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vg
tools for working with variation graphs
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This is the complete list of members for vg::Aligner, including all inherited members.
| align(Alignment &alignment, const HandleGraph &g, bool traceback_aln) const | vg::Aligner | virtual |
| align(Alignment &alignment, const HandleGraph &g, const std::vector< handle_t > &topological_order) const | vg::Aligner | |
| align_global_banded(Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true) const | vg::Aligner | virtual |
| align_global_banded_multi(Alignment &alignment, vector< Alignment > &alt_alignments, const HandleGraph &g, int32_t max_alt_alns, int32_t band_padding=0, bool permissive_banding=true) const | vg::Aligner | virtual |
| align_internal(Alignment &alignment, vector< Alignment > *multi_alignments, const HandleGraph &g, bool pinned, bool pin_left, int32_t max_alt_alns, bool traceback_aln) const | vg::Aligner | private |
| align_pinned(Alignment &alignment, const HandleGraph &g, bool pin_left, bool xdrop=false, uint16_t xdrop_max_gap_length=default_xdrop_max_gap_length) const | vg::Aligner | virtual |
| align_pinned_multi(Alignment &alignment, vector< Alignment > &alt_alignments, const HandleGraph &g, bool pin_left, int32_t max_alt_alns) const | vg::Aligner | virtual |
| align_xdrop(Alignment &alignment, const HandleGraph &g, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const | vg::Aligner | virtual |
| align_xdrop(Alignment &alignment, const HandleGraph &g, const vector< handle_t > &order, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const | vg::Aligner | virtual |
| Aligner(const int8_t *_score_matrix=default_score_matrix, int8_t _gap_open=default_gap_open, int8_t _gap_extension=default_gap_extension, int8_t _full_length_bonus=default_full_length_bonus, double _gc_content=default_gc_content) | vg::Aligner | |
| alignment_score_partition_function(double lambda, const int8_t *score_matrix, const double *nt_freqs) const | vg::GSSWAligner | protected |
| all_mapping_qualities_exact(const vector< double > &scaled_scores, const vector< double > *multiplicities=nullptr) const | vg::GSSWAligner | protected |
| compute_all_mapping_qualities(const vector< double > &scores, const vector< double > *multiplicities=nullptr) const | vg::GSSWAligner | |
| compute_first_mapping_quality(const vector< double > &scores, bool fast_approximation, const vector< double > *multiplicities=nullptr) const | vg::GSSWAligner | |
| compute_group_mapping_quality(const vector< double > &scores, const vector< size_t > &group, const vector< double > *multiplicities=nullptr) const | vg::GSSWAligner | |
| compute_mapping_quality(vector< Alignment > &alignments, int max_mapping_quality, bool fast_approximation, double cluster_mq, bool use_cluster_mq, int overlap_count, double mq_estimate, double maybe_mq_threshold, double identity_weight) const | vg::GSSWAligner | |
| compute_max_mapping_quality(const vector< double > &scores, bool fast_approximation, const vector< double > *multiplicities=nullptr) const | vg::GSSWAligner | |
| compute_paired_mapping_quality(pair< vector< Alignment >, vector< Alignment >> &alignment_pairs, const vector< double > &frag_weights, int max_mapping_quality1, int max_mapping_quality2, bool fast_approximation, double cluster_mq, bool use_cluster_mq, int overlap_count1, int overlap_count2, double mq_estimate1, double mq_estimate2, double maybe_mq_threshold, double identity_weight) const | vg::GSSWAligner | |
| create_gssw_graph(const HandleGraph &g) const | vg::GSSWAligner | protected |
| deletion_aligner | vg::GSSWAligner | |
| estimate_max_possible_mapping_quality(int length, double min_diffs, double next_min_diffs) const | vg::GSSWAligner | |
| estimate_next_best_score(int length, double min_diffs) const | vg::GSSWAligner | protected |
| first_mapping_quality_approx(const vector< double > &scaled_scores, const vector< double > *multiplicities=nullptr) | vg::GSSWAligner | static |
| first_mapping_quality_exact(const vector< double > &scaled_scores, const vector< double > *multiplicities=nullptr) | vg::GSSWAligner | static |
| full_length_bonus | vg::GSSWAligner | |
| gap_extension | vg::GSSWAligner | |
| gap_open | vg::GSSWAligner | |
| graph_cigar(gssw_graph_mapping *gm) const | vg::GSSWAligner | protected |
| group_mapping_quality_exact(const vector< double > &scaled_scores, const vector< size_t > &group, const vector< double > *multiplicities=nullptr) const | vg::GSSWAligner | protected |
| gssw_mapping_to_alignment(gssw_graph *graph, gssw_graph_mapping *gm, Alignment &alignment, bool pinned, bool pin_left) const | vg::GSSWAligner | protected |
| GSSWAligner()=default | vg::GSSWAligner | protected |
| GSSWAligner(const int8_t *_score_matrix, int8_t _gap_open, int8_t _gap_extension, int8_t _full_length_bonus, double _gc_content) | vg::GSSWAligner | protected |
| identify_pinning_points(const HandleGraph &graph) const | vg::GSSWAligner | protected |
| log_base | vg::GSSWAligner | |
| longest_detectable_gap(const Alignment &alignment, const string::const_iterator &read_pos) const | vg::GSSWAligner | |
| longest_detectable_gap(size_t read_length, size_t read_pos) const | vg::GSSWAligner | |
| longest_detectable_gap(const Alignment &alignment) const | vg::GSSWAligner | |
| longest_detectable_gap(size_t read_length) const | vg::GSSWAligner | |
| mapping_quality_score_diff(double mapping_quality) const | vg::GSSWAligner | |
| match | vg::GSSWAligner | |
| max_possible_mapping_quality(int length) const | vg::GSSWAligner | |
| maximum_mapping_quality_approx(const vector< double > &scaled_scores, size_t *max_idx_out, const vector< double > *multiplicities=nullptr) | vg::GSSWAligner | static |
| maximum_mapping_quality_exact(const vector< double > &scaled_scores, size_t *max_idx_out, const vector< double > *multiplicities=nullptr) | vg::GSSWAligner | static |
| mismatch | vg::GSSWAligner | |
| nt_table | vg::GSSWAligner | |
| recover_log_base(const int8_t *score_matrix, double gc_content, double tol) const | vg::GSSWAligner | protected |
| remove_bonuses(const Alignment &aln, bool pinned=false, bool pin_left=false) const | vg::GSSWAligner | virtual |
| score_contiguous_alignment(const Alignment &aln, bool strip_bonuses=false) const | vg::GSSWAligner | virtual |
| score_discontiguous_alignment(const Alignment &aln, const function< size_t(pos_t, pos_t, size_t)> &estimate_distance, bool strip_bonuses=false) const | vg::GSSWAligner | virtual |
| score_exact_match(const Alignment &aln, size_t read_offset, size_t length) const | vg::Aligner | virtual |
| score_exact_match(const string &sequence, const string &base_quality) const | vg::Aligner | virtual |
| score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const | vg::Aligner | virtual |
| score_exact_match(const string &sequence) const | vg::Aligner | |
| score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end) const | vg::Aligner | |
| score_full_length_bonus(bool left_side, string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const | vg::Aligner | virtual |
| score_full_length_bonus(bool left_side, const Alignment &alignment) const | vg::Aligner | virtual |
| score_gap(size_t gap_length) const | vg::GSSWAligner | |
| score_matrix | vg::GSSWAligner | |
| score_mismatch(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const | vg::Aligner | virtual |
| score_mismatch(size_t length) const | vg::Aligner | |
| score_partial_alignment(const Alignment &alignment, const HandleGraph &graph, const path_t &path, string::const_iterator seq_begin, bool no_read_end_scoring=false) const | vg::Aligner | virtual |
| score_to_unnormalized_likelihood_ln(double score) const | vg::GSSWAligner | |
| unreverse_graph(gssw_graph *graph) const | vg::GSSWAligner | protected |
| unreverse_graph_mapping(gssw_graph_mapping *gm) const | vg::GSSWAligner | protected |
| verify_valid_log_odds_score_matrix(const int8_t *score_matrix, const double *nt_freqs) const | vg::GSSWAligner | protected |
| xdrops | vg::Aligner | private |
| ~Aligner(void)=default | vg::Aligner | |
| ~GSSWAligner() | vg::GSSWAligner | protected |
1.8.17