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vg
tools for working with variation graphs
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This is the complete list of members for vg::MinimizerMapper, including all inherited members.
| adjust_alignments_for_base_quality | vg::AlignerClient | |
| align_from_chains | vg::MinimizerMapper | |
| align_sequence_between(const pos_t &left_anchor, const pos_t &right_anchor, size_t max_path_length, const HandleGraph *graph, const GSSWAligner *aligner, Alignment &alignment, size_t max_dp_cells=std::numeric_limits< size_t >::max()) | vg::MinimizerMapper | protectedstatic |
| AlignerClient(double gc_content_estimate=vg::default_gc_content) | vg::AlignerClient | protected |
| annotate_with_minimizer_statistics(Alignment &target, const VectorView< Minimizer > &minimizers, const std::vector< Seed > &seeds, size_t old_seed_count, size_t new_seed_offset, const Funnel &funnel) const | vg::MinimizerMapper | protected |
| attempt_rescue(const Alignment &aligned_read, Alignment &rescued_alignment, const VectorView< Minimizer > &minimizers, bool rescue_forward) | vg::MinimizerMapper | protected |
| chain_info_to_seed(const pos_t &hit, size_t minimizer, const gbwtgraph::Payload &chain_info) | vg::MinimizerMapper | inlineprotectedstatic |
| chain_min_score | vg::MinimizerMapper | |
| chain_score_threshold | vg::MinimizerMapper | |
| chaining_cluster_distance | vg::MinimizerMapper | |
| Cluster typedef | vg::MinimizerMapper | protected |
| cluster_coverage_threshold | vg::MinimizerMapper | |
| cluster_score_threshold | vg::MinimizerMapper | |
| clusterer | vg::MinimizerMapper | protected |
| compute_mapq_caps(const Alignment &aln, const VectorView< Minimizer > &minimizers, const SmallBitset &explored) | vg::MinimizerMapper | protected |
| default_align_from_chains | vg::MinimizerMapper | static |
| default_chain_min_score | vg::MinimizerMapper | static |
| default_chain_score_threshold | vg::MinimizerMapper | static |
| default_chaining_cluster_distance | vg::MinimizerMapper | static |
| default_cluster_coverage_threshold | vg::MinimizerMapper | static |
| default_cluster_score_threshold | vg::MinimizerMapper | static |
| default_distance_limit | vg::MinimizerMapper | static |
| default_do_dp | vg::MinimizerMapper | static |
| default_exclude_overlapping_min | vg::MinimizerMapper | static |
| default_extension_score_threshold | vg::MinimizerMapper | static |
| default_extension_set_min_score | vg::MinimizerMapper | static |
| default_extension_set_score_threshold | vg::MinimizerMapper | static |
| default_hard_hit_cap | vg::MinimizerMapper | static |
| default_hit_cap | vg::MinimizerMapper | static |
| default_initial_lookback_threshold | vg::MinimizerMapper | static |
| default_item_bonus | vg::MinimizerMapper | static |
| default_lookback_item_hard_cap | vg::MinimizerMapper | static |
| default_lookback_scale_factor | vg::MinimizerMapper | static |
| default_max_alignments | vg::MinimizerMapper | static |
| default_max_chain_connection | vg::MinimizerMapper | static |
| default_max_clusters_to_chain | vg::MinimizerMapper | static |
| default_max_dozeu_cells | vg::MinimizerMapper | static |
| default_max_dp_cells | vg::MinimizerMapper | static |
| default_max_extensions | vg::MinimizerMapper | static |
| default_max_fragment_length | vg::MinimizerMapper | static |
| default_max_indel_bases | vg::MinimizerMapper | static |
| default_max_local_extensions | vg::MinimizerMapper | static |
| default_max_lookback_bases | vg::MinimizerMapper | static |
| default_max_multimaps | vg::MinimizerMapper | static |
| default_max_precluster_connections | vg::MinimizerMapper | static |
| default_max_rescue_attempts | vg::MinimizerMapper | static |
| default_max_tail_length | vg::MinimizerMapper | static |
| default_max_unique_min | vg::MinimizerMapper | static |
| default_min_chains | vg::MinimizerMapper | static |
| default_min_clusters_to_chain | vg::MinimizerMapper | static |
| default_min_extension_sets | vg::MinimizerMapper | static |
| default_min_extensions | vg::MinimizerMapper | static |
| default_min_good_transition_score_per_base | vg::MinimizerMapper | static |
| default_min_lookback_items | vg::MinimizerMapper | static |
| default_min_precluster_connections | vg::MinimizerMapper | static |
| default_minimizer_score_fraction | vg::MinimizerMapper | static |
| default_num_bp_per_min | vg::MinimizerMapper | static |
| default_pad_cluster_score_threshold | vg::MinimizerMapper | static |
| default_paired_distance_stdevs | vg::MinimizerMapper | static |
| default_paired_rescue_score_limit | vg::MinimizerMapper | static |
| default_precluster_connection_coverage_threshold | vg::MinimizerMapper | static |
| default_rescue_seed_limit | vg::MinimizerMapper | static |
| default_rescue_subgraph_stdevs | vg::MinimizerMapper | static |
| default_reseed_search_distance | vg::MinimizerMapper | static |
| default_show_work | vg::MinimizerMapper | static |
| default_track_correctness | vg::MinimizerMapper | static |
| default_track_provenance | vg::MinimizerMapper | static |
| dfs_gbwt(const Position &from, size_t walk_distance, const function< void(const handle_t &)> &enter_handle, const function< void(void)> exit_handle) const | vg::MinimizerMapper | protected |
| dfs_gbwt(handle_t from_handle, size_t from_offset, size_t walk_distance, const function< void(const handle_t &)> &enter_handle, const function< void(void)> exit_handle) const | vg::MinimizerMapper | protected |
| dfs_gbwt(const gbwt::SearchState &start_state, size_t from_offset, size_t walk_distance, const function< void(const handle_t &)> &enter_handle, const function< void(void)> exit_handle) const | vg::MinimizerMapper | protected |
| distance_between(const pos_t &pos1, const pos_t &pos2) | vg::MinimizerMapper | protected |
| distance_between(const Alignment &aln1, const Alignment &aln2) | vg::MinimizerMapper | protected |
| distance_index | vg::MinimizerMapper | protected |
| distance_limit | vg::MinimizerMapper | |
| distance_to_annotation(int64_t distance) const | vg::MinimizerMapper | protected |
| do_dp | vg::MinimizerMapper | |
| dump_chaining_problem(const std::vector< algorithms::Anchor > &anchors, const std::vector< size_t > &cluster_seeds_sorted, const HandleGraph &graph) | vg::MinimizerMapper | protectedstatic |
| dump_debug_clustering(const Cluster &cluster, size_t cluster_number, const VectorView< Minimizer > &minimizers, const std::vector< Seed > &seeds) | vg::MinimizerMapper | protectedstatic |
| dump_debug_extension_set(const HandleGraph &graph, const Alignment &aln, const vector< GaplessExtension > &extended_seeds) | vg::MinimizerMapper | protectedstatic |
| dump_debug_minimizers(const VectorView< Minimizer > &minimizers, const string &sequence, const vector< size_t > *to_include=nullptr, size_t start_offset=0, size_t length_limit=std::numeric_limits< size_t >::max()) | vg::MinimizerMapper | protectedstatic |
| dump_debug_query(const Alignment &aln) | vg::MinimizerMapper | protectedstatic |
| dump_debug_query(const Alignment &aln1, const Alignment &aln2) | vg::MinimizerMapper | protectedstatic |
| dump_debug_seeds(const VectorView< Minimizer > &minimizers, const std::vector< Seed > &seeds, const std::vector< size_t > &selected_seeds) | vg::MinimizerMapper | protectedstatic |
| dump_debug_sequence(ostream &out, const string &sequence, size_t start_offset=0, size_t length_limit=std::numeric_limits< size_t >::max()) | vg::MinimizerMapper | protectedstatic |
| exclude_overlapping_min | vg::MinimizerMapper | |
| extend_cluster(const Cluster &cluster, size_t cluster_num, const VectorView< Minimizer > &minimizers, const std::vector< Seed > &seeds, const string &sequence, vector< vector< size_t >> &minimizer_kept_cluster_count, Funnel &funnel) const | vg::MinimizerMapper | protected |
| extender | vg::MinimizerMapper | protected |
| extension_score_threshold | vg::MinimizerMapper | |
| extension_set_min_score | vg::MinimizerMapper | |
| extension_set_score_threshold | vg::MinimizerMapper | |
| extension_to_alignment(const GaplessExtension &extension, Alignment &alignment) const | vg::MinimizerMapper | protected |
| faster_cap(const VectorView< Minimizer > &minimizers, vector< size_t > &minimizers_explored, const string &sequence, const string &quality_bytes) | vg::MinimizerMapper | protectedstatic |
| finalize_fragment_length_distr() | vg::MinimizerMapper | inline |
| find_chain_alignment(const Alignment &aln, const VectorView< algorithms::Anchor > &to_chain, const std::vector< size_t > &chain) const | vg::MinimizerMapper | protected |
| find_minimizers(const std::string &sequence, Funnel &funnel) const | vg::MinimizerMapper | protected |
| find_optimal_tail_alignments(const Alignment &aln, const vector< GaplessExtension > &extended_seeds, LazyRNG &rng, Alignment &best, Alignment &second_best) const | vg::MinimizerMapper | protected |
| find_seeds(const VectorView< Minimizer > &minimizers, const Alignment &aln, Funnel &funnel) const | vg::MinimizerMapper | protected |
| fix_dozeu_end_deletions(Alignment &rescued_alignment) const | vg::MinimizerMapper | protected |
| fix_dozeu_score(Alignment &rescued_alignment, const HandleGraph &rescue_graph, const std::vector< handle_t > &topological_order) const | vg::MinimizerMapper | protected |
| for_each_agglomeration_interval(const VectorView< Minimizer > &minimizers, const string &sequence, const string &quality_bytes, const vector< size_t > &minimizer_indices, const function< void(size_t, size_t, size_t, size_t)> &iteratee) | vg::MinimizerMapper | protectedstatic |
| force_fragment_length_distr(double mean, double stdev) | vg::MinimizerMapper | inline |
| fragment_distr_is_finalized() | vg::MinimizerMapper | inline |
| fragment_length_distr | vg::MinimizerMapper | protected |
| gbwt_graph | vg::MinimizerMapper | protected |
| gc_content_estimate | vg::AlignerClient | private |
| get_aligner(bool have_qualities=true) const | vg::AlignerClient | protected |
| get_best_alignment_against_any_tree(const vector< TreeSubgraph > &trees, const string &sequence, const Position &default_position, bool pin_left, size_t longest_detectable_gap, LazyRNG &rng) const | vg::MinimizerMapper | protected |
| get_distance_limit(size_t read_length) const | vg::MinimizerMapper | inline |
| get_fragment_length_mean() const | vg::MinimizerMapper | inline |
| get_fragment_length_sample_size() const | vg::MinimizerMapper | inline |
| get_fragment_length_stdev() const | vg::MinimizerMapper | inline |
| get_log10_prob_of_disruption_in_interval(const VectorView< Minimizer > &minimizers, const string &sequence, const string &quality_bytes, const vector< size_t >::iterator &disrupt_begin, const vector< size_t >::iterator &disrupt_end, size_t left, size_t right) | vg::MinimizerMapper | protectedstatic |
| get_prob_of_disruption_in_column(const VectorView< Minimizer > &minimizers, const string &sequence, const string &quality_bytes, const vector< size_t >::iterator &disrupt_begin, const vector< size_t >::iterator &disrupt_end, size_t index) | vg::MinimizerMapper | protectedstatic |
| get_qual_adj_aligner() const | vg::AlignerClient | protected |
| get_regular_aligner() const | vg::AlignerClient | protected |
| get_tail_forest(const GaplessExtension &extended_seed, size_t read_length, bool left_tails, size_t *longest_detectable_gap=nullptr) const | vg::MinimizerMapper | protected |
| hard_hit_cap | vg::MinimizerMapper | |
| hit_cap | vg::MinimizerMapper | |
| immutable_path_from_length(const ImmutablePath &path) | vg::MinimizerMapper | protectedstatic |
| ImmutablePath typedef | vg::MinimizerMapper | protected |
| initial_lookback_threshold | vg::MinimizerMapper | |
| item_bonus | vg::MinimizerMapper | |
| log_alignment(const Alignment &aln) | vg::MinimizerMapper | protectedstatic |
| log_alignment(const Path &path, bool force_condensed=false) | vg::MinimizerMapper | protectedstatic |
| log_bits(const std::vector< bool > &bits) | vg::MinimizerMapper | protectedstatic |
| log_name() | vg::MinimizerMapper | protectedstatic |
| LONG_LIMIT | vg::MinimizerMapper | protectedstatic |
| lookback_item_hard_cap | vg::MinimizerMapper | |
| lookback_scale_factor | vg::MinimizerMapper | |
| MANY_LIMIT | vg::MinimizerMapper | protectedstatic |
| map(Alignment &aln, AlignmentEmitter &alignment_emitter) | vg::MinimizerMapper | |
| map(Alignment &aln) | vg::MinimizerMapper | |
| map_from_chains(Alignment &aln) | vg::MinimizerMapper | |
| map_from_extensions(Alignment &aln) | vg::MinimizerMapper | |
| map_paired(Alignment &aln1, Alignment &aln2, vector< pair< Alignment, Alignment >> &ambiguous_pair_buffer) | vg::MinimizerMapper | |
| map_paired(Alignment &aln1, Alignment &aln2) | vg::MinimizerMapper | |
| max_alignments | vg::MinimizerMapper | |
| max_chain_connection | vg::MinimizerMapper | |
| max_clusters_to_chain | vg::MinimizerMapper | |
| max_dozeu_cells | vg::MinimizerMapper | |
| max_dp_cells | vg::MinimizerMapper | |
| MAX_DP_LENGTH | vg::MinimizerMapper | static |
| max_extensions | vg::MinimizerMapper | |
| max_fragment_length | vg::MinimizerMapper | |
| max_indel_bases | vg::MinimizerMapper | |
| max_local_extensions | vg::MinimizerMapper | |
| max_lookback_bases | vg::MinimizerMapper | |
| max_multimaps | vg::MinimizerMapper | |
| max_precluster_connections | vg::MinimizerMapper | |
| max_rescue_attempts | vg::MinimizerMapper | |
| max_tail_length | vg::MinimizerMapper | |
| max_unique_min | vg::MinimizerMapper | |
| min_chains | vg::MinimizerMapper | |
| min_clusters_to_chain | vg::MinimizerMapper | |
| min_extension_sets | vg::MinimizerMapper | |
| min_extensions | vg::MinimizerMapper | |
| min_good_transition_score_per_base | vg::MinimizerMapper | |
| min_lookback_items | vg::MinimizerMapper | |
| min_precluster_connections | vg::MinimizerMapper | |
| minimizer_index | vg::MinimizerMapper | protected |
| minimizer_score_fraction | vg::MinimizerMapper | |
| MinimizerMapper(const gbwtgraph::GBWTGraph &graph, const gbwtgraph::DefaultMinimizerIndex &minimizer_index, SnarlDistanceIndex *distance_index, const PathPositionHandleGraph *path_graph=nullptr) | vg::MinimizerMapper | |
| no_chain_info() | vg::MinimizerMapper | inlineprotectedstatic |
| num_bp_per_min | vg::MinimizerMapper | |
| pad_cluster_score_threshold | vg::MinimizerMapper | |
| pair_all(std::array< vector< Alignment >, 2 > &mappings) const | vg::MinimizerMapper | protected |
| paired_distance_stdevs | vg::MinimizerMapper | |
| paired_rescue_score_limit | vg::MinimizerMapper | |
| parse_matrix(std::istream &matrix_stream) | vg::AlignerClient | static |
| path_graph | vg::MinimizerMapper | protected |
| precluster_connection_coverage_threshold | vg::MinimizerMapper | |
| process_until_threshold_a(size_t items, const function< Score(size_t)> &get_score, double threshold, size_t min_count, size_t max_count, LazyRNG &rng, const function< bool(size_t)> &process_item, const function< void(size_t)> &discard_item_by_count, const function< void(size_t)> &discard_item_by_score) const | vg::MinimizerMapper | protected |
| process_until_threshold_b(const vector< Score > &scores, double threshold, size_t min_count, size_t max_count, LazyRNG &rng, const function< bool(size_t)> &process_item, const function< void(size_t)> &discard_item_by_count, const function< void(size_t)> &discard_item_by_score) const | vg::MinimizerMapper | protected |
| process_until_threshold_c(size_t items, const function< Score(size_t)> &get_score, const function< bool(size_t, size_t)> &comparator, double threshold, size_t min_count, size_t max_count, LazyRNG &get_seed, const function< bool(size_t)> &process_item, const function< void(size_t)> &discard_item_by_count, const function< void(size_t)> &discard_item_by_score) const | vg::MinimizerMapper | protected |
| qual_adj_aligner | vg::AlignerClient | private |
| read_group | vg::MinimizerMapper | |
| regular_aligner | vg::AlignerClient | private |
| rescue_algorithm | vg::MinimizerMapper | |
| rescue_dozeu enum value | vg::MinimizerMapper | |
| rescue_gssw enum value | vg::MinimizerMapper | |
| rescue_none enum value | vg::MinimizerMapper | |
| rescue_seed_limit | vg::MinimizerMapper | |
| rescue_subgraph_stdevs | vg::MinimizerMapper | |
| RescueAlgorithm enum name | vg::MinimizerMapper | |
| reseed_between(size_t read_region_start, size_t read_region_end, pos_t left_graph_pos, pos_t right_graph_pos, const HandleGraph &graph, const VectorView< Minimizer > &minimizers, const std::function< void(const Minimizer &, const std::vector< nid_t > &, const std::function< void(const pos_t &)> &)> &for_each_pos_for_source_in_subgraph) const | vg::MinimizerMapper | protected |
| reseed_search_distance | vg::MinimizerMapper | |
| sample_name | vg::MinimizerMapper | |
| score_alignment_pair(Alignment &aln1, Alignment &aln2, int64_t fragment_distance) | vg::MinimizerMapper | protected |
| score_cluster(Cluster &cluster, size_t i, const VectorView< Minimizer > &minimizers, const std::vector< Seed > &seeds, size_t seq_length, Funnel &funnel) const | vg::MinimizerMapper | protected |
| score_extension_group(const Alignment &aln, const vector< GaplessExtension > &extended_seeds, int gap_open_penalty, int gap_extend_penalty) | vg::MinimizerMapper | protectedstatic |
| score_extensions(const std::vector< std::vector< GaplessExtension >> &extensions, const Alignment &aln, Funnel &funnel) const | vg::MinimizerMapper | protected |
| score_extensions(const std::vector< std::pair< std::vector< GaplessExtension >, size_t >> &extensions, const Alignment &aln, Funnel &funnel) const | vg::MinimizerMapper | protected |
| score_merged_cluster(Cluster &cluster, size_t i, const VectorView< Minimizer > &minimizers, const std::vector< Seed > &seeds, size_t first_new_seed, const std::vector< size_t > &seed_to_precluster, const std::vector< Cluster > &preclusters, size_t seq_length, Funnel &funnel) const | vg::MinimizerMapper | protected |
| Seed typedef | vg::MinimizerMapper | |
| seeds_in_subgraph(const VectorView< Minimizer > &minimizers, const std::unordered_set< nid_t > &subgraph) const | vg::MinimizerMapper | protected |
| set_alignment_scores(const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus) | vg::MinimizerMapper | virtual |
| set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus) | vg::MinimizerMapper | |
| set_alignment_scores(std::istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus) | vg::MinimizerMapper | |
| set_alignment_scores(const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus) | vg::MinimizerMapper | |
| vg::AlignerClient::set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus) | vg::AlignerClient | virtual |
| vg::AlignerClient::set_alignment_scores(std::istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus) | vg::AlignerClient | virtual |
| show_work | vg::MinimizerMapper | |
| sort_minimizers_by_score(const std::vector< Minimizer > &minimizers) const | vg::MinimizerMapper | protected |
| tag_seeds(const Alignment &aln, const std::vector< Seed >::const_iterator &begin, const std::vector< Seed >::const_iterator &end, const VectorView< Minimizer > &minimizers, size_t funnel_offset, Funnel &funnel) const | vg::MinimizerMapper | protected |
| TestMinimizerMapper class | vg::MinimizerMapper | friend |
| to_anchor(const Alignment &aln, const VectorView< Minimizer > &minimizers, const Seed &seed) const | vg::MinimizerMapper | protected |
| to_anchors(const Alignment &aln, const VectorView< Minimizer > &minimizers, const std::vector< Seed > &seeds) const | vg::MinimizerMapper | protected |
| to_path(const ImmutablePath &path) | vg::MinimizerMapper | protectedstatic |
| to_wfa_alignment(const algorithms::Anchor &anchor) const | vg::MinimizerMapper | protected |
| track_correctness | vg::MinimizerMapper | |
| track_provenance | vg::MinimizerMapper | |
| unoriented_distance_between(const pos_t &pos1, const pos_t &pos2) const | vg::MinimizerMapper | protected |
| validate_clusters(const std::vector< std::vector< Cluster >> &clusters, const std::vector< std::vector< Seed >> &seeds, size_t read_limit, size_t fragment_limit) const | vg::MinimizerMapper | protected |
| warned_about_bad_distribution | vg::MinimizerMapper | protected |
| warned_about_rescue_size | vg::MinimizerMapper | |
| warned_about_tail_size | vg::MinimizerMapper | mutable |
| wfa_alignment_to_alignment(const WFAAlignment &wfa_alignment, Alignment &alignment) const | vg::MinimizerMapper | protected |
| window_breaking_quality(const VectorView< Minimizer > &minimizers, vector< size_t > &broken, const string &sequence, const string &quality_bytes) | vg::MinimizerMapper | protectedstatic |
| with_dagified_local_graph(const pos_t &left_anchor, const pos_t &right_anchor, size_t max_path_length, const HandleGraph &graph, const std::function< void(DeletableHandleGraph &, const std::function< std::pair< nid_t, bool >(const handle_t &)> &)> &callback) | vg::MinimizerMapper | protectedstatic |
1.8.17