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.
adaptive_diff_exponent | vg::BaseMapper | |
adaptive_reseed_diff | vg::BaseMapper | |
adaptive_reseed_length_memo | vg::BaseMapper | static |
adjust_alignments_for_base_quality | vg::AlignerClient | |
align_to_cluster_graph_pairs(const Alignment &alignment1, const Alignment &alignment2, vector< clustergraph_t > &cluster_graphs1, vector< clustergraph_t > &cluster_graphs2, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< pair< MultipathAlignment, MultipathAlignment >> &multipath_aln_pairs_out, vector< pair< size_t, size_t >> &duplicate_pairs_out) | vg::MultipathMapper | protected |
align_to_cluster_graphs(const Alignment &alignment, MappingQualityMethod mapq_method, vector< clustergraph_t > &cluster_graphs, vector< MultipathAlignment > &multipath_alns_out, size_t num_mapping_attempts, 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, bool block_rescue_from_1, bool block_rescue_from_2, vector< pair< MultipathAlignment, MultipathAlignment >> &multipath_aln_pairs_out, vector< pair< pair< size_t, size_t >, int64_t >> &pair_distances) | 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 MultipathAlignment &multipath_aln_1, const MultipathAlignment &multipath_aln_2) const | vg::MultipathMapper | protected |
assume_acyclic | vg::BaseMapper | |
attempt_rescue(const MultipathAlignment &multipath_aln, const Alignment &other_aln, bool rescue_forward, MultipathAlignment &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< MultipathAlignment, MultipathAlignment >> &multipath_aln_pairs_out, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs) | vg::MultipathMapper | protected |
attempt_rescue_of_repeat_from_non_repeat(const Alignment &alignment1, const Alignment &alignment2, const vector< MaximalExactMatch > &mems1, const vector< MaximalExactMatch > &mems2, bool do_repeat_rescue_from_1, bool do_repeat_rescue_from_2, vector< memcluster_t > &clusters1, vector< memcluster_t > &clusters2, vector< clustergraph_t > &cluster_graphs1, vector< clustergraph_t > &cluster_graphs2, vector< pair< MultipathAlignment, MultipathAlignment >> &multipath_aln_pairs_out, vector< pair< pair< size_t, size_t >, int64_t >> &pair_distances, OrientedDistanceMeasurer &distance_measurer) | vg::MultipathMapper | protected |
attempt_unpaired_multipath_map_of_pair(const Alignment &alignment1, const Alignment &alignment2, vector< pair< MultipathAlignment, MultipathAlignment >> &multipath_aln_pairs_out, vector< pair< Alignment, Alignment >> &ambiguous_pair_buffer) | vg::MultipathMapper | protected |
avg_node_length | vg::BaseMapper | |
band_padding_memo | vg::MultipathMapper | protected |
band_padding_memo_size | vg::MultipathMapper | |
band_padding_multiplier | vg::MultipathMapper | |
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 | |
cap_mapping_quality_by_hit_sampling_probability(vector< MultipathAlignment > &multipath_alns_out, vector< size_t > &cluster_idxs, vector< clustergraph_t > &cluster_graphs) const | vg::MultipathMapper | protected |
cap_mapping_quality_by_hit_sampling_probability(vector< pair< MultipathAlignment, MultipathAlignment >> &multipath_aln_pairs_out, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< clustergraph_t > &cluster_graphs1, vector< clustergraph_t > &cluster_graphs2, bool did_secondary_rescue) const | vg::MultipathMapper | protected |
cap_mapping_quality_by_rescue_probability(vector< pair< MultipathAlignment, MultipathAlignment >> &multipath_aln_pairs_out, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< clustergraph_t > &cluster_graphs1, vector< clustergraph_t > &cluster_graphs2, bool from_secondary_rescue) const | vg::MultipathMapper | protected |
clustergraph_t typedef | vg::MultipathMapper | |
compute_raw_mapping_quality_from_scores(const vector< double > &scores, MappingQualityMethod mapq_method) const | vg::MultipathMapper | protected |
debug | vg::BaseMapper | |
delay_population_scoring | vg::MultipathMapper | |
distance_between(const MultipathAlignment &multipath_aln_1, const MultipathAlignment &multipath_aln_2, bool full_fragment=false, bool forward_strand=false) const | vg::MultipathMapper | protected |
distance_index | vg::MultipathMapper | protected |
dynamic_max_alt_alns | vg::MultipathMapper | |
establish_strand_consistency(vector< pair< MultipathAlignment, MultipathAlignment >> &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 |
exclude_unaligned | vg::BaseMapper | |
fast_reseed | vg::BaseMapper | |
fast_reseed_length_diff | 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_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 | |
fragment_length_distr | vg::PairedEndMapper | protected |
fragment_length_log_likelihood(int64_t length) const | vg::MultipathMapper | 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_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 | vg::MultipathMapper | protected |
get_qual_adj_aligner() const | vg::AlignerClient | protected |
get_regular_aligner() const | vg::AlignerClient | protected |
get_rr_memo(double recombination_penalty, size_t population_size) const | vg::MultipathMapper | protected |
haplo_score_provider | vg::BaseMapper | |
haplotype_consistency_exponent | vg::BaseMapper | |
has_fixed_fragment_length_distr() | vg::PairedEndMapper | |
hit_max | vg::BaseMapper | |
init_band_padding_memo() | vg::MultipathMapper | |
is_consistent(int64_t distance) const | vg::MultipathMapper | protected |
lcp | vg::BaseMapper | |
likely_mismapping(const MultipathAlignment &multipath_aln) | vg::MultipathMapper | protected |
load_scoring_matrix(std::ifstream &matrix_stream) | vg::AlignerClient | |
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, SnarlManager &snarl_manager, MultipathAlignment &multipath_aln_out) const | vg::MultipathMapper | protected |
mapping_quality_method | vg::BaseMapper | |
mapq_scaling_factor | vg::MultipathMapper | |
max_alt_mappings | vg::MultipathMapper | |
max_branch_trim_length | 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_mapping_p_value | vg::MultipathMapper | |
max_mapping_quality | vg::BaseMapper | |
max_p_value_memo_size | vg::MultipathMapper | |
max_rescue_attempts | vg::MultipathMapper | |
max_single_end_mappings_for_rescue | vg::MultipathMapper | |
max_snarl_cut_size | vg::MultipathMapper | |
max_sub_mem_recursion_depth | vg::BaseMapper | |
max_suboptimal_path_score_ratio | vg::MultipathMapper | |
mem_coverage_min_ratio | vg::MultipathMapper | |
mem_reseed_length | vg::BaseMapper | |
memcluster_t typedef | vg::MultipathMapper | |
merge_rescued_mappings(vector< pair< MultipathAlignment, MultipathAlignment >> &multipath_aln_pairs_out, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< pair< MultipathAlignment, MultipathAlignment >> &rescued_multipath_aln_pairs, vector< pair< pair< size_t, size_t >, int64_t >> &rescued_cluster_pairs) const | vg::MultipathMapper | protected |
min_clustering_mem_length | vg::MultipathMapper | |
min_median_mem_coverage_for_split | vg::MultipathMapper | |
min_mem_length | vg::BaseMapper | |
min_tail_anchor_length | vg::MultipathMapper | |
multipath_align(const Alignment &alignment, const bdsg::HashGraph *graph, memcluster_t &graph_mems, MultipathAlignment &multipath_aln_out) const | vg::MultipathMapper | protected |
multipath_map(const Alignment &alignment, vector< MultipathAlignment > &multipath_alns_out) | vg::MultipathMapper | |
multipath_map_internal(const Alignment &alignment, MappingQualityMethod mapq_method, vector< MultipathAlignment > &multipath_alns_out) | vg::MultipathMapper | protected |
multipath_map_paired(const Alignment &alignment1, const Alignment &alignment2, vector< pair< MultipathAlignment, MultipathAlignment >> &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, MinimumDistanceIndex *distance_index=nullptr) | vg::MultipathMapper | |
num_alt_alns | vg::MultipathMapper | |
num_mapping_attempts | vg::MultipathMapper | |
order_length_repeat_hit_max | vg::MultipathMapper | |
p_value_memo | vg::MultipathMapper | protectedstatic |
path_component_index | vg::MultipathMapper | protected |
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 | |
prob_equivalent_clusters_hits_missed(const memcluster_t &cluster) const | vg::MultipathMapper | protected |
pseudo_length(const MultipathAlignment &multipath_aln) const | vg::MultipathMapper | protected |
qual_adj_aligner | vg::AlignerClient | private |
query_cluster_graphs(const Alignment &alignment, const vector< MaximalExactMatch > &mems, const vector< memcluster_t > &clusters) | vg::MultipathMapper | protected |
random_match_length(double chance_random) | vg::BaseMapper | |
random_match_p_value(size_t match_length, size_t read_length) | vg::MultipathMapper | protected |
read_coverage(const memcluster_t &mem_hits) | vg::MultipathMapper | protectedstatic |
read_coverage_z_score(int64_t coverage, const Alignment &alignment) const | vg::MultipathMapper | protected |
recombination_penalty | vg::MultipathMapper | |
reduce_to_single_path(const MultipathAlignment &multipath_aln, vector< Alignment > &alns_out, size_t max_number) const | vg::MultipathMapper | |
regular_aligner | vg::AlignerClient | private |
report_group_mapq | 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 | |
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(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, uint32_t xdrop_max_gap_length=default_xdrop_max_gap_length, 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, uint32_t xdrop_max_gap_length=default_xdrop_max_gap_length) | vg::AlignerClient | |
set_automatic_min_clustering_length(double random_mem_probability=0.5) | vg::MultipathMapper | |
set_cache_size(int new_cache_size) | vg::BaseMapper | |
set_fragment_length_distr_params(size_t maximum_sample_size=1000, size_t reestimation_frequency=1000, double robust_estimation_fraction=0.95) | vg::PairedEndMapper | |
share_terminal_positions(const MultipathAlignment &multipath_aln_1, const MultipathAlignment &multipath_aln_2) const | vg::MultipathMapper | protected |
simplify_topologies | vg::MultipathMapper | |
snarl_manager | vg::MultipathMapper | protected |
sort_and_compute_mapping_quality(vector< MultipathAlignment > &multipath_alns, MappingQualityMethod mapq_method, vector< size_t > *cluster_idxs=nullptr) const | vg::MultipathMapper | protected |
sort_and_compute_mapping_quality(vector< pair< MultipathAlignment, MultipathAlignment >> &multipath_aln_pairs, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, bool allow_population_component, vector< pair< size_t, size_t >> *duplicate_pairs_out=nullptr) const | vg::MultipathMapper | protected |
split_multicomponent_alignments(vector< MultipathAlignment > &multipath_alns_out, vector< size_t > *cluster_idxs=nullptr) const | vg::MultipathMapper | protected |
split_multicomponent_alignments(vector< pair< MultipathAlignment, MultipathAlignment >> &multipath_aln_pairs_out, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs) const | vg::MultipathMapper | protected |
strip_bonuses | vg::BaseMapper | |
strip_full_length_bonuses(MultipathAlignment &multipath_aln) const | vg::MultipathMapper | protected |
sub_mem_count_thinning | vg::BaseMapper | |
sub_mem_thinning_burn_in | vg::BaseMapper | |
suppress_cluster_merging | vg::MultipathMapper | |
suppress_tail_anchors | vg::MultipathMapper | |
top_tracebacks | vg::MultipathMapper | |
total_seq_length | vg::BaseMapper | |
unpaired_penalty | vg::BaseMapper | |
use_approx_sub_mem_count | vg::BaseMapper | |
use_min_dist_clusterer | vg::MultipathMapper | |
use_population_mapqs | vg::MultipathMapper | |
use_tvs_clusterer | vg::MultipathMapper | |
use_weibull_calibration | vg::MultipathMapper | |
weibull_offset_intercept | vg::MultipathMapper | |
weibull_offset_slope | vg::MultipathMapper | |
weibull_scale_intercept | vg::MultipathMapper | |
weibull_scale_slope | vg::MultipathMapper | |
weibull_shape_intercept | vg::MultipathMapper | |
weibull_shape_slope | vg::MultipathMapper | |
xindex | vg::BaseMapper | |
~MultipathMapper() | vg::MultipathMapper |