batched_banded_inl.h File Reference

#include <nvbio/basic/types.h>
#include <nvbio/basic/thrust_view.h>
#include <nvbio/alignment/utils.h>
#include <nvbio/basic/cuda/work_queue.h>
#include <nvbio/basic/strided_iterator.h>
#include <nvbio/alignment/batched_stream.h>

Go to the source code of this file.

Classes
struct	nvbio::aln::BatchedBandedAlignmentScore< BAND_LEN, stream_type, HostThreadScheduler >
struct	nvbio::aln::BatchedBandedAlignmentScore< BAND_LEN, stream_type, DeviceThreadBlockScheduler< BLOCKDIM, MINBLOCKS > >
struct	nvbio::aln::BatchedBandedAlignmentScore< BAND_LEN, stream_type, DeviceStagedThreadScheduler >
struct	nvbio::aln::BatchedBandedAlignmentTraceback< BAND_LEN, CHECKPOINTS, stream_type, DeviceThreadScheduler >

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

Functions
template<uint32 BAND_LEN, typename stream_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::aln::batched_banded_alignment_score (const stream_type &stream, const uint32 work_id)
template<uint32 BLOCKDIM, uint32 MINBLOCKS, uint32 BAND_LEN, typename stream_type >
__global__ void	nvbio::aln::__launch_bounds__ (BLOCKDIM, MINBLOCKS) batched_banded_alignment_score_kernel(const stream_type stream)
template<uint32 BAND_LEN, uint32 CHECKPOINTS, typename stream_type , typename cell_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::aln::batched_banded_alignment_traceback (stream_type &stream, cell_type *checkpoints, uint32 *submatrices, const uint32 stride, const uint32 work_id, const uint32 thread_id)
template<uint32 BLOCKDIM, uint32 BAND_LEN, uint32 CHECKPOINTS, typename stream_type , typename cell_type >
__global__ void	nvbio::aln::batched_banded_alignment_traceback_kernel (stream_type stream, cell_type *checkpoints, uint32 *submatrices, const uint32 stride)
template<uint32 BLOCKDIM, uint32 BAND_LEN, uint32 CHECKPOINTS, typename stream_type , typename cell_type >
__global__ void	nvbio::aln::persistent_banded_batched_alignment_traceback_kernel (stream_type stream, cell_type *checkpoints, uint32 *submatrices, const uint32 stride)