vg
tools for working with variation graphs
vg::MultipathMapper Member List

This is the complete list of members for vg::MultipathMapper, including all inherited members.

adaptive_diff_exponentvg::BaseMapper
adaptive_reseed_diffvg::BaseMapper
adaptive_reseed_length_memovg::BaseMapperstatic
adjust_alignments_for_base_qualityvg::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::MultipathMapperprotected
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::MultipathMapperprotected
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::MultipathMapperprotected
AlignerClient(double gc_content_estimate=vg::default_gc_content)vg::AlignerClientprotected
alt_anchor_max_length_diffvg::MultipathMapper
always_check_populationvg::MultipathMapper
apply_haplotype_consistency_scores(const vector< Alignment * > &alns)vg::BaseMapper
are_consistent(const MultipathAlignment &multipath_aln_1, const MultipathAlignment &multipath_aln_2) constvg::MultipathMapperprotected
assume_acyclicvg::BaseMapper
attempt_rescue(const MultipathAlignment &multipath_aln, const Alignment &other_aln, bool rescue_forward, MultipathAlignment &rescue_multipath_aln)vg::MultipathMapperprotected
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::MultipathMapperprotected
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::MultipathMapperprotected
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::MultipathMapperprotected
avg_node_lengthvg::BaseMapper
band_padding_memovg::MultipathMapperprotected
band_padding_memo_sizevg::MultipathMapper
band_padding_multipliervg::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) constvg::MultipathMapperprotected
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) constvg::MultipathMapperprotected
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) constvg::MultipathMapperprotected
clustergraph_t typedefvg::MultipathMapper
compute_raw_mapping_quality_from_scores(const vector< double > &scores, MappingQualityMethod mapq_method) constvg::MultipathMapperprotected
debugvg::BaseMapper
delay_population_scoringvg::MultipathMapper
distance_between(const MultipathAlignment &multipath_aln_1, const MultipathAlignment &multipath_aln_2, bool full_fragment=false, bool forward_strand=false) constvg::MultipathMapperprotected
distance_indexvg::MultipathMapperprotected
dynamic_max_alt_alnsvg::MultipathMapper
establish_strand_consistency(vector< pair< MultipathAlignment, MultipathAlignment >> &multipath_aln_pairs, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs)vg::MultipathMapperprotected
estimate_gc_content(const gcsa::GCSA *gcsa)vg::BaseMapperstatic
exclude_unalignedvg::BaseMapper
fast_reseedvg::BaseMapper
fast_reseed_length_diffvg::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_countvg::MultipathMapper
fragment_length_distrvg::PairedEndMapperprotected
fragment_length_log_likelihood(int64_t length) constvg::MultipathMapperprotected
gc_content_estimatevg::AlignerClientprivate
gcsavg::BaseMapper
get_adaptive_min_reseed_length(size_t parent_mem_length)vg::BaseMapper
get_aligner(bool have_qualities=true) constvg::AlignerClientprotected
get_cluster_pairs(const Alignment &alignment1, const Alignment &alignment2, vector< clustergraph_t > &cluster_graphs1, vector< clustergraph_t > &cluster_graphs2, OrientedDistanceMeasurer *distance_measurer=nullptr)vg::MultipathMapperprotected
get_clusters(const Alignment &alignment, const vector< MaximalExactMatch > &mems, OrientedDistanceMeasurer *distance_measurer=nullptr) constvg::MultipathMapperprotected
get_qual_adj_aligner() constvg::AlignerClientprotected
get_regular_aligner() constvg::AlignerClientprotected
get_rr_memo(double recombination_penalty, size_t population_size) constvg::MultipathMapperprotected
haplo_score_providervg::BaseMapper
haplotype_consistency_exponentvg::BaseMapper
has_fixed_fragment_length_distr()vg::PairedEndMapper
hit_maxvg::BaseMapper
init_band_padding_memo()vg::MultipathMapper
is_consistent(int64_t distance) constvg::MultipathMapperprotected
lcpvg::BaseMapper
likely_mismapping(const MultipathAlignment &multipath_aln)vg::MultipathMapperprotected
load_scoring_matrix(std::ifstream &matrix_stream)vg::AlignerClient
log_likelihood_approx_factorvg::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) constvg::MultipathMapperprotected
mapping_quality_methodvg::BaseMapper
mapq_scaling_factorvg::MultipathMapper
max_alt_mappingsvg::MultipathMapper
max_branch_trim_lengthvg::MultipathMapper
max_expected_dist_approx_errorvg::MultipathMapper
max_exponential_rate_interceptvg::MultipathMapper
max_exponential_rate_slopevg::MultipathMapper
max_exponential_shape_interceptvg::MultipathMapper
max_exponential_shape_slopevg::MultipathMapper
max_mapping_p_valuevg::MultipathMapper
max_mapping_qualityvg::BaseMapper
max_p_value_memo_sizevg::MultipathMapper
max_rescue_attemptsvg::MultipathMapper
max_single_end_mappings_for_rescuevg::MultipathMapper
max_snarl_cut_sizevg::MultipathMapper
max_sub_mem_recursion_depthvg::BaseMapper
max_suboptimal_path_score_ratiovg::MultipathMapper
mem_coverage_min_ratiovg::MultipathMapper
mem_reseed_lengthvg::BaseMapper
memcluster_t typedefvg::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) constvg::MultipathMapperprotected
min_clustering_mem_lengthvg::MultipathMapper
min_median_mem_coverage_for_splitvg::MultipathMapper
min_mem_lengthvg::BaseMapper
min_tail_anchor_lengthvg::MultipathMapper
multipath_align(const Alignment &alignment, const bdsg::HashGraph *graph, memcluster_t &graph_mems, MultipathAlignment &multipath_aln_out) constvg::MultipathMapperprotected
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::MultipathMapperprotected
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_alnsvg::MultipathMapper
num_mapping_attemptsvg::MultipathMapper
order_length_repeat_hit_maxvg::MultipathMapper
p_value_memovg::MultipathMapperprotectedstatic
path_component_indexvg::MultipathMapperprotected
plausible_rescue_cluster_coverage_diffvg::MultipathMapper
population_max_pathsvg::MultipathMapper
population_paths_hard_capvg::MultipathMapper
precollapse_order_length_hitsvg::BaseMapper
precollapse_order_length_runs(string::const_iterator seq_begin, vector< MaximalExactMatch > &mems)vg::BaseMapper
prefilter_redundant_hitsvg::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) constvg::MultipathMapperprotected
pseudo_length(const MultipathAlignment &multipath_aln) constvg::MultipathMapperprotected
qual_adj_alignervg::AlignerClientprivate
query_cluster_graphs(const Alignment &alignment, const vector< MaximalExactMatch > &mems, const vector< memcluster_t > &clusters)vg::MultipathMapperprotected
random_match_length(double chance_random)vg::BaseMapper
random_match_p_value(size_t match_length, size_t read_length)vg::MultipathMapperprotected
read_coverage(const memcluster_t &mem_hits)vg::MultipathMapperprotectedstatic
read_coverage_z_score(int64_t coverage, const Alignment &alignment) constvg::MultipathMapperprotected
recombination_penaltyvg::MultipathMapper
reduce_to_single_path(const MultipathAlignment &multipath_aln, vector< Alignment > &alns_out, size_t max_number) constvg::MultipathMapper
regular_alignervg::AlignerClientprivate
report_group_mapqvg::MultipathMapper
rescue_high_count_order_length_mems(vector< MaximalExactMatch > &mems, size_t max_rescue_hit_count)vg::BaseMapper
rescue_only_anchor_maxvg::MultipathMapper
rescue_only_minvg::MultipathMapper
reversing_walk_lengthvg::MultipathMapper
rr_memosvg::MultipathMapperprotectedstatic
secondary_rescue_attemptsvg::MultipathMapper
secondary_rescue_score_diffvg::MultipathMapper
secondary_rescue_subopt_diffvg::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) constvg::MultipathMapperprotected
simplify_topologiesvg::MultipathMapper
snarl_managervg::MultipathMapperprotected
sort_and_compute_mapping_quality(vector< MultipathAlignment > &multipath_alns, MappingQualityMethod mapq_method, vector< size_t > *cluster_idxs=nullptr) constvg::MultipathMapperprotected
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) constvg::MultipathMapperprotected
split_multicomponent_alignments(vector< MultipathAlignment > &multipath_alns_out, vector< size_t > *cluster_idxs=nullptr) constvg::MultipathMapperprotected
split_multicomponent_alignments(vector< pair< MultipathAlignment, MultipathAlignment >> &multipath_aln_pairs_out, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs) constvg::MultipathMapperprotected
strip_bonusesvg::BaseMapper
strip_full_length_bonuses(MultipathAlignment &multipath_aln) constvg::MultipathMapperprotected
sub_mem_count_thinningvg::BaseMapper
sub_mem_thinning_burn_invg::BaseMapper
suppress_cluster_mergingvg::MultipathMapper
suppress_tail_anchorsvg::MultipathMapper
top_tracebacksvg::MultipathMapper
total_seq_lengthvg::BaseMapper
unpaired_penaltyvg::BaseMapper
use_approx_sub_mem_countvg::BaseMapper
use_min_dist_clusterervg::MultipathMapper
use_population_mapqsvg::MultipathMapper
use_tvs_clusterervg::MultipathMapper
use_weibull_calibrationvg::MultipathMapper
weibull_offset_interceptvg::MultipathMapper
weibull_offset_slopevg::MultipathMapper
weibull_scale_interceptvg::MultipathMapper
weibull_scale_slopevg::MultipathMapper
weibull_shape_interceptvg::MultipathMapper
weibull_shape_slopevg::MultipathMapper
xindexvg::BaseMapper
~MultipathMapper()vg::MultipathMapper