesDeviceView hits, flags_iterator flags, const ParamsPOD params)