| aligner_tag typedef | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| base1() | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | static |
| cumulative_deletion(const uint32 i) const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| cumulative_insertion(const uint32 i) const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| end_to_end_aligner() const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| end_to_end_aligner_type typedef | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| inf_score | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | static |
| local() | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | static |
| local_aligner() const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| local_aligner_type typedef | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| m_gap_free | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| m_local | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| m_match | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| m_mmp | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| m_monotone | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| m_n_ceil_coeff | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| m_n_ceil_const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| m_np | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| m_read_gap_coeff | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| m_read_gap_const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| m_ref_gap_coeff | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| m_ref_gap_const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| m_score_min | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| match(const uint8 q=0) const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| match_cost_function typedef | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| MatchCost typedef | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| min_score(const uint32 len) const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| mismatch(const uint8 q=0) const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| mismatch(const uint8 r, const uint8 q, const uint8 qq=0) const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| mismatch_cost_function typedef | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| MismatchCost typedef | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| n(int q) const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| N_cost_function typedef | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| pattern_gap_extension() const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| pattern_gap_open() const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| perfect_score(const uint32 read_len) const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| scheme_type typedef | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| score(const uint8 read, const uint8 ref_mask, int q) const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| SmithWatermanScoringScheme() | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| SmithWatermanScoringScheme(const std::map< std::string, std::string > &options, const AlignmentType type=LocalAlignment) | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| substitution(const uint32 r_i, const uint32 q_j, const uint8 r, const uint8 q, const uint8 qq=0) const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| text_gap_extension() const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| text_gap_open() const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| threshold_score() const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| threshold_score_type typedef | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| ungapped_end_to_end_aligner() const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| ungapped_end_to_end_aligner_type typedef | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| ungapped_local_aligner() const | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | inline |
| ungapped_local_aligner_type typedef | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | |
| worst_score | nvbio::bowtie2::cuda::SmithWatermanScoringScheme< MMCost, NCost > | static |
1.8.4