NVBIO
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This class implements a scoring scheme for short read alignment, taking into account matches, mismatches, insertions, deletions, ambiguous bases and base qualities. In practice, it reproduces exactly bowtie2's original scoring scheme employing a Gotoh aligner.
#include <scoring.h>
Public Types | |
typedef SmithWatermanScoringScheme < MMCost, NCost > | scheme_type |
typedef aln::GotohTag | aligner_tag |
typedef aln::GotohAligner < aln::LOCAL, scheme_type > | local_aligner_type |
typedef aln::GotohAligner < aln::SEMI_GLOBAL, scheme_type > | end_to_end_aligner_type |
typedef aln::HammingDistanceAligner < aln::LOCAL, scheme_type > | ungapped_local_aligner_type |
typedef aln::HammingDistanceAligner < aln::SEMI_GLOBAL, scheme_type > | ungapped_end_to_end_aligner_type |
typedef ConstantCost< int > | MatchCost |
typedef MMCost | MismatchCost |
typedef MatchCost | match_cost_function |
typedef MismatchCost | mismatch_cost_function |
typedef NCost | N_cost_function |
typedef SimpleFunc | threshold_score_type |
Static Public Methods | |
static SmithWatermanScoringScheme | base1 () |
static SmithWatermanScoringScheme | local () |
Public Members | |
SimpleFunc | m_score_min |
float | m_n_ceil_const |
float | m_n_ceil_coeff |
int | m_read_gap_const |
int | m_read_gap_coeff |
int | m_ref_gap_const |
int | m_ref_gap_coeff |
int | m_gap_free |
MatchCost | m_match |
MMCost | m_mmp |
NCost | m_np |
bool | m_monotone |
bool | m_local |
Static Public Members | |
static const int32 | inf_score = -(1 << 16) |
static const int32 | worst_score = inf_score |
typedef aln::GotohTag nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::aligner_tag |
typedef aln::GotohAligner<aln::SEMI_GLOBAL,scheme_type> nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::end_to_end_aligner_type |
typedef aln::GotohAligner<aln::LOCAL,scheme_type> nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::local_aligner_type |
typedef MatchCost nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::match_cost_function |
typedef ConstantCost<int> nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::MatchCost |
typedef MismatchCost nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::mismatch_cost_function |
typedef MMCost nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::MismatchCost |
typedef NCost nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::N_cost_function |
typedef SmithWatermanScoringScheme<MMCost,NCost> nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::scheme_type |
typedef SimpleFunc nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::threshold_score_type |
typedef aln::HammingDistanceAligner<aln::SEMI_GLOBAL,scheme_type> nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::ungapped_end_to_end_aligner_type |
typedef aln::HammingDistanceAligner<aln::LOCAL,scheme_type> nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::ungapped_local_aligner_type |
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::SmithWatermanScoringScheme | ( | ) |
default constructor
Definition at line 108 of file scoring_inl.h.
nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::SmithWatermanScoringScheme | ( | const std::map< std::string, std::string > & | options, |
const AlignmentType | type = LocalAlignment |
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constructor
options | key/value string options |
Definition at line 130 of file scoring_inl.h.
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return a preconfigured scoring scheme
Definition at line 58 of file scoring_inl.h.
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return preconfigured scoring scheme for local mapping
Definition at line 81 of file scoring_inl.h.
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int nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::m_gap_free |
bool nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::m_local |
MatchCost nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::m_match |
MMCost nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::m_mmp |
bool nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::m_monotone |
float nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::m_n_ceil_coeff |
float nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::m_n_ceil_const |
NCost nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::m_np |
int nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::m_read_gap_coeff |
int nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::m_read_gap_const |
int nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::m_ref_gap_coeff |
int nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::m_ref_gap_const |
SimpleFunc nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost >::m_score_min |
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