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AlignmentDetail

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

Enumerator
SCORE_STREAM 
OPPOSITE_SCORE_STREAM 
TRACEBACK_STREAM 

Definition at line 114 of file alignment_utils.h.

Function Documentation

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
policyinput paired end policy
anchor0 iff anchor is mate 1, 1 otherwise
anchor_fwtrue iff anchor aligned forward
lefttrue iff opposite mate must be to the left of the anchor
fwtrue iff opposite mate must align forward

Definition at line 62 of file alignment_utils.h.