nvbio::bowtie2::cuda::EditDistanceScoringScheme Struct Reference

Detailed description

This class implements an edit-distance based scoring scheme for short read alignment. While the original bowtie2 code base always performs alignment using Gotoh's algorithm (i.e. Smith-Waterman with affine gap penalties), nvBowtie also supports edit-distance, which is sometimes better suited for very short reads (e.g. ~100bps).

Definition at line 133 of file scoring.h.

#include <scoring.h>

Public Types
typedef EditDistanceScoringScheme	scheme_type
typedef SimpleFunc	threshold_score_type
typedef aln::EditDistanceTag	aligner_tag
typedef aln::EditDistanceAligner < aln::LOCAL >	local_aligner_type
typedef aln::EditDistanceAligner < aln::SEMI_GLOBAL >	end_to_end_aligner_type
typedef aln::EditDistanceAligner < aln::LOCAL >	ungapped_local_aligner_type
typedef aln::EditDistanceAligner < aln::SEMI_GLOBAL >	ungapped_end_to_end_aligner_type

Public Methods
local_aligner_type	local_aligner () const
end_to_end_aligner_type	end_to_end_aligner () const
ungapped_local_aligner_type	ungapped_local_aligner () const
ungapped_end_to_end_aligner_type	ungapped_end_to_end_aligner () const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	EditDistanceScoringScheme ()
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	perfect_score (const uint32 read_len) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	min_score (const uint32 len) const
SimpleFunc	threshold_score () const

Public Members
SimpleFunc	m_score_min

Static Public Members
static const int32	inf_score = 0
static const int32	worst_score = -(1 << 8)

Member Typedef Documentation

typedef aln::EditDistanceTag nvbio::bowtie2::cuda::EditDistanceScoringScheme::aligner_tag

Definition at line 137 of file scoring.h.

typedef aln::EditDistanceAligner<aln::SEMI_GLOBAL> nvbio::bowtie2::cuda::EditDistanceScoringScheme::end_to_end_aligner_type

Definition at line 140 of file scoring.h.

typedef aln::EditDistanceAligner<aln::LOCAL> nvbio::bowtie2::cuda::EditDistanceScoringScheme::local_aligner_type

Definition at line 139 of file scoring.h.

typedef EditDistanceScoringScheme nvbio::bowtie2::cuda::EditDistanceScoringScheme::scheme_type

Definition at line 135 of file scoring.h.

typedef SimpleFunc nvbio::bowtie2::cuda::EditDistanceScoringScheme::threshold_score_type

Definition at line 136 of file scoring.h.

typedef aln::EditDistanceAligner<aln::SEMI_GLOBAL> nvbio::bowtie2::cuda::EditDistanceScoringScheme::ungapped_end_to_end_aligner_type

Definition at line 143 of file scoring.h.

typedef aln::EditDistanceAligner<aln::LOCAL> nvbio::bowtie2::cuda::EditDistanceScoringScheme::ungapped_local_aligner_type

Definition at line 142 of file scoring.h.

Constructor & Destructor Documentation

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::bowtie2::cuda::EditDistanceScoringScheme::EditDistanceScoringScheme ( )

inline

default constructor

Definition at line 169 of file scoring.h.

Member Function Documentation

end_to_end_aligner_type nvbio::bowtie2::cuda::EditDistanceScoringScheme::end_to_end_aligner ( ) const

inline

return the end_to_end aligner

Definition at line 154 of file scoring.h.

local_aligner_type nvbio::bowtie2::cuda::EditDistanceScoringScheme::local_aligner ( ) const

inline

return the local aligner

Definition at line 150 of file scoring.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 nvbio::bowtie2::cuda::EditDistanceScoringScheme::min_score ( const uint32  len) const

inline

min score

Definition at line 181 of file scoring.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 nvbio::bowtie2::cuda::EditDistanceScoringScheme::perfect_score ( const uint32  read_len) const

inline

best achievable score for a read of given length

Definition at line 176 of file scoring.h.

SimpleFunc nvbio::bowtie2::cuda::EditDistanceScoringScheme::threshold_score ( ) const

inline

min score function

Definition at line 185 of file scoring.h.

ungapped_end_to_end_aligner_type nvbio::bowtie2::cuda::EditDistanceScoringScheme::ungapped_end_to_end_aligner ( ) const

inline

return the end_to_end aligner

Definition at line 162 of file scoring.h.

ungapped_local_aligner_type nvbio::bowtie2::cuda::EditDistanceScoringScheme::ungapped_local_aligner ( ) const

inline

return the local aligner

Definition at line 158 of file scoring.h.

Member Data Documentation

const int32 nvbio::bowtie2::cuda::EditDistanceScoringScheme::inf_score = 0

static

Definition at line 145 of file scoring.h.

SimpleFunc nvbio::bowtie2::cuda::EditDistanceScoringScheme::m_score_min

Definition at line 193 of file scoring.h.

const int32 nvbio::bowtie2::cuda::EditDistanceScoringScheme::worst_score = -(1 << 8)

static

Definition at line 146 of file scoring.h.

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The documentation for this struct was generated from the following file:

• E:/git/nvbio/nvBowtie/bowtie2/cuda/scoring.h