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vg
tools for working with variation graphs
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This is the complete list of members for vg::MultipathMapper, including all inherited members.
| accelerate_mem_query(string::const_iterator begin, string::const_iterator &cursor) const | vg::BaseMapper | |
| accelerator | vg::BaseMapper | |
| adaptive_diff_exponent | vg::BaseMapper | |
| adaptive_reseed_diff | vg::BaseMapper | |
| adaptive_reseed_length_memo | vg::BaseMapper | static |
| adjust_alignments_for_base_quality | vg::AlignerClient | |
| agglomerate(size_t idx, multipath_alignment_t &agglomerating, const multipath_alignment_t &multipath_aln, vector< size_t > &agglomerated_group, unordered_set< pos_t > &agg_start_positions, unordered_set< pos_t > &agg_end_positions) const | vg::MultipathMapper | protected |
| agglomerate_alignment_pairs(vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< double > &multiplicities) | vg::MultipathMapper | protected |
| agglomerate_alignments(vector< multipath_alignment_t > &multipath_alns_out, vector< double > *multiplicities=nullptr) | vg::MultipathMapper | protected |
| agglomerate_multipath_alns | vg::MultipathMapper | |
| align_to_cluster_graph_pairs(const Alignment &alignment1, const Alignment &alignment2, vector< clustergraph_t > &cluster_graphs1, vector< clustergraph_t > &cluster_graphs2, vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< double > &pair_multiplicities, vector< pair< size_t, size_t >> &duplicate_pairs_out, const match_fanouts_t *fanouts1, const match_fanouts_t *fanouts2) | vg::MultipathMapper | protected |
| align_to_cluster_graphs(const Alignment &alignment, vector< clustergraph_t > &cluster_graphs, vector< multipath_alignment_t > &multipath_alns_out, vector< double > &multiplicities_out, size_t num_mapping_attempts, const match_fanouts_t *fanouts=nullptr, vector< size_t > *cluster_idxs=nullptr) | vg::MultipathMapper | protected |
| align_to_cluster_graphs_with_rescue(const Alignment &alignment1, const Alignment &alignment2, vector< clustergraph_t > &cluster_graphs1, vector< clustergraph_t > &cluster_graphs2, vector< MaximalExactMatch > &mems1, vector< MaximalExactMatch > &mems2, vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, vector< pair< pair< size_t, size_t >, int64_t >> &pair_distances_out, vector< double > &pair_multiplicities_out, const match_fanouts_t *fanouts1, const match_fanouts_t *fanouts2) | vg::MultipathMapper | protected |
| align_to_splice_candidates(const Alignment &alignment, vector< clustergraph_t > &cluster_graphs, const vector< MaximalExactMatch > &mems, const vector< size_t > &cluster_candidates, const vector< pair< const MaximalExactMatch *, pos_t >> &hit_candidates, const pair< int64_t, int64_t > &primary_interval, bool searching_left, bool is_read_1, unordered_map< candidate_id_t, pair< multipath_alignment_t, double >> &unaligned_candidate_bank, vector< candidate_id_t > &candidates_out, const match_fanouts_t *mem_fanouts=nullptr) const | vg::MultipathMapper | protected |
| AlignerClient(double gc_content_estimate=vg::default_gc_content) | vg::AlignerClient | protected |
| alt_anchor_max_length_diff | vg::MultipathMapper | |
| always_check_population | vg::MultipathMapper | |
| apply_haplotype_consistency_scores(const vector< Alignment * > &alns) | vg::BaseMapper | |
| are_consistent(const multipath_alignment_t &multipath_aln_1, const multipath_alignment_t &multipath_aln_2) const | vg::MultipathMapper | protected |
| assume_acyclic | vg::BaseMapper | |
| attempt_rescue(const multipath_alignment_t &multipath_aln, const Alignment &other_aln, bool rescue_forward, multipath_alignment_t &rescue_multipath_aln) | vg::MultipathMapper | protected |
| attempt_rescue_for_secondaries(const Alignment &alignment1, const Alignment &alignment2, vector< clustergraph_t > &cluster_graphs1, vector< clustergraph_t > &cluster_graphs2, vector< pair< size_t, size_t >> &duplicate_pairs, vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< double > &pair_multiplicities, const match_fanouts_t *fanouts1, const match_fanouts_t *fanouts2) | vg::MultipathMapper | protected |
| attempt_rescue_for_splice_segment(const Alignment &alignment, const pair< int64_t, int64_t > &primary_interval, const multipath_alignment_t &rescue_anchor, bool rescue_left, multipath_alignment_t &rescued_out) const | vg::MultipathMapper | protected |
| attempt_unpaired_multipath_map_of_pair(const Alignment &alignment1, const Alignment &alignment2, vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, vector< pair< Alignment, Alignment >> &ambiguous_pair_buffer) | vg::MultipathMapper | protected |
| avg_node_length | vg::BaseMapper | |
| BaseMapper(PathPositionHandleGraph *xidex, gcsa::GCSA *g, gcsa::LCPArray *a, haplo::ScoreProvider *haplo_score_provider=nullptr) | vg::BaseMapper | |
| BaseMapper(void) | vg::BaseMapper | |
| calibrate_mismapping_detection(size_t num_simulations, const vector< size_t > &simulated_read_lengths) | vg::MultipathMapper | |
| candidate_id_t typedef | vg::MultipathMapper | |
| choose_band_padding | vg::MultipathMapper | |
| cluster_multiplicity(const memcluster_t &cluster) const | vg::MultipathMapper | protected |
| clustergraph_t typedef | vg::MultipathMapper | |
| component_min_dist | vg::MultipathMapper | |
| compute_raw_mapping_qualities_from_scores(const vector< double > &scores, bool have_qualities, const vector< double > *multiplicities=nullptr) const | vg::MultipathMapper | protected |
| covered_intervals(const Alignment &alignment, const clustergraph_t &cluster) const | vg::MultipathMapper | protected |
| debug | vg::BaseMapper | |
| determine_distance_correlation() | vg::MultipathMapper | |
| dinuc_machine | vg::MultipathMapper | protected |
| distance(const pos_t &pos_1, const pos_t &pos_2) const | vg::MultipathMapper | protected |
| distance_between(const multipath_alignment_t &multipath_aln_1, const multipath_alignment_t &multipath_aln_2, bool full_fragment=false, bool forward_strand=false) const | vg::MultipathMapper | protected |
| distance_index | vg::MultipathMapper | protected |
| do_rescue_alignment(const multipath_alignment_t &multipath_aln, const Alignment &other_aln, bool rescue_forward, multipath_alignment_t &rescue_multipath_aln, double rescue_mean_length, double num_std_devs) const | vg::MultipathMapper | protected |
| do_spliced_alignment | vg::MultipathMapper | |
| dynamic_max_alt_alns | vg::MultipathMapper | |
| establish_strand_consistency(vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs) | vg::MultipathMapper | protected |
| estimate_gc_content(const gcsa::GCSA *gcsa) | vg::BaseMapper | static |
| estimate_missed_rescue_multiplicity(size_t which_pair, const vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, const vector< clustergraph_t > &cluster_graphs1, const vector< clustergraph_t > &cluster_graphs2, bool from_secondary_rescue) const | vg::MultipathMapper | protected |
| exclude_unaligned | vg::BaseMapper | |
| expand_for_softclips(clustergraph_t &cluster_graph, const multipath_alignment_t &multipath_aln) const | vg::MultipathMapper | protected |
| extract_cluster_graph(const Alignment &alignment, const memcluster_t &mem_cluster) const | vg::MultipathMapper | protected |
| extract_maximal_graph(const Alignment &alignment, const memcluster_t &mem_cluster) const | vg::MultipathMapper | protected |
| extract_rescue_graph(const multipath_alignment_t &multipath_aln, const Alignment &other_aln, bool rescue_forward, MutableHandleGraph *rescue_graph, double rescue_mean_length, double num_std_devs) const | vg::MultipathMapper | protected |
| extract_restrained_graph(const Alignment &alignment, const memcluster_t &mem_cluster) const | vg::MultipathMapper | protected |
| fanout_length_threshold | vg::BaseMapper | |
| fast_reseed | vg::BaseMapper | |
| fast_reseed_length_diff | vg::BaseMapper | |
| filter_short_mems | vg::BaseMapper | |
| find_fanout_mems(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator qual_begin, int max_fans_out, char max_fanout_base_quality, vector< deque< pair< string::const_iterator, char >>> *mem_fanout_breaks=nullptr) | vg::BaseMapper | |
| find_mems(const Alignment &alignment, vector< deque< pair< string::const_iterator, char >>> *mem_fanout_breaks=nullptr) | vg::MultipathMapper | protected |
| find_mems_deep(string::const_iterator seq_begin, string::const_iterator seq_end, double &lcp_avg, double &fraction_filtered, int max_mem_length=0, int min_mem_length=1, int reseed_length=0, bool use_lcp_reseed_heuristic=false, bool use_diff_based_fast_reseed=false, bool include_parent_in_sub_mem_count=false, bool record_max_lcp=false, int reseed_below_count=0) | vg::BaseMapper | |
| find_mems_simple(string::const_iterator seq_begin, string::const_iterator seq_end, int max_mem_length=0, int min_mem_length=1, int reseed_length=0) | vg::BaseMapper | |
| find_rescuable_spliced_alignments(const Alignment &alignment, multipath_alignment_t &splice_anchor, double &anchor_multiplicity, SpliceStrand &strand, const multipath_alignment_t &rescue_anchor, double rescue_multiplicity, bool rescue_left, const pair< int64_t, int64_t > &primary_interval) const | vg::MultipathMapper | protected |
| find_spliced_alignments(const Alignment &alignment, vector< multipath_alignment_t > &multipath_alns_out, vector< double > &multiplicities, vector< size_t > &cluster_idxs, const vector< MaximalExactMatch > &mems, vector< clustergraph_t > &cluster_graphs, const match_fanouts_t *fanouts=nullptr, const multipath_alignment_t *rescue_anchor=nullptr, bool rescue_left=false, double rescue_multiplicity=1.0) | vg::MultipathMapper | protected |
| find_spliced_alignments(const Alignment &alignment1, const Alignment &alignment2, vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< double > &pair_multiplicities, const vector< MaximalExactMatch > &mems1, const vector< MaximalExactMatch > &mems2, vector< clustergraph_t > &cluster_graphs1, vector< clustergraph_t > &cluster_graphs2, const match_fanouts_t *fanouts=nullptr) | vg::MultipathMapper | protected |
| find_stripped_matches(string::const_iterator seq_begin, string::const_iterator seq_end, size_t strip_length, size_t max_match_length, size_t target_count) | vg::BaseMapper | |
| find_sub_mems(const vector< MaximalExactMatch > &mems, int parent_layer_begin, int parent_layer_end, int mem_idx, string::const_iterator next_mem_end, int min_mem_length, vector< pair< MaximalExactMatch, vector< size_t >>> &sub_mems_out) | vg::BaseMapper | |
| find_sub_mems_fast(const vector< MaximalExactMatch > &mems, int parent_layer_begin, int parent_layer_end, int mem_idx, string::const_iterator leftmost_guaranteed_disjoint_bound, string::const_iterator leftmost_seeding_bound, int min_sub_mem_length, vector< pair< MaximalExactMatch, vector< size_t >>> &sub_mems_out) | vg::BaseMapper | |
| force_fragment_length_distr(double mean, double stddev) | vg::PairedEndMapper | |
| force_haplotype_count | vg::MultipathMapper | |
| Forward enum value | vg::MultipathMapper | protected |
| fragment_length_distr | vg::PairedEndMapper | protected |
| fragment_length_log_likelihood(int64_t length) const | vg::MultipathMapper | protected |
| fragment_length_warning_factor | vg::MultipathMapper | |
| gap_memo_max_size | vg::MultipathMapper | protectedstatic |
| gc_content_estimate | vg::AlignerClient | private |
| gcsa | vg::BaseMapper | |
| get_adaptive_min_reseed_length(size_t parent_mem_length) | vg::BaseMapper | |
| get_aligner(bool have_qualities=true) const | vg::AlignerClient | protected |
| get_cluster_pairs(const Alignment &alignment1, const Alignment &alignment2, vector< clustergraph_t > &cluster_graphs1, vector< clustergraph_t > &cluster_graphs2, OrientedDistanceMeasurer *distance_measurer=nullptr) | vg::MultipathMapper | protected |
| get_clusters(const Alignment &alignment, const vector< MaximalExactMatch > &mems, OrientedDistanceMeasurer *distance_measurer=nullptr, const match_fanouts_t *fanouts=nullptr) const | vg::MultipathMapper | protected |
| get_distance_measurer(MemoizingGraph &memoizing_graph) const | vg::MultipathMapper | protected |
| get_qual_adj_aligner() const | vg::AlignerClient | protected |
| get_regular_aligner() const | vg::AlignerClient | protected |
| get_rescue_graph_from_paths | vg::MultipathMapper | |
| get_rr_memo(double recombination_penalty, size_t population_size) const | vg::MultipathMapper | protected |
| greedy_min_dist | vg::MultipathMapper | |
| greedy_restart_assume_substitution | vg::BaseMapper | |
| greedy_restart_max_count | vg::BaseMapper | |
| greedy_restart_max_lcp | vg::BaseMapper | |
| greedy_restart_min_length | vg::BaseMapper | |
| haplo_score_provider | vg::BaseMapper | |
| haplotype_consistency_exponent | vg::BaseMapper | |
| hard_hit_max | vg::BaseMapper | |
| has_fixed_fragment_length_distr() | vg::PairedEndMapper | |
| hit_max | vg::BaseMapper | |
| identify_aligned_splice_candidates(const Alignment &alignment, bool search_left, const pair< int64_t, int64_t > &primary_interval, const vector< multipath_alignment_t > &multipath_alns, const vector< size_t > &cluster_idxs, const vector< int64_t > ¤t_index, int64_t anchor, unordered_set< size_t > &clusters_used_out, vector< size_t > &mp_aln_candidates_out) const | vg::MultipathMapper | protected |
| identify_aligned_splice_candidates(const Alignment &alignment, bool read_1, bool search_left, const pair< int64_t, int64_t > &primary_interval, const vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs, const vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, const vector< int64_t > ¤t_index, int64_t anchor, unordered_set< size_t > &clusters_used_out, vector< size_t > &mp_aln_candidates_out) const | vg::MultipathMapper | protected |
| identify_unaligned_splice_candidates(const Alignment &alignment, bool search_left, const pair< int64_t, int64_t > &primary_interval, const vector< MaximalExactMatch > &mems, const vector< clustergraph_t > &cluster_graphs, const unordered_set< size_t > &clusters_already_used, vector< size_t > &cluster_candidates_out, vector< pair< const MaximalExactMatch *, pos_t >> &hit_candidates_out) const | vg::MultipathMapper | protected |
| is_consistent(int64_t distance) const | vg::MultipathMapper | protected |
| lcp | vg::BaseMapper | |
| likely_mismapping(const multipath_alignment_t &multipath_aln) | vg::MultipathMapper | protected |
| likely_misrescue(const multipath_alignment_t &multipath_aln) | vg::MultipathMapper | protected |
| log_likelihood_approx_factor | vg::MultipathMapper | |
| make_nontrivial_multipath_alignment(const Alignment &alignment, const HandleGraph &subgraph, const function< pair< id_t, bool >(id_t)> &translator, multipath_alignment_t &multipath_aln_out) const | vg::MultipathMapper | protected |
| mapping_likelihoods(vector< multipath_alignment_t > &multipath_alns) const | vg::MultipathMapper | protected |
| mapping_quality_method | vg::BaseMapper | |
| mapq_scaling_factor | vg::MultipathMapper | |
| match_fanouts_t typedef | vg::MultipathMapper | |
| max_alignment_gap | vg::MultipathMapper | |
| max_alt_mappings | vg::MultipathMapper | |
| max_branch_trim_length | vg::MultipathMapper | |
| max_dagify_duplications | vg::MultipathMapper | |
| max_expected_dist_approx_error | vg::MultipathMapper | |
| max_exponential_rate_intercept | vg::MultipathMapper | |
| max_exponential_rate_slope | vg::MultipathMapper | |
| max_exponential_shape_intercept | vg::MultipathMapper | |
| max_exponential_shape_slope | vg::MultipathMapper | |
| max_fanout_base_quality | vg::MultipathMapper | |
| max_fans_out | vg::MultipathMapper | |
| max_intron_length | vg::MultipathMapper | |
| max_mapping_p_value | vg::MultipathMapper | |
| max_mapping_quality | vg::BaseMapper | |
| max_motif_pairs | vg::MultipathMapper | |
| max_p_value_memo_size | vg::MultipathMapper | |
| max_rescue_attempts | vg::MultipathMapper | |
| max_rescue_p_value | vg::MultipathMapper | |
| max_single_end_mappings_for_rescue | vg::MultipathMapper | |
| max_snarl_cut_size | vg::MultipathMapper | |
| max_softclip_overlap | vg::MultipathMapper | |
| max_splice_overhang | vg::MultipathMapper | |
| max_splice_ref_search_length | vg::MultipathMapper | |
| max_sub_mem_recursion_depth | vg::BaseMapper | |
| max_suboptimal_path_score_ratio | vg::MultipathMapper | |
| max_tail_merge_supress_length | vg::MultipathMapper | |
| mem_coverage_min_ratio | vg::MultipathMapper | |
| mem_reseed_length | vg::BaseMapper | |
| memcluster_t typedef | vg::MultipathMapper | |
| merge_rescued_mappings(vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< double > &pair_multiplicities, vector< pair< multipath_alignment_t, multipath_alignment_t >> &rescued_multipath_aln_pairs, vector< pair< pair< size_t, size_t >, int64_t >> &rescued_cluster_pairs, vector< double > &rescued_multiplicities) const | vg::MultipathMapper | protected |
| min_clustering_mem_length | vg::MultipathMapper | |
| min_median_mem_coverage_for_split | vg::MultipathMapper | |
| min_mem_length | vg::BaseMapper | |
| min_softclip_length_for_splice | vg::MultipathMapper | protected |
| min_softclipped_score_for_splice | vg::MultipathMapper | protected |
| min_splice_rescue_matches | vg::MultipathMapper | |
| min_tail_anchor_length | vg::MultipathMapper | |
| multipath_align(const Alignment &alignment, clustergraph_t &cluster_graph, multipath_alignment_t &multipath_aln_out, const match_fanouts_t *fanouts) const | vg::MultipathMapper | protected |
| multipath_map(const Alignment &alignment, vector< multipath_alignment_t > &multipath_alns_out) | vg::MultipathMapper | |
| multipath_map_paired(const Alignment &alignment1, const Alignment &alignment2, vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, vector< pair< Alignment, Alignment >> &ambiguous_pair_buffer) | vg::MultipathMapper | |
| MultipathMapper(PathPositionHandleGraph *graph, gcsa::GCSA *gcsa_index, gcsa::LCPArray *lcp_array, haplo::ScoreProvider *haplo_score_provider=nullptr, SnarlManager *snarl_manager=nullptr, SnarlDistanceIndex *distance_index=nullptr) | vg::MultipathMapper | |
| no_clustering | vg::MultipathMapper | |
| no_splice_log_odds | vg::MultipathMapper | protected |
| no_splice_natural_log_odds | vg::MultipathMapper | protected |
| num_alt_alns | vg::MultipathMapper | |
| num_mapping_attempts | vg::MultipathMapper | |
| order_length_repeat_hit_max | vg::MultipathMapper | |
| p_value_memo | vg::MultipathMapper | protectedstatic |
| pair_cluster_multiplicity(const memcluster_t &cluster_1, const memcluster_t &cluster_2) const | vg::MultipathMapper | protected |
| pair_mapping_likelihoods(vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs, const vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs) const | vg::MultipathMapper | protected |
| parse_matrix(std::istream &matrix_stream) | vg::AlignerClient | static |
| path_component_index | vg::MultipathMapper | protected |
| pessimistic_gap(int64_t length, double multiplier) const | vg::MultipathMapper | protected |
| pessimistic_gap_memo | vg::MultipathMapper | protectedstatic |
| pessimistic_gap_multiplier | vg::MultipathMapper | |
| plausible_rescue_cluster_coverage_diff | vg::MultipathMapper | |
| population_max_paths | vg::MultipathMapper | |
| population_paths_hard_cap | vg::MultipathMapper | |
| precollapse_order_length_hits | vg::BaseMapper | |
| precollapse_order_length_runs(string::const_iterator seq_begin, vector< MaximalExactMatch > &mems) | vg::BaseMapper | |
| prefilter_redundant_hits | vg::BaseMapper | |
| prefilter_redundant_sub_mems(vector< MaximalExactMatch > &mems, vector< pair< int, vector< size_t >>> &sub_mem_containment_graph) | vg::BaseMapper | |
| prune_subpaths_multiplier | vg::MultipathMapper | |
| pseudo_length(const multipath_alignment_t &multipath_aln) const | vg::MultipathMapper | protected |
| purge_unmapped_alignments(vector< multipath_alignment_t > &multipath_alns_out) | vg::MultipathMapper | protected |
| purge_unmapped_alignments(vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, bool proper_paired) | vg::MultipathMapper | protected |
| qual_adj_aligner | vg::AlignerClient | private |
| query_cluster_graphs(const Alignment &alignment, const vector< MaximalExactMatch > &mems, const vector< memcluster_t > &clusters) const | vg::MultipathMapper | protected |
| random_match_length(double chance_random) | vg::BaseMapper | |
| random_match_p_value(int64_t match_length, size_t read_length) | vg::MultipathMapper | protected |
| read_1_adapter | vg::MultipathMapper | protected |
| read_1_adapter_lps | vg::MultipathMapper | protected |
| read_2_adapter | vg::MultipathMapper | protected |
| read_2_adapter_lps | vg::MultipathMapper | protected |
| reassign_split_clusters(const Alignment &alignment, vector< clustergraph_t > &cluster_graphs, const vector< const multipath_alignment_t * > &split_mp_alns, const vector< size_t * > &cluster_assignments, const vector< size_t * > &all_cluster_assignments) const | vg::MultipathMapper | protected |
| recombination_penalty | vg::MultipathMapper | |
| record_fanouts(const vector< MaximalExactMatch > &mems, vector< deque< pair< string::const_iterator, char >>> &fanouts) const | vg::MultipathMapper | protected |
| reduce_to_single_path(const multipath_alignment_t &multipath_aln, vector< Alignment > &alns_out, size_t max_number) const | vg::MultipathMapper | |
| ref_path_handles | vg::MultipathMapper | |
| regular_aligner | vg::AlignerClient | private |
| report_allelic_mapq | vg::MultipathMapper | |
| report_group_mapq | vg::MultipathMapper | |
| rescue_graph_std_devs | vg::MultipathMapper | |
| rescue_high_count_order_length_mems(vector< MaximalExactMatch > &mems, size_t max_rescue_hit_count) | vg::BaseMapper | |
| rescue_only_anchor_max | vg::MultipathMapper | |
| rescue_only_min | vg::MultipathMapper | |
| RESCUED | vg::MultipathMapper | protectedstatic |
| restrained_graph_extraction | vg::MultipathMapper | |
| retry_pairing_spliced_alignments(const Alignment &alignment1, const Alignment &alignment2, vector< multipath_alignment_t > &multipath_alns_1, vector< multipath_alignment_t > &multipath_alns_2, const vector< size_t > &cluster_idxs_1, const vector< size_t > &cluster_idxs_2, const vector< double > &multiplicities_1, const vector< double > &multiplicities_2, vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs_out, vector< double > &pair_multiplicities_out) const | vg::MultipathMapper | protected |
| Reverse enum value | vg::MultipathMapper | protected |
| reversing_walk_length | vg::MultipathMapper | |
| rr_memos | vg::MultipathMapper | protectedstatic |
| secondary_rescue_attempts | vg::MultipathMapper | |
| secondary_rescue_score_diff | vg::MultipathMapper | |
| secondary_rescue_subopt_diff | vg::MultipathMapper | |
| sequence_positions(const string &seq) | vg::BaseMapper | |
| set_alignment_scores(const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus) | vg::MultipathMapper | virtual |
| set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus) | vg::MultipathMapper | |
| set_alignment_scores(std::istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus) | vg::MultipathMapper | |
| set_alignment_scores(const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus) | vg::MultipathMapper | |
| vg::BaseMapper::set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, double haplotype_consistency_exponent=1) | vg::BaseMapper | |
| vg::BaseMapper::set_alignment_scores(istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, double haplotype_consistency_exponent=1) | vg::BaseMapper | |
| 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 |
| set_automatic_min_clustering_length(double random_mem_probability=0.5) | vg::MultipathMapper | |
| set_fragment_length_distr_params(size_t maximum_sample_size=1000, size_t reestimation_frequency=1000, double robust_estimation_fraction=0.95) | vg::PairedEndMapper | |
| set_intron_length_distribution(const vector< double > &intron_mixture_weights, const vector< pair< double, double >> &intron_component_params) | vg::MultipathMapper | |
| set_log_odds_against_splice(double log_odds) | vg::MultipathMapper | |
| set_max_merge_supression_length() | vg::MultipathMapper | |
| set_min_softclip_length_for_splice(size_t length) | vg::MultipathMapper | |
| set_read_1_adapter(const string &adapter) | vg::MultipathMapper | |
| set_read_2_adapter(const string &adapter) | vg::MultipathMapper | |
| set_read_coverage(clustergraph_t &cluster_graph) | vg::MultipathMapper | protectedstatic |
| share_terminal_positions(const multipath_alignment_t &multipath_aln_1, const multipath_alignment_t &multipath_aln_2) const | vg::MultipathMapper | protected |
| short_mem_filter_factor | vg::BaseMapper | |
| simplify_complicated_multipath_alignment(multipath_alignment_t &multipath_aln) const | vg::MultipathMapper | protected |
| simplify_topologies | vg::MultipathMapper | |
| snarl_manager | vg::MultipathMapper | protected |
| sort_and_compute_mapping_quality(vector< multipath_alignment_t > &multipath_alns, vector< size_t > *cluster_idxs=nullptr, vector< double > *multiplicities=nullptr) const | vg::MultipathMapper | protected |
| sort_and_compute_mapping_quality(vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< pair< size_t, size_t >> *duplicate_pairs_out=nullptr, vector< double > *pair_multiplicities=nullptr) const | vg::MultipathMapper | protected |
| splice_rescue_graph_std_devs | vg::MultipathMapper | |
| splice_stats | vg::MultipathMapper | protected |
| SpliceStrand enum name | vg::MultipathMapper | protected |
| split_multicomponent_alignments(vector< multipath_alignment_t > &multipath_alns_out, const Alignment *alignment=nullptr, vector< clustergraph_t > *cluster_graphs=nullptr, vector< size_t > *cluster_idxs=nullptr, vector< double > *multiplicities=nullptr) const | vg::MultipathMapper | protected |
| split_multicomponent_alignments(const Alignment &alignment1, const Alignment &alignment2, vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, vector< clustergraph_t > &cluster_graphs1, vector< clustergraph_t > &cluster_graphs2, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< double > &multiplicities) const | vg::MultipathMapper | protected |
| strip_bonuses | vg::BaseMapper | |
| strip_full_length_bonuses(multipath_alignment_t &multipath_aln) const | vg::MultipathMapper | protected |
| stripped_match_alg_max_length | vg::MultipathMapper | |
| stripped_match_alg_strip_length | vg::MultipathMapper | |
| stripped_match_alg_target_count | vg::MultipathMapper | |
| sub_mem_count_thinning | vg::BaseMapper | |
| sub_mem_thinning_burn_in | vg::BaseMapper | |
| suppress_cluster_merging | vg::MultipathMapper | |
| suppress_mismapping_detection | vg::MultipathMapper | |
| suppress_multicomponent_splitting | vg::MultipathMapper | |
| suppress_p_value_memoization | vg::MultipathMapper | |
| suppress_tail_anchors | vg::MultipathMapper | |
| test_splice_candidates(const Alignment &alignment, bool searching_left, multipath_alignment_t &anchor_mp_aln, double *anchor_multiplicity_out, SpliceStrand &strand, int64_t num_candidates, const function< const multipath_alignment_t &(int64_t)> &get_candidate, const function< double(int64_t)> &get_multiplicity, const function< multipath_alignment_t &&(int64_t)> &consume_candidate) const | vg::MultipathMapper | protected |
| top_tracebacks | vg::MultipathMapper | |
| total_seq_length | vg::BaseMapper | |
| truncation_multiplicity_mq_limit | vg::MultipathMapper | |
| Undetermined enum value | vg::MultipathMapper | protected |
| unpaired_penalty | vg::BaseMapper | |
| use_approx_sub_mem_count | vg::BaseMapper | |
| use_fanout_match_alg | vg::MultipathMapper | |
| use_greedy_mem_restarts | vg::BaseMapper | |
| use_min_dist_clusterer | vg::MultipathMapper | |
| use_pessimistic_tail_alignment | vg::MultipathMapper | |
| use_population_mapqs | vg::MultipathMapper | |
| use_stripped_match_alg | vg::MultipathMapper | |
| use_tvs_clusterer | vg::MultipathMapper | |
| walk_fanout_path(string::const_iterator begin, string::const_iterator end, const deque< pair< string::const_iterator, char >> &fanout_breaks, gcsa::node_type pos) | vg::BaseMapper | |
| xindex | vg::BaseMapper | |
| ~MultipathMapper() | vg::MultipathMapper |
1.8.17