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LocateDetail

Detailed Description

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)
 

Function Documentation

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 
)

transform an SA index to linear coordinates using either the forward or reverse FM-index

Definition at line 55 of file locate_inl.h.

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 
)

first pass of a two pass method to transform an SA index to linear coordinates using either the forward or reverse FM-index

Definition at line 78 of file locate_inl.h.

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 
)

Locate the next SA row in the queue. Since the input loc_queue might have been sorted to gather locality, the corresponding entry in seed_queue is now specified by an index (idx_queue).

Definition at line 154 of file locate_inl.h.

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 
)

Locate the next SA row in the queue. Since the input loc_queue might have been sorted to gather locality, the corresponding entry in seed_queue is now specified by an index (idx_queue).

Definition at line 123 of file locate_inl.h.

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 
)

second pass of a two pass method to transform an SA index to linear coordinates using either the forward or reverse FM-index

Definition at line 99 of file locate_inl.h.

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 
)

Locate the next SA row in the queue. Since the input loc_queue might have been sorted to gather locality, the corresponding entry in seed_queue is now specified by an index (idx_queue).

Definition at line 184 of file locate_inl.h.

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 
)

mark seeds straddling the reference boundaries.

Definition at line 214 of file locate_inl.h.