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
AlignerClient(double gc_content_estimate=vg::default_gc_content)vg::AlignerClientprotected
attempt_rescue(const Alignment &aligned_read, Alignment &rescued_alignment, const std::vector< Minimizer > &minimizers, bool rescue_forward)vg::MinimizerMapperprotected
Cluster typedefvg::MinimizerMapperprotected
cluster_coverage_thresholdvg::MinimizerMapper
cluster_score_thresholdvg::MinimizerMapper
clusterervg::MinimizerMapperprotected
compute_mapq_caps(const Alignment &aln, const std::vector< Minimizer > &minimizers, const SmallBitset &explored)vg::MinimizerMapperprotected
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 Alignment &aln1, const Alignment &aln2)vg::MinimizerMapperprotected
distance_indexvg::MinimizerMapperprotected
distance_limitvg::MinimizerMapper
do_dpvg::MinimizerMapper
dump_debug_extension_set(const HandleGraph &graph, const Alignment &aln, const vector< GaplessExtension > &extended_seeds)vg::MinimizerMapperprotectedstatic
dump_debug_minimizers(const vector< Minimizer > &minimizers, const string &sequence, const vector< size_t > *to_include=nullptr)vg::MinimizerMapperprotectedstatic
dump_debug_sequence(ostream &out, const string &sequence)vg::MinimizerMapperprotectedstatic
extendervg::MinimizerMapperprotected
extension_score_thresholdvg::MinimizerMapper
extension_set_score_thresholdvg::MinimizerMapper
extension_to_alignment(const GaplessExtension &extension, Alignment &alignment) constvg::MinimizerMapperprotected
faster_cap(const vector< Minimizer > &minimizers, vector< size_t > &minimizers_explored, const string &sequence, const string &quality_bytes)vg::MinimizerMapperprotectedstatic
finalize_fragment_length_distr()vg::MinimizerMapperinline
find_connecting_paths(const vector< GaplessExtension > &extended_seeds, size_t read_length) constvg::MinimizerMapperprotected
find_minimizers(const std::string &sequence, Funnel &funnel) constvg::MinimizerMapperprotected
find_optimal_tail_alignments(const Alignment &aln, const vector< GaplessExtension > &extended_seeds, Alignment &best, Alignment &second_best) constvg::MinimizerMapperprotected
find_seeds(const std::vector< Minimizer > &minimizers, const Alignment &aln, Funnel &funnel) constvg::MinimizerMapperprotected
fix_dozeu_score(Alignment &rescued_alignment, const HandleGraph &rescue_graph, const std::vector< handle_t > &topological_order) constvg::MinimizerMapperprotected
for_each_aglomeration_interval(const vector< 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) 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 vector< 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 vector< 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
map(Alignment &aln, AlignmentEmitter &alignment_emitter)vg::MinimizerMapper
map(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_extensionsvg::MinimizerMapper
max_local_extensionsvg::MinimizerMapper
max_multimapsvg::MinimizerMapper
max_rescue_attemptsvg::MinimizerMapper
min_extensionsvg::MinimizerMapper
minimizer_indexesvg::MinimizerMapperprotected
minimizer_score_fractionvg::MinimizerMapper
MinimizerMapper(const gbwtgraph::GBWTGraph &graph, const std::vector< gbwtgraph::DefaultMinimizerIndex * > &minimizer_indexes, MinimumDistanceIndex &distance_index, const PathPositionHandleGraph *path_graph=nullptr)vg::MinimizerMapper
pad_cluster_score_thresholdvg::MinimizerMapper
paired_distance_stdevsvg::MinimizerMapper
paired_rescue_score_limitvg::MinimizerMapper
parse_matrix(std::istream &matrix_stream)vg::AlignerClientstatic
path_graphvg::MinimizerMapperprotected
process_until_threshold_a(const vector< Item > &items, const function< Score(size_t)> &get_score, double threshold, size_t min_count, size_t max_count, 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< Item > &items, const vector< Score > &scores, double threshold, size_t min_count, size_t max_count, 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(const vector< Item > &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, 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_haplotypes enum valuevg::MinimizerMapper
rescue_none enum valuevg::MinimizerMapper
rescue_subgraph_stdevsvg::MinimizerMapper
RescueAlgorithm enum namevg::MinimizerMapper
sample_namevg::MinimizerMapper
score_cluster(Cluster &cluster, size_t i, const std::vector< 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
Seed typedefvg::MinimizerMapperprotected
seeds_in_subgraph(const std::vector< Minimizer > &minimizers, const std::unordered_set< id_t > &subgraph) constvg::MinimizerMapperprotected
set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)vg::AlignerClient
set_alignment_scores(std::istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)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
to_path(const ImmutablePath &path)vg::MinimizerMapperprotectedstatic
track_correctnessvg::MinimizerMapper
track_provenancevg::MinimizerMapper
warned_about_bad_distributionvg::MinimizerMapperprotected
window_breaking_quality(const vector< Minimizer > &minimizers, vector< size_t > &broken, const string &sequence, const string &quality_bytes)vg::MinimizerMapperprotectedstatic