Detailed Description

The functions in this module implement the very first pipeline stage: seed mapping. In this stage each read is broken up into many short, possibly overlapping seeds which get mapped against the reference genome using an FM-index. The output is a vector of variable-lenth "priority deques", one for each read, containing the set of Suffix Array ranges (SeedHits) where the seeds align, prioritized by the inverse of the range size (see SeedHitDequeArray).

The module implements many mapping algorithms:

exact: allowing exact matches only
approx-hybrid: allowing 0 mismatches in a subseed of the seed, and up to 1 mismatch in the rest
approx-case-pruning: allowing 1 mismatch across the entire seed, using 2 FM-indices to perform the search with case pruning (i.e. searching an alignment with 0 mismatches in the first half of the seed in the forward FM-index, and an alignment with 0 mismatches in the second half in the reverse FM-index).

Modules
	MappingDetail

Functions
void	nvbio::bowtie2::cuda::gather_ranges (const uint32 count, const uint32 n_reads, SeedHitDequeArrayDeviceView hits, const uint32 hit_counts_scan, uint64 out_ranges)

void	nvbio::bowtie2::cuda::map_whole_read (const ReadsDef::type &read_batch, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, const nvbio::cuda::PingPongQueuesView< uint32 > queues, uint8 *reseed, SeedHitDequeArrayDeviceView hits, const ParamsPOD params, const bool fw, const bool rc)

void	nvbio::bowtie2::cuda::map_exact (const ReadsDef::type &read_batch, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, const uint32 retry, const nvbio::cuda::PingPongQueuesView< uint32 > queues, uint8 *reseed, SeedHitDequeArrayDeviceView hits, const ParamsPOD params, const bool fw, const bool rc)

void	nvbio::bowtie2::cuda::map_exact (const ReadsDef::type &read_batch, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, SeedHitDequeArrayDeviceView hits, const uint2 seed_range, const ParamsPOD params, const bool fw, const bool rc)

void	nvbio::bowtie2::cuda::map_approx (const ReadsDef::type &read_batch, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, const uint32 retry, const nvbio::cuda::PingPongQueuesView< uint32 > queues, uint8 *reseed, SeedHitDequeArrayDeviceView hits, const ParamsPOD params, const bool fw, const bool rc)

void	nvbio::bowtie2::cuda::map_approx (const ReadsDef::type &read_batch, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, SeedHitDequeArrayDeviceView hits, const uint2 seed_range, const ParamsPOD params, const bool fw, const bool rc)

void	nvbio::bowtie2::cuda::map (const ReadsDef::type &read_batch, const FMIndexDef::type fmi, const FMIndexDef::type rfmi, const uint32 retry, const nvbio::cuda::PingPongQueuesView< uint32 > queues, uint8 *reseed, SeedHitDequeArrayDeviceView hits, const ParamsPOD params, const bool fw, const bool rc)

template<typename BatchType , typename FMType , typename rFMType >
void	nvbio::bowtie2::cuda::map_whole_read_t (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<typename BatchType , typename FMType , typename rFMType >
void	nvbio::bowtie2::cuda::map_exact_t (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<typename BatchType , typename FMType , typename rFMType >
void	nvbio::bowtie2::cuda::map_exact_t (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 BatchType , typename FMType , typename rFMType >
void	nvbio::bowtie2::cuda::map_case_pruning_t (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<typename BatchType , typename FMType , typename rFMType >
void	nvbio::bowtie2::cuda::map_approx_t (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<typename BatchType , typename FMType , typename rFMType >
void	nvbio::bowtie2::cuda::map_approx_t (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 BatchType , typename FMType , typename rFMType >
void	nvbio::bowtie2::cuda::map_t (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)

Function Documentation

void nvbio::bowtie2::cuda::gather_ranges	(	const uint32	count,
		const uint32	n_reads,
		SeedHitDequeArrayDeviceView	hits,
		const uint32 *	hit_counts_scan,
		uint64 *	out_ranges
	)

For all the seed hit ranges, output the range size in out_ranges.

void nvbio::bowtie2::cuda::map	(	const ReadsDef::type &	read_batch,
		const FMIndexDef::type	fmi,
		const FMIndexDef::type	rfmi,
		const uint32	retry,
		const nvbio::cuda::PingPongQueuesView< uint32 >	queues,
		uint8 *	reseed,
		SeedHitDequeArrayDeviceView	hits,
		const ParamsPOD	params,
		const bool	fw,
		const bool	rc
	)

perform one run of seed mapping

void nvbio::bowtie2::cuda::map_approx	(	const ReadsDef::type &	read_batch,
		const FMIndexDef::type	fmi,
		const FMIndexDef::type	rfmi,
		const uint32	retry,
		const nvbio::cuda::PingPongQueuesView< uint32 >	queues,
		uint8 *	reseed,
		SeedHitDequeArrayDeviceView	hits,
		const ParamsPOD	params,
		const bool	fw,
		const bool	rc
	)

perform one run of approximate seed mapping for all the reads in the input queue, writing reads that need another run in the output queue

void nvbio::bowtie2::cuda::map_approx	(	const ReadsDef::type &	read_batch,
		const FMIndexDef::type	fmi,
		const FMIndexDef::type	rfmi,
		SeedHitDequeArrayDeviceView	hits,
		const uint2	seed_range,
		const ParamsPOD	params,
		const bool	fw,
		const bool	rc
	)

perform multiple runs of approximate seed mapping in one go and keep the best

template<typename BatchType , typename FMType , typename rFMType >

void nvbio::bowtie2::cuda::map_approx_t	(	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
	)

perform one run of approximate seed mapping for all the reads in the input queue, writing reads that need another run in the output queue

Definition at line 721 of file mapping_inl.h.

template<typename BatchType , typename FMType , typename rFMType >

void nvbio::bowtie2::cuda::map_approx_t	(	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
	)

perform multiple runs of approximate seed mapping in one go and keep the best

Definition at line 740 of file mapping_inl.h.

template<typename BatchType , typename FMType , typename rFMType >

void nvbio::bowtie2::cuda::map_case_pruning_t	(	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
	)

perform one run of approximate seed mapping using case pruning for all the reads in the input queue, writing reads that need another run in the output queue

Definition at line 702 of file mapping_inl.h.

void nvbio::bowtie2::cuda::map_exact	(	const ReadsDef::type &	read_batch,
		const FMIndexDef::type	fmi,
		const FMIndexDef::type	rfmi,
		const uint32	retry,
		const nvbio::cuda::PingPongQueuesView< uint32 >	queues,
		uint8 *	reseed,
		SeedHitDequeArrayDeviceView	hits,
		const ParamsPOD	params,
		const bool	fw,
		const bool	rc
	)

perform one run of exact seed mapping for all the reads in the input queue, writing reads that need another run in the output queue

void nvbio::bowtie2::cuda::map_exact	(	const ReadsDef::type &	read_batch,
		const FMIndexDef::type	fmi,
		const FMIndexDef::type	rfmi,
		SeedHitDequeArrayDeviceView	hits,
		const uint2	seed_range,
		const ParamsPOD	params,
		const bool	fw,
		const bool	rc
	)

perform multiple runs of exact seed mapping in one go and keep the best

template<typename BatchType , typename FMType , typename rFMType >

void nvbio::bowtie2::cuda::map_exact_t	(	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
	)

perform one run of exact seed mapping for all the reads in the input queue, writing reads that need another run in the output queue

Definition at line 775 of file mapping_inl.h.

template<typename BatchType , typename FMType , typename rFMType >

void nvbio::bowtie2::cuda::map_exact_t	(	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
	)

perform multiple runs of exact seed mapping in one go and keep the best

Definition at line 794 of file mapping_inl.h.

template<typename BatchType , typename FMType , typename rFMType >

void nvbio::bowtie2::cuda::map_t	(	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
	)

perform one run of seed mapping

Definition at line 811 of file mapping_inl.h.

void nvbio::bowtie2::cuda::map_whole_read	(	const ReadsDef::type &	read_batch,
		const FMIndexDef::type	fmi,
		const FMIndexDef::type	rfmi,
		const nvbio::cuda::PingPongQueuesView< uint32 >	queues,
		uint8 *	reseed,
		SeedHitDequeArrayDeviceView	hits,
		const ParamsPOD	params,
		const bool	fw,
		const bool	rc
	)

perform exact read mapping

template<typename BatchType , typename FMType , typename rFMType >

void nvbio::bowtie2::cuda::map_whole_read_t	(	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
	)

perform exact read mapping

Definition at line 757 of file mapping_inl.h.

Detailed Description

Modules

Functions

Function Documentation