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vg
tools for working with variation graphs
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This is the complete list of members for vg::EditAlignmentScorer, including all inherited members.
| alignment_score_partition_function(double lambda, const double matrix[16], const double nt_freqs[4]) | vg::AlignmentScorer | privatestatic |
| EditAlignmentScorer(int8_t match=default_match, int8_t mismatch=default_mismatch, int8_t gap_open=default_gap_open, int8_t gap_extension=default_gap_extension, int8_t full_length_bonus=default_full_length_bonus) | vg::EditAlignmentScorer | |
| full_length_bonus | vg::EditAlignmentScorer | |
| gap_extension | vg::EditAlignmentScorer | |
| gap_open | vg::EditAlignmentScorer | |
| get_log_base() const =0 | vg::AlignmentScorer | pure virtual |
| longest_detectable_gap(const Alignment &alignment, const std::string::const_iterator &read_pos) const | vg::EditAlignmentScorer | |
| longest_detectable_gap(size_t read_length, size_t read_pos) const | vg::EditAlignmentScorer | |
| longest_detectable_gap(const Alignment &alignment) const | vg::EditAlignmentScorer | |
| longest_detectable_gap(size_t read_length) const | vg::EditAlignmentScorer | |
| match | vg::EditAlignmentScorer | |
| mismatch | vg::EditAlignmentScorer | |
| recover_log_base(const double matrix[16], double gc_content, double tol=1e-12) | vg::AlignmentScorer | protectedstatic |
| remove_bonuses(const Alignment &aln, bool pinned=false, bool pin_left=false) const | vg::EditAlignmentScorer | virtual |
| score_alignment(const Alignment &aln) const override | vg::EditAlignmentScorer | virtual |
| score_contiguous_alignment(const Alignment &aln, bool allow_left_bonus=true, bool allow_right_bonus=true) const | vg::EditAlignmentScorer | virtual |
| score_discontiguous_alignment(const Alignment &aln, const std::function< size_t(pos_t, pos_t, size_t)> &estimate_distance, bool allow_left_bonus=true, bool allow_right_bonus=true) const | vg::EditAlignmentScorer | virtual |
| score_exact_match(const Alignment &aln, size_t read_offset, size_t length) const =0 | vg::EditAlignmentScorer | pure virtual |
| score_exact_match(const std::string &sequence, const std::string &base_quality) const =0 | vg::EditAlignmentScorer | pure virtual |
| score_exact_match(std::string::const_iterator seq_begin, std::string::const_iterator seq_end, std::string::const_iterator base_qual_begin) const =0 | vg::EditAlignmentScorer | pure virtual |
| score_full_length_bonus(bool left_side, std::string::const_iterator seq_begin, std::string::const_iterator seq_end, std::string::const_iterator base_qual_begin) const =0 | vg::EditAlignmentScorer | pure virtual |
| score_full_length_bonus(bool left_side, const Alignment &alignment) const =0 | vg::EditAlignmentScorer | pure virtual |
| score_gap(size_t gap_length) const | vg::EditAlignmentScorer | virtual |
| score_mismatch(std::string::const_iterator seq_begin, std::string::const_iterator seq_end, std::string::const_iterator base_qual_begin) const =0 | vg::EditAlignmentScorer | pure virtual |
| score_partial_alignment(const Alignment &alignment, const HandleGraph &graph, const path_t &path, std::string::const_iterator seq_begin, bool no_read_end_scoring=false) const =0 | vg::EditAlignmentScorer | pure virtual |
| verify_valid_log_odds_score_matrix(const double matrix[16], const double nt_freqs[4]) | vg::AlignmentScorer | privatestatic |
| ~AlignmentScorer()=default | vg::AlignmentScorer | virtual |
1.9.1