locate_inl.h File Reference

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

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

Functions
template<typename FMType , typename rFMType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::bowtie2::cuda::detail::locate (const FMType &fmi, const rFMType &rfmi, const uint32 dir, const uint32 r)
template<typename FMType , typename rFMType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint2	nvbio::bowtie2::cuda::detail::locate_init (const FMType &fmi, const rFMType &rfmi, const uint32 dir, const uint32 r)
template<typename FMType , typename rFMType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nvbio::bowtie2::cuda::detail::locate_lookup (const FMType &fmi, const rFMType &rfmi, const uint32 dir, const uint2 it)
template<typename BatchType , typename FMType , typename rFMType >
__global__ void	nvbio::bowtie2::cuda::detail::locate_kernel (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 >
__global__ void	nvbio::bowtie2::cuda::detail::locate_init_kernel (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 >
__global__ void	nvbio::bowtie2::cuda::detail::locate_lookup_kernel (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 index_iterator , typename flags_iterator >
__global__ void	nvbio::bowtie2::cuda::detail::mark_straddling_kernel (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)
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 ScoringScheme >
void	nvbio::bowtie2::cuda::locate_init (const BaseScoringPipelineState< ScoringScheme > &pipeline, 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_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)