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

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

adjust_alignments_for_base_qualityvg::AlignerClient
align_from_chainsvg::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::MinimizerMapperprotectedstatic
AlignerClient(double gc_content_estimate=vg::default_gc_content)vg::AlignerClientprotected
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) constvg::MinimizerMapperprotected
attempt_rescue(const Alignment &aligned_read, Alignment &rescued_alignment, const VectorView< Minimizer > &minimizers, bool rescue_forward)vg::MinimizerMapperprotected
chain_info_to_seed(const pos_t &hit, size_t minimizer, const gbwtgraph::Payload &chain_info)vg::MinimizerMapperinlineprotectedstatic
chain_min_scorevg::MinimizerMapper
chain_score_thresholdvg::MinimizerMapper
chaining_cluster_distancevg::MinimizerMapper
Cluster typedefvg::MinimizerMapperprotected
cluster_coverage_thresholdvg::MinimizerMapper
cluster_score_thresholdvg::MinimizerMapper
clusterervg::MinimizerMapperprotected
compute_mapq_caps(const Alignment &aln, const VectorView< Minimizer > &minimizers, const SmallBitset &explored)vg::MinimizerMapperprotected
default_align_from_chainsvg::MinimizerMapperstatic
default_chain_min_scorevg::MinimizerMapperstatic
default_chain_score_thresholdvg::MinimizerMapperstatic
default_chaining_cluster_distancevg::MinimizerMapperstatic
default_cluster_coverage_thresholdvg::MinimizerMapperstatic
default_cluster_score_thresholdvg::MinimizerMapperstatic
default_distance_limitvg::MinimizerMapperstatic
default_do_dpvg::MinimizerMapperstatic
default_exclude_overlapping_minvg::MinimizerMapperstatic
default_extension_score_thresholdvg::MinimizerMapperstatic
default_extension_set_min_scorevg::MinimizerMapperstatic
default_extension_set_score_thresholdvg::MinimizerMapperstatic
default_hard_hit_capvg::MinimizerMapperstatic
default_hit_capvg::MinimizerMapperstatic
default_initial_lookback_thresholdvg::MinimizerMapperstatic
default_item_bonusvg::MinimizerMapperstatic
default_lookback_item_hard_capvg::MinimizerMapperstatic
default_lookback_scale_factorvg::MinimizerMapperstatic
default_max_alignmentsvg::MinimizerMapperstatic
default_max_chain_connectionvg::MinimizerMapperstatic
default_max_clusters_to_chainvg::MinimizerMapperstatic
default_max_dozeu_cellsvg::MinimizerMapperstatic
default_max_dp_cellsvg::MinimizerMapperstatic
default_max_extensionsvg::MinimizerMapperstatic
default_max_fragment_lengthvg::MinimizerMapperstatic
default_max_indel_basesvg::MinimizerMapperstatic
default_max_local_extensionsvg::MinimizerMapperstatic
default_max_lookback_basesvg::MinimizerMapperstatic
default_max_multimapsvg::MinimizerMapperstatic
default_max_precluster_connectionsvg::MinimizerMapperstatic
default_max_rescue_attemptsvg::MinimizerMapperstatic
default_max_tail_lengthvg::MinimizerMapperstatic
default_max_unique_minvg::MinimizerMapperstatic
default_min_chainsvg::MinimizerMapperstatic
default_min_clusters_to_chainvg::MinimizerMapperstatic
default_min_extension_setsvg::MinimizerMapperstatic
default_min_extensionsvg::MinimizerMapperstatic
default_min_good_transition_score_per_basevg::MinimizerMapperstatic
default_min_lookback_itemsvg::MinimizerMapperstatic
default_min_precluster_connectionsvg::MinimizerMapperstatic
default_minimizer_score_fractionvg::MinimizerMapperstatic
default_num_bp_per_minvg::MinimizerMapperstatic
default_pad_cluster_score_thresholdvg::MinimizerMapperstatic
default_paired_distance_stdevsvg::MinimizerMapperstatic
default_paired_rescue_score_limitvg::MinimizerMapperstatic
default_precluster_connection_coverage_thresholdvg::MinimizerMapperstatic
default_rescue_seed_limitvg::MinimizerMapperstatic
default_rescue_subgraph_stdevsvg::MinimizerMapperstatic
default_reseed_search_distancevg::MinimizerMapperstatic
default_show_workvg::MinimizerMapperstatic
default_track_correctnessvg::MinimizerMapperstatic
default_track_provenancevg::MinimizerMapperstatic
dfs_gbwt(const Position &from, size_t walk_distance, const function< void(const handle_t &)> &enter_handle, const function< void(void)> exit_handle) constvg::MinimizerMapperprotected
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) constvg::MinimizerMapperprotected
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) constvg::MinimizerMapperprotected
distance_between(const pos_t &pos1, const pos_t &pos2)vg::MinimizerMapperprotected
distance_between(const Alignment &aln1, const Alignment &aln2)vg::MinimizerMapperprotected
distance_indexvg::MinimizerMapperprotected
distance_limitvg::MinimizerMapper
distance_to_annotation(int64_t distance) constvg::MinimizerMapperprotected
do_dpvg::MinimizerMapper
dump_chaining_problem(const std::vector< algorithms::Anchor > &anchors, const std::vector< size_t > &cluster_seeds_sorted, const HandleGraph &graph)vg::MinimizerMapperprotectedstatic
dump_debug_clustering(const Cluster &cluster, size_t cluster_number, const VectorView< Minimizer > &minimizers, const std::vector< Seed > &seeds)vg::MinimizerMapperprotectedstatic
dump_debug_extension_set(const HandleGraph &graph, const Alignment &aln, const vector< GaplessExtension > &extended_seeds)vg::MinimizerMapperprotectedstatic
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::MinimizerMapperprotectedstatic
dump_debug_query(const Alignment &aln)vg::MinimizerMapperprotectedstatic
dump_debug_query(const Alignment &aln1, const Alignment &aln2)vg::MinimizerMapperprotectedstatic
dump_debug_seeds(const VectorView< Minimizer > &minimizers, const std::vector< Seed > &seeds, const std::vector< size_t > &selected_seeds)vg::MinimizerMapperprotectedstatic
dump_debug_sequence(ostream &out, const string &sequence, size_t start_offset=0, size_t length_limit=std::numeric_limits< size_t >::max())vg::MinimizerMapperprotectedstatic
exclude_overlapping_minvg::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) constvg::MinimizerMapperprotected
extendervg::MinimizerMapperprotected
extension_score_thresholdvg::MinimizerMapper
extension_set_min_scorevg::MinimizerMapper
extension_set_score_thresholdvg::MinimizerMapper
extension_to_alignment(const GaplessExtension &extension, Alignment &alignment) constvg::MinimizerMapperprotected
faster_cap(const VectorView< Minimizer > &minimizers, vector< size_t > &minimizers_explored, const string &sequence, const string &quality_bytes)vg::MinimizerMapperprotectedstatic
finalize_fragment_length_distr()vg::MinimizerMapperinline
find_chain_alignment(const Alignment &aln, const VectorView< algorithms::Anchor > &to_chain, const std::vector< size_t > &chain) constvg::MinimizerMapperprotected
find_minimizers(const std::string &sequence, Funnel &funnel) constvg::MinimizerMapperprotected
find_optimal_tail_alignments(const Alignment &aln, const vector< GaplessExtension > &extended_seeds, LazyRNG &rng, Alignment &best, Alignment &second_best) constvg::MinimizerMapperprotected
find_seeds(const VectorView< Minimizer > &minimizers, const Alignment &aln, Funnel &funnel) constvg::MinimizerMapperprotected
fix_dozeu_end_deletions(Alignment &rescued_alignment) constvg::MinimizerMapperprotected
fix_dozeu_score(Alignment &rescued_alignment, const HandleGraph &rescue_graph, const std::vector< handle_t > &topological_order) constvg::MinimizerMapperprotected
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::MinimizerMapperprotectedstatic
force_fragment_length_distr(double mean, double stdev)vg::MinimizerMapperinline
fragment_distr_is_finalized()vg::MinimizerMapperinline
fragment_length_distrvg::MinimizerMapperprotected
gbwt_graphvg::MinimizerMapperprotected
gc_content_estimatevg::AlignerClientprivate
get_aligner(bool have_qualities=true) constvg::AlignerClientprotected
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) constvg::MinimizerMapperprotected
get_distance_limit(size_t read_length) constvg::MinimizerMapperinline
get_fragment_length_mean() constvg::MinimizerMapperinline
get_fragment_length_sample_size() constvg::MinimizerMapperinline
get_fragment_length_stdev() constvg::MinimizerMapperinline
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::MinimizerMapperprotectedstatic
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::MinimizerMapperprotectedstatic
get_qual_adj_aligner() constvg::AlignerClientprotected
get_regular_aligner() constvg::AlignerClientprotected
get_tail_forest(const GaplessExtension &extended_seed, size_t read_length, bool left_tails, size_t *longest_detectable_gap=nullptr) constvg::MinimizerMapperprotected
hard_hit_capvg::MinimizerMapper
hit_capvg::MinimizerMapper
immutable_path_from_length(const ImmutablePath &path)vg::MinimizerMapperprotectedstatic
ImmutablePath typedefvg::MinimizerMapperprotected
initial_lookback_thresholdvg::MinimizerMapper
item_bonusvg::MinimizerMapper
log_alignment(const Alignment &aln)vg::MinimizerMapperprotectedstatic
log_alignment(const Path &path, bool force_condensed=false)vg::MinimizerMapperprotectedstatic
log_bits(const std::vector< bool > &bits)vg::MinimizerMapperprotectedstatic
log_name()vg::MinimizerMapperprotectedstatic
LONG_LIMITvg::MinimizerMapperprotectedstatic
lookback_item_hard_capvg::MinimizerMapper
lookback_scale_factorvg::MinimizerMapper
MANY_LIMITvg::MinimizerMapperprotectedstatic
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_alignmentsvg::MinimizerMapper
max_chain_connectionvg::MinimizerMapper
max_clusters_to_chainvg::MinimizerMapper
max_dozeu_cellsvg::MinimizerMapper
max_dp_cellsvg::MinimizerMapper
MAX_DP_LENGTHvg::MinimizerMapperstatic
max_extensionsvg::MinimizerMapper
max_fragment_lengthvg::MinimizerMapper
max_indel_basesvg::MinimizerMapper
max_local_extensionsvg::MinimizerMapper
max_lookback_basesvg::MinimizerMapper
max_multimapsvg::MinimizerMapper
max_precluster_connectionsvg::MinimizerMapper
max_rescue_attemptsvg::MinimizerMapper
max_tail_lengthvg::MinimizerMapper
max_unique_minvg::MinimizerMapper
min_chainsvg::MinimizerMapper
min_clusters_to_chainvg::MinimizerMapper
min_extension_setsvg::MinimizerMapper
min_extensionsvg::MinimizerMapper
min_good_transition_score_per_basevg::MinimizerMapper
min_lookback_itemsvg::MinimizerMapper
min_precluster_connectionsvg::MinimizerMapper
minimizer_indexvg::MinimizerMapperprotected
minimizer_score_fractionvg::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::MinimizerMapperinlineprotectedstatic
num_bp_per_minvg::MinimizerMapper
pad_cluster_score_thresholdvg::MinimizerMapper
pair_all(std::array< vector< Alignment >, 2 > &mappings) constvg::MinimizerMapperprotected
paired_distance_stdevsvg::MinimizerMapper
paired_rescue_score_limitvg::MinimizerMapper
parse_matrix(std::istream &matrix_stream)vg::AlignerClientstatic
path_graphvg::MinimizerMapperprotected
precluster_connection_coverage_thresholdvg::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) constvg::MinimizerMapperprotected
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) constvg::MinimizerMapperprotected
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) constvg::MinimizerMapperprotected
qual_adj_alignervg::AlignerClientprivate
read_groupvg::MinimizerMapper
regular_alignervg::AlignerClientprivate
rescue_algorithmvg::MinimizerMapper
rescue_dozeu enum valuevg::MinimizerMapper
rescue_gssw enum valuevg::MinimizerMapper
rescue_none enum valuevg::MinimizerMapper
rescue_seed_limitvg::MinimizerMapper
rescue_subgraph_stdevsvg::MinimizerMapper
RescueAlgorithm enum namevg::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) constvg::MinimizerMapperprotected
reseed_search_distancevg::MinimizerMapper
sample_namevg::MinimizerMapper
score_alignment_pair(Alignment &aln1, Alignment &aln2, int64_t fragment_distance)vg::MinimizerMapperprotected
score_cluster(Cluster &cluster, size_t i, const VectorView< Minimizer > &minimizers, const std::vector< Seed > &seeds, size_t seq_length, Funnel &funnel) constvg::MinimizerMapperprotected
score_extension_group(const Alignment &aln, const vector< GaplessExtension > &extended_seeds, int gap_open_penalty, int gap_extend_penalty)vg::MinimizerMapperprotectedstatic
score_extensions(const std::vector< std::vector< GaplessExtension >> &extensions, const Alignment &aln, Funnel &funnel) constvg::MinimizerMapperprotected
score_extensions(const std::vector< std::pair< std::vector< GaplessExtension >, size_t >> &extensions, const Alignment &aln, Funnel &funnel) constvg::MinimizerMapperprotected
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) constvg::MinimizerMapperprotected
Seed typedefvg::MinimizerMapper
seeds_in_subgraph(const VectorView< Minimizer > &minimizers, const std::unordered_set< nid_t > &subgraph) constvg::MinimizerMapperprotected
set_alignment_scores(const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)vg::MinimizerMappervirtual
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::AlignerClientvirtual
vg::AlignerClient::set_alignment_scores(std::istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)vg::AlignerClientvirtual
show_workvg::MinimizerMapper
sort_minimizers_by_score(const std::vector< Minimizer > &minimizers) constvg::MinimizerMapperprotected
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) constvg::MinimizerMapperprotected
TestMinimizerMapper classvg::MinimizerMapperfriend
to_anchor(const Alignment &aln, const VectorView< Minimizer > &minimizers, const Seed &seed) constvg::MinimizerMapperprotected
to_anchors(const Alignment &aln, const VectorView< Minimizer > &minimizers, const std::vector< Seed > &seeds) constvg::MinimizerMapperprotected
to_path(const ImmutablePath &path)vg::MinimizerMapperprotectedstatic
to_wfa_alignment(const algorithms::Anchor &anchor) constvg::MinimizerMapperprotected
track_correctnessvg::MinimizerMapper
track_provenancevg::MinimizerMapper
unoriented_distance_between(const pos_t &pos1, const pos_t &pos2) constvg::MinimizerMapperprotected
validate_clusters(const std::vector< std::vector< Cluster >> &clusters, const std::vector< std::vector< Seed >> &seeds, size_t read_limit, size_t fragment_limit) constvg::MinimizerMapperprotected
warned_about_bad_distributionvg::MinimizerMapperprotected
warned_about_rescue_sizevg::MinimizerMapper
warned_about_tail_sizevg::MinimizerMappermutable
wfa_alignment_to_alignment(const WFAAlignment &wfa_alignment, Alignment &alignment) constvg::MinimizerMapperprotected
window_breaking_quality(const VectorView< Minimizer > &minimizers, vector< size_t > &broken, const string &sequence, const string &quality_bytes)vg::MinimizerMapperprotectedstatic
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::MinimizerMapperprotectedstatic