Locate

Detailed Description

The functions in this module implement a pipeline stage in which all the previously selected hits (Select) locations are converted from Suffix Array coordinates to linear genome coordinates. In terms of inputs and outputs, this stage takes the HitQueues::seed and HitQueues::loc fields, and rewrite the HitQueues::loc field with the linear value.

inputs:

• HitQueues::seed
• HitQueues::loc

outputs:

• HitQueues::loc

Modules
	LocateDetail

Functions
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 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_init (const BaseScoringPipelineState< ScoringScheme > &pipeline, 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)

Function Documentation

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
	)

Locate the SA row of the the hits in the HitQueues. Since the input might have been sorted to gather locality, the entries in the HitQueues are now specified by an index (idx_queue). This function reads HitQueues::seed and HitQueues::loc fields and rewrites the HitQueues::loc field.

Definition at line 259 of file locate_inl.h.

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
	)

Locate the SA row of the the hits in the HitQueues. Since the input might have been sorted to gather locality, the entries in the HitQueues are now specified by an index (idx_queue). This function reads HitQueues::seed and HitQueues::loc fields and writes the HitQueues::loc and HitQueues::ssa fields with temporary values that can be later consumed by locate_lookup.

Definition at line 282 of file locate_inl.h.

template<typename ScoringScheme >

void nvbio::bowtie2::cuda::locate_init	(	const BaseScoringPipelineState< ScoringScheme > &	pipeline,
		const ParamsPOD	params
	)

Locate the SA row of the the hits in the HitQueues. This function reads HitQueues::seed and HitQueues::loc fields and writes the HitQueues::loc and HitQueues::ssa fields with temporary values that can be later consumed by locate_lookup.

Definition at line 305 of file locate_inl.h.

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
	)

Locate the SA row of the the hits in the HitQueues. Since the input might have been sorted to gather locality, the entries in the HitQueues are now specified by an index (idx_queue). This function reads HitQueues::seed, HitQueues::loc and HitQueues::ssa fields (which must have been previously produced by a call to locate_init) and rewrites the HitQueues::loc field with the final linear coordinate value.

Definition at line 325 of file locate_inl.h.

template<typename ScoringScheme >

void nvbio::bowtie2::cuda::locate_lookup	(	const BaseScoringPipelineState< ScoringScheme > &	pipeline,
		const ParamsPOD	params
	)

Locate the SA row of the the hits in the HitQueues. This function reads HitQueues::seed, HitQueues::loc and HitQueues::ssa fields (which must have been previously produced by a call to locate_init) and rewrites the HitQueues::loc field with the final linear coordinate value.

Definition at line 348 of file locate_inl.h.

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
	)

mark seeds straddling the reference boundaries.

Definition at line 368 of file locate_inl.h.