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vg
tools for working with variation graphs
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This is the complete list of members for vg::Mapper, 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 |
| adjacent_positions(const Position &pos1, const Position &pos2) | vg::Mapper | |
| adjust_alignments_for_base_quality | vg::AlignerClient | |
| align(const string &seq, int kmer_size=0, int stride=0, int max_mem_length=0, int band_width=1000, int band_overlap=500, bool xdrop_alignment=false) | vg::Mapper | |
| align(const Alignment &read, int kmer_size=0, int stride=0, int max_mem_length=0, int band_width=1000, int band_overlap=500, bool xdrop_alignment=false) | vg::Mapper | |
| align_banded(const Alignment &read, int kmer_size=0, int stride=0, int max_mem_length=0, int band_width=1000, int band_overlap=500, bool xdrop_alignment=false) | vg::Mapper | private |
| align_cluster(const Alignment &aln, const vector< MaximalExactMatch > &mems, bool traceback, bool xdrop_alignment=false) | vg::Mapper | |
| align_maybe_flip(const Alignment &base, HandleGraph &graph, bool flip, bool traceback, bool banded_global=false, bool xdrop_alignment=false) | vg::Mapper | |
| align_maybe_flip(const Alignment &base, HandleGraph &graph, const vector< MaximalExactMatch > &mems, bool flip, bool traceback, bool banded_global=false, bool xdrop_alignment=false) | vg::Mapper | |
| align_mem_multi(const Alignment &aln, vector< MaximalExactMatch > &mems, double &cluster_mq, double lcp_avg, double fraction_filtered, int max_mem_length, int keep_multimaps, int additional_multimaps, bool xdrop_alignment=false) | vg::Mapper | private |
| align_multi(const Alignment &aln, int kmer_size=0, int stride=0, int max_mem_length=0, int band_width=1000, int band_overlap=500, bool xdrop_alignment=false) | vg::Mapper | |
| align_multi_internal(bool compute_unpaired_qualities, const Alignment &aln, int kmer_size, int stride, int max_mem_length, int band_width, int band_overlap, double &cluster_mq, int keep_multimaps=0, int additional_multimaps=0, vector< MaximalExactMatch > *restricted_mems=nullptr, bool xdrop_alignment=false) | vg::Mapper | private |
| align_paired_multi(const Alignment &read1, const Alignment &read2, bool &queued_resolve_later, int max_mem_length=0, bool only_top_scoring_pair=false, bool retrying=false, bool xdrop_alignment=false) | vg::Mapper | |
| align_to_graph(const Alignment &aln, HandleGraph &graph, bool do_flip, bool traceback, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, bool keep_bonuses=true) | vg::Mapper | protected |
| align_to_graph(const Alignment &aln, HandleGraph &graph, const vector< MaximalExactMatch > &mems, bool do_flip, bool traceback, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, int xdrop_alignment=0, bool keep_bonuses=true) | vg::Mapper | protected |
| AlignerClient(double gc_content_estimate=vg::default_gc_content) | vg::AlignerClient | protected |
| alignment_end_position(const Alignment &aln) | vg::Mapper | |
| alignments_consistent(const map< string, double > &pos1, const map< string, double > &pos2, int fragment_size_bound) | vg::Mapper | |
| always_rescue | vg::Mapper | |
| apply_haplotype_consistency_scores(const vector< Alignment * > &alns) | vg::BaseMapper | |
| approx_alignment_position(const Alignment &aln) | vg::Mapper | |
| approx_distance(pos_t pos1, pos_t pos2) | vg::Mapper | |
| approx_fragment_length(const Alignment &aln1, const Alignment &aln2) | vg::Mapper | |
| approx_position(pos_t pos) | vg::Mapper | |
| assume_acyclic | vg::BaseMapper | |
| avg_node_length | vg::BaseMapper | |
| band_multimaps | vg::Mapper | |
| BaseMapper(PathPositionHandleGraph *xidex, gcsa::GCSA *g, gcsa::LCPArray *a, haplo::ScoreProvider *haplo_score_provider=nullptr) | vg::BaseMapper | |
| BaseMapper(void) | vg::BaseMapper | |
| check_alignment(const Alignment &aln) | vg::Mapper | |
| clusters_to_drop(const vector< vector< MaximalExactMatch > > &clusters) | vg::Mapper | |
| compute_cluster_mapping_quality(const vector< vector< MaximalExactMatch > > &clusters, int read_length) | vg::Mapper | |
| compute_mapping_qualities(vector< Alignment > &alns, double cluster_mq, double mq_estimate, double mq_cap) | vg::Mapper | private |
| compute_mapping_qualities(pair< vector< Alignment >, vector< Alignment >> &pair_alns, double cluster_mq, double mq_estmate1, double mq_estimate2, double mq_cap1, double mq_cap2) | vg::Mapper | private |
| compute_uniqueness(const Alignment &aln, const vector< MaximalExactMatch > &mems) | vg::Mapper | |
| debug | vg::BaseMapper | |
| drop_chain | vg::Mapper | |
| estimate_gc_content(const gcsa::GCSA *gcsa) | vg::BaseMapper | static |
| estimate_max_possible_mapping_quality(int length, double min_diffs, double next_min_diffs) | vg::Mapper | |
| exclude_unaligned | vg::BaseMapper | |
| extra_multimaps | vg::Mapper | |
| fanout_length_threshold | vg::BaseMapper | |
| fast_reseed | vg::BaseMapper | |
| fast_reseed_length_diff | vg::BaseMapper | |
| filter_and_process_multimaps(vector< Alignment > &all_alns, int total_multimaps) | vg::Mapper | private |
| 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_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_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 | |
| frag_stats | vg::Mapper | |
| fragment_length_distr | vg::PairedEndMapper | protected |
| 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_node_length(int64_t node_id) | vg::Mapper | |
| get_qual_adj_aligner() const | vg::AlignerClient | protected |
| get_regular_aligner() const | vg::AlignerClient | protected |
| graph_mixed_distance_estimate(pos_t pos1, pos_t pos2, int64_t maximum) | vg::Mapper | |
| 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 | |
| identity_weight | vg::Mapper | |
| imperfect_pairs_to_retry | vg::Mapper | |
| include_full_length_bonuses | vg::Mapper | |
| lcp | vg::BaseMapper | |
| likely_mate_positions(const Alignment &aln, bool is_first) | vg::Mapper | |
| make_bands(const Alignment &read, int band_width, int band_overlap, vector< pair< int, int >> &to_strip) | vg::Mapper | protected |
| Mapper(PathPositionHandleGraph *xidex, gcsa::GCSA *g, gcsa::LCPArray *a, haplo::ScoreProvider *haplo_score_provider=nullptr) | vg::Mapper | |
| Mapper(void) | vg::Mapper | |
| mapping_quality_method | vg::BaseMapper | |
| mate_rescues | vg::Mapper | |
| max_attempts | vg::Mapper | |
| max_band_jump | vg::Mapper | |
| max_cluster_mapping_quality | vg::Mapper | |
| max_mapping_quality | vg::BaseMapper | |
| max_multimaps | vg::Mapper | |
| max_possible_mapping_quality(int length) | vg::Mapper | |
| max_softclip_iterations | vg::Mapper | |
| max_sub_mem_recursion_depth | vg::BaseMapper | |
| max_target_factor | vg::Mapper | |
| max_xdrop_gap_length | vg::Mapper | |
| maybe_mq_threshold | vg::Mapper | |
| mem_reseed_length | vg::BaseMapper | |
| mems_id_clusters_to_alignments(const Alignment &alignment, vector< MaximalExactMatch > &mems, int additional_multimaps) | vg::Mapper | |
| min_banded_mq | vg::Mapper | |
| min_cluster_length | vg::Mapper | |
| min_identity | vg::Mapper | |
| min_mem_length | vg::BaseMapper | |
| min_multimaps | vg::Mapper | |
| min_pair_fragment_length(const Alignment &aln1, const Alignment &aln2) | vg::Mapper | |
| mq_overlap | vg::Mapper | |
| pair_consistent(Alignment &aln1, Alignment &aln2, double pval) | vg::Mapper | |
| pair_rescue(Alignment &mate1, Alignment &mate2, bool &tried1, bool &tried2, int match_score, int full_length_bonus, bool traceback, bool xdrop_alignment) | vg::Mapper | |
| pair_rescue_hang_threshold | vg::Mapper | |
| pair_rescue_retry_threshold | vg::Mapper | |
| parse_matrix(std::istream &matrix_stream) | vg::AlignerClient | static |
| patch_alignment(const Alignment &aln, int max_patch_length, bool trim_internal_deletions=true, bool xdrop_alignment=false) | vg::Mapper | |
| patch_alignments | vg::Mapper | |
| 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 | |
| qual_adj_aligner | vg::AlignerClient | private |
| random_match_length(double chance_random) | vg::BaseMapper | |
| recombination_penalty | vg::BaseMapper | |
| regular_aligner | vg::AlignerClient | private |
| remove_full_length_bonuses(Alignment &aln) | vg::Mapper | |
| rescue_high_count_order_length_mems(vector< MaximalExactMatch > &mems, size_t max_rescue_hit_count) | vg::BaseMapper | |
| score_alignment(const Alignment &aln, bool use_approx_distance=false) | vg::Mapper | |
| score_sort_and_deduplicate_alignments(vector< Alignment > &all_alns, const Alignment &original_alignment) | vg::Mapper | private |
| sequence_positions(const string &seq) | 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 | |
| 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 |
| vg::AlignerClient::set_alignment_scores(const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus) | vg::AlignerClient | virtual |
| set_fragment_length_distr_params(size_t maximum_sample_size=1000, size_t reestimation_frequency=1000, double robust_estimation_fraction=0.95) | vg::PairedEndMapper | |
| short_mem_filter_factor | vg::BaseMapper | |
| simultaneous_pair_alignment | vg::Mapper | |
| softclip_threshold | vg::Mapper | |
| strip_bonuses | vg::BaseMapper | |
| sub_mem_count_thinning | vg::BaseMapper | |
| sub_mem_thinning_burn_in | vg::BaseMapper | |
| thread_extension | vg::Mapper | |
| total_seq_length | vg::BaseMapper | |
| unpaired_penalty | vg::BaseMapper | |
| use_approx_sub_mem_count | vg::BaseMapper | |
| use_cluster_mq | vg::Mapper | |
| use_greedy_mem_restarts | vg::BaseMapper | |
| 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 | |
| warned_about_chunking | vg::Mapper | |
| xindex | vg::BaseMapper | |
| ~Mapper(void) | vg::Mapper |
1.8.17