nvbio::bowtie2::cuda::detail Namespace Reference

Classes
struct	Backtracker
struct	AlignmentStrings
struct	AlignmentStreamContext
struct	AlignmentStreamContext< SCORE_STREAM >
struct	AlignmentStreamContext< OPPOSITE_SCORE_STREAM >
struct	AlignmentStreamContext< TRACEBACK_STREAM >
struct	AlignmentStreamBase
struct	seed_mapper
	abstract seed-mapper interface More...
struct	seed_mapper< EXACT_MAPPING >
struct	seed_mapper< APPROX_MAPPING >
struct	seed_mapper< CASE_PRUNING_MAPPING >
struct	AllScoreStream
struct	BestScoreStream
struct	BestOppositeScoreStream
struct	BestAnchorScoreStream
struct	BestTracebackStream
struct	AllTracebackStream

Enumerations
enum	AlignmentStreamType { SCORE_STREAM = 0, OPPOSITE_SCORE_STREAM = 1, TRACEBACK_STREAM = 2 }
enum	{ CHECK_EXACT =1u, IGNORE_EXACT =0u }
enum	MappingAlgorithm { EXACT_MAPPING = 0u, APPROX_MAPPING = 1u, CASE_PRUNING_MAPPING = 2u }

Functions
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	frame_opposite_mate (const int policy, const uint32 anchor, const bool anchor_fw, bool &left, bool &fw)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	compute_target_score (const io::BestPairedAlignments &best, const int32 a_worst_score, const int32 o_worst_score)
template<typename FMType , typename rFMType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	locate (const FMType &fmi, const rFMType &rfmi, const uint32 dir, const uint32 r)
template<typename FMType , typename rFMType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint2	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	locate_lookup (const FMType &fmi, const rFMType &rfmi, const uint32 dir, const uint2 it)
template<typename BatchType , typename FMType , typename rFMType >
__global__ void	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	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	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	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 ReadStream >
NVBIO_DEVICE NVBIO_FORCEINLINE bool	check_N (const ReadStream &seed, const uint32 exact_len, const uint32 seed_len)
template<typename FMType , typename StreamType >
NVBIO_DEVICE NVBIO_FORCEINLINE uint2	match_range (uint2 range, const FMType index, StreamType query, uint32 begin, uint32 end)
NVBIO_DEVICE NVBIO_FORCEINLINE void	store_deque (SeedHitDequeArrayDeviceView hit_deques, const uint32 read_id, const uint32 n_hits, const SeedHit *hitstorage)
template<bool find_exact, typename Stream , typename FMType , typename HitType >
NVBIO_DEVICE NVBIO_FORCEINLINE void	map (const Stream query, uint32 len1, const uint32 len2, const FMType index, const SeedHit::Flags hit_flags, HitType &hitheap, uint32 max_hits, uint32 &range_sum, uint32 &range_count)
template<typename BatchType , typename FMType , typename rFMType >
__global__ void	map_whole_read_kernel (const BatchType read_batch, const FMType fmi, const rFMType rfmi, const nvbio::cuda::PingPongQueuesView< uint32 > queues, uint8 *reseed, SeedHitDequeArrayDeviceView hits, const ParamsPOD params, const bool fw, const bool rc)
template<MappingAlgorithm ALGO, typename BatchType , typename FMType , typename rFMType >
__global__ void	map_queues_kernel (const BatchType read_batch, const FMType fmi, const rFMType rfmi, const uint32 retry, const nvbio::cuda::PingPongQueuesView< uint32 > queues, uint8 *reseed, SeedHitDequeArrayDeviceView hits, const ParamsPOD params, const bool fw, const bool rc)
template<MappingAlgorithm ALGO, typename BatchType , typename FMType , typename rFMType >
__global__ void	map_kernel (const BatchType read_batch, const FMType fmi, const rFMType rfmi, SeedHitDequeArrayDeviceView hits, const uint2 seed_range, const ParamsPOD params, const bool fw, const bool rc)
template<typename ScoringScheme , typename PipelineType , typename ReduceContext >
__global__ void	score_reduce_kernel (const ReduceContext context, PipelineType pipeline, const ParamsPOD params)
template<typename ReduceContext >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	update_best (const uint32 read_id, io::BestPairedAlignments &best_pairs, const io::PairedAlignments &pair, ReduceContext &context, const ParamsPOD params)
template<typename ReduceContext >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	replace_best (const uint32 read_id, io::BestPairedAlignments &best_pairs, const io::PairedAlignments &pair, ReduceContext &context, const ParamsPOD params)
template<typename ReduceContext >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	update_second (const uint32 read_id, io::BestPairedAlignments &best_pairs, const io::PairedAlignments &pair, ReduceContext &context, const ParamsPOD params)
template<typename ReduceContext >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	try_update (const uint32 read_id, io::BestPairedAlignments &best_pairs, const io::PairedAlignments &pair, const uint32 min_distance, ReduceContext &context, const ParamsPOD params)
template<typename ReduceContext >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	update_best (const uint32 read_id, io::Alignment &a1, io::Alignment &a2, const io::Alignment &a, ReduceContext &context, const ParamsPOD params)
template<typename ReduceContext >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	replace_best (const uint32 read_id, io::Alignment &a1, io::Alignment &a2, const io::Alignment &a, ReduceContext &context, const ParamsPOD params)
template<typename ReduceContext >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	update_second (const uint32 read_id, io::Alignment &a1, io::Alignment &a2, const io::Alignment &a, ReduceContext &context, const ParamsPOD params)
template<typename ReduceContext >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	try_update (const uint32 read_id, io::Alignment &a1, io::Alignment &a2, const io::Alignment &a, const uint32 min_distance, ReduceContext &context, const ParamsPOD params)
template<typename ScoringScheme , typename PipelineType , typename ReduceContext >
__global__ void	score_reduce_paired_kernel (const ReduceContext context, PipelineType pipeline, const ParamsPOD params)
template<typename aligner_type , typename pipeline_type >
void	banded_score_all (const uint32 band_len, const pipeline_type &pipeline, const aligner_type aligner, const ParamsPOD params, const uint32 buffer_offset, const uint32 buffer_size, uint32 *counter)
template<typename aligner_type , typename pipeline_type >
void	banded_score_best (const uint32 band_len, const pipeline_type &pipeline, const aligner_type aligner, const ParamsPOD params)
template<typename aligner_type , typename pipeline_type >
void	opposite_score_best (const pipeline_type &pipeline, const aligner_type aligner, const ParamsPOD params)
template<typename aligner_type , typename pipeline_type >
void	banded_anchor_score_best (const uint32 band_len, const pipeline_type &pipeline, const aligner_type aligner, const ParamsPOD params)
template<uint32 ALN_IDX, typename aligner_type , typename pipeline_type >
void	banded_traceback_best (const MateType mate_type, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const pipeline_type &pipeline, const aligner_type aligner, const ParamsPOD params)
template<uint32 ALN_IDX, typename aligner_type , typename pipeline_type >
void	traceback_best (const MateType mate_type, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const pipeline_type &pipeline, const aligner_type aligner, const ParamsPOD params)
template<typename aligner_type , typename pipeline_type >
void	banded_traceback_all (const uint32 count, const uint32 *idx, const uint32 buffer_offset, const uint32 buffer_size, io::Alignment *alignments, const uint32 band_len, const pipeline_type &pipeline, const aligner_type aligner, const ParamsPOD params)
template<typename stream_type , typename scheme_type , typename pipeline_type >
__global__ void	finish_alignment_kernel (stream_type stream, pipeline_type pipeline, const scheme_type scoring_scheme, const ParamsPOD params)
template<uint32 ALN_IDX, typename scheme_type , typename pipeline_type >
void	finish_alignment_best (const MateType mate_type, const uint32 count, const uint32 *idx, io::Alignment *best_data, const uint32 best_stride, const uint32 band_len, const pipeline_type &pipeline, const scheme_type scoring_scheme, const ParamsPOD params)
template<typename scheme_type , typename pipeline_type >
void	finish_alignment_all (const uint32 count, const uint32 *idx, const uint32 buffer_offset, const uint32 buffer_size, io::Alignment *alignments, const uint32 band_len, const pipeline_type &pipeline, const scheme_type scoring_scheme, const ParamsPOD params)