Detailed Description

Classes
struct	nvbio::bowtie2::cuda::detail::Backtracker< vector >

struct	nvbio::bowtie2::cuda::detail::AlignmentStrings< AlignerType, PipelineType >

struct	nvbio::bowtie2::cuda::detail::AlignmentStreamContext< TYPE >

struct	nvbio::bowtie2::cuda::detail::AlignmentStreamContext< SCORE_STREAM >

struct	nvbio::bowtie2::cuda::detail::AlignmentStreamContext< OPPOSITE_SCORE_STREAM >

struct	nvbio::bowtie2::cuda::detail::AlignmentStreamContext< TRACEBACK_STREAM >

struct	nvbio::bowtie2::cuda::detail::AlignmentStreamBase< TYPE, AlignerType, PipelineType >

Enumerations
enum	nvbio::bowtie2::cuda::detail::AlignmentStreamType { nvbio::bowtie2::cuda::detail::SCORE_STREAM = 0, nvbio::bowtie2::cuda::detail::OPPOSITE_SCORE_STREAM = 1, nvbio::bowtie2::cuda::detail::TRACEBACK_STREAM = 2 }

Functions
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	nvbio::bowtie2::cuda::detail::frame_opposite_mate (const int policy, const uint32 anchor, const bool anchor_fw, bool &left, bool &fw)

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	nvbio::bowtie2::cuda::detail::compute_target_score (const io::BestPairedAlignments &best, const int32 a_worst_score, const int32 o_worst_score)

Enumeration Type Documentation

Definition at line 114 of file alignment_utils.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 nvbio::bowtie2::cuda::detail::compute_target_score	(	const io::BestPairedAlignments &	best,
		const int32	a_worst_score,
		const int32	o_worst_score
	)

compute the target minimum score for a valid extension of a paired-end alignment

Definition at line 104 of file alignment_utils.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::bowtie2::cuda::detail::frame_opposite_mate	(	const int	policy,
		const uint32	anchor,
		const bool	anchor_fw,
		bool &	left,
		bool &	fw
	)

Frame the opposite mate alignment's direction & orientation

Parameters

policy	input paired end policy
anchor	0 iff anchor is mate 1, 1 otherwise
anchor_fw	true iff anchor aligned forward
left	true iff opposite mate must be to the left of the anchor
fw	true iff opposite mate must align forward

Definition at line 62 of file alignment_utils.h.