scoring.h File Reference

#include <nvbio/basic/types.h>
#include <nvbio/basic/options.h>
#include <nvbio/alignment/alignment_base.h>
#include <nvBowtie/bowtie2/quality_coeffs.h>
#include <nvBowtie/bowtie2/cuda/defs.h>
#include <nvBowtie/bowtie2/cuda/func.h>
#include <string>
#include <map>
#include <nvBowtie/bowtie2/cuda/scoring_inl.h>

Go to the source code of this file.

Classes
struct	nvbio::bowtie2::cuda::RoundedQualCost< T >
struct	nvbio::bowtie2::cuda::QualCost< T >
struct	nvbio::bowtie2::cuda::ConstantCost< T >
struct	nvbio::bowtie2::cuda::EditDistanceScoringScheme
struct	nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >
struct	nvbio::bowtie2::cuda::make_aligner_dispatch< TYPE, scheme_type >
struct	nvbio::bowtie2::cuda::make_aligner_dispatch< LocalAlignment, scheme_type >
struct	nvbio::bowtie2::cuda::make_aligner_dispatch< EndToEndAlignment, scheme_type >
struct	nvbio::bowtie2::cuda::UberScoringScheme
struct	nvbio::bowtie2::cuda::ScoringSchemeSelector< ScoringTagType >
struct	nvbio::bowtie2::cuda::ScoringSchemeSelector< edit_distance_scoring_tag >
struct	nvbio::bowtie2::cuda::ScoringSchemeSelector< smith_waterman_scoring_tag >
struct	nvbio::bowtie2::cuda::ScoringSchemeTag< ScoringSchemeType >
struct	nvbio::bowtie2::cuda::ScoringSchemeTag< EditDistanceScoringScheme >
struct	nvbio::bowtie2::cuda::ScoringSchemeTag< SmithWatermanScoringScheme< MMCost, NCost > >

Namespaces
	nvbio
	Define a vector_view POD type and plain_view() for std::vector.
	nvbio::bowtie2
	nvbio::bowtie2::cuda

Enumerations
enum	nvbio::bowtie2::cuda::AlignmentType { nvbio::bowtie2::cuda::EndToEndAlignment = 0, nvbio::bowtie2::cuda::LocalAlignment = 1 }
enum	nvbio::bowtie2::cuda::CostType { nvbio::bowtie2::cuda::ROUNDED_QUAL_COST = 1, nvbio::bowtie2::cuda::QUAL_COST = 2, nvbio::bowtie2::cuda::CONSTANT_COST = 3 }

Functions
template<AlignmentType TYPE, typename scheme_type >
make_aligner_dispatch< TYPE, scheme_type >::type	nvbio::bowtie2::cuda::make_aligner (const scheme_type &scheme)
SmithWatermanScoringScheme	nvbio::bowtie2::cuda::load_scoring_scheme (const char *name, const AlignmentType type)