vg
tools for working with variation graphs
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This is the complete list of members for vg::MinimizerMapper, including all inherited members.
adjust_alignments_for_base_quality | vg::AlignerClient | |
AlignerClient(double gc_content_estimate=vg::default_gc_content) | vg::AlignerClient | protected |
attempt_rescue(const Alignment &aligned_read, Alignment &rescued_alignment, const std::vector< Minimizer > &minimizers, bool rescue_forward) | vg::MinimizerMapper | protected |
Cluster typedef | vg::MinimizerMapper | protected |
cluster_coverage_threshold | vg::MinimizerMapper | |
cluster_score_threshold | vg::MinimizerMapper | |
clusterer | vg::MinimizerMapper | protected |
compute_mapq_caps(const Alignment &aln, const std::vector< Minimizer > &minimizers, const SmallBitset &explored) | vg::MinimizerMapper | protected |
dfs_gbwt(const Position &from, size_t walk_distance, const function< void(const handle_t &)> &enter_handle, const function< void(void)> exit_handle) const | vg::MinimizerMapper | protected |
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) const | vg::MinimizerMapper | protected |
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) const | vg::MinimizerMapper | protected |
distance_between(const Alignment &aln1, const Alignment &aln2) | vg::MinimizerMapper | protected |
distance_index | vg::MinimizerMapper | protected |
distance_limit | vg::MinimizerMapper | |
do_dp | vg::MinimizerMapper | |
dump_debug_extension_set(const HandleGraph &graph, const Alignment &aln, const vector< GaplessExtension > &extended_seeds) | vg::MinimizerMapper | protectedstatic |
dump_debug_minimizers(const vector< Minimizer > &minimizers, const string &sequence, const vector< size_t > *to_include=nullptr) | vg::MinimizerMapper | protectedstatic |
dump_debug_sequence(ostream &out, const string &sequence) | vg::MinimizerMapper | protectedstatic |
extender | vg::MinimizerMapper | protected |
extension_score_threshold | vg::MinimizerMapper | |
extension_set_score_threshold | vg::MinimizerMapper | |
extension_to_alignment(const GaplessExtension &extension, Alignment &alignment) const | vg::MinimizerMapper | protected |
faster_cap(const vector< Minimizer > &minimizers, vector< size_t > &minimizers_explored, const string &sequence, const string &quality_bytes) | vg::MinimizerMapper | protectedstatic |
finalize_fragment_length_distr() | vg::MinimizerMapper | inline |
find_connecting_paths(const vector< GaplessExtension > &extended_seeds, size_t read_length) const | vg::MinimizerMapper | protected |
find_minimizers(const std::string &sequence, Funnel &funnel) const | vg::MinimizerMapper | protected |
find_optimal_tail_alignments(const Alignment &aln, const vector< GaplessExtension > &extended_seeds, Alignment &best, Alignment &second_best) const | vg::MinimizerMapper | protected |
find_seeds(const std::vector< Minimizer > &minimizers, const Alignment &aln, Funnel &funnel) const | vg::MinimizerMapper | protected |
fix_dozeu_score(Alignment &rescued_alignment, const HandleGraph &rescue_graph, const std::vector< handle_t > &topological_order) const | vg::MinimizerMapper | protected |
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::MinimizerMapper | protectedstatic |
force_fragment_length_distr(double mean, double stdev) | vg::MinimizerMapper | inline |
fragment_distr_is_finalized() | vg::MinimizerMapper | inline |
fragment_length_distr | vg::MinimizerMapper | protected |
gbwt_graph | vg::MinimizerMapper | protected |
gc_content_estimate | vg::AlignerClient | private |
get_aligner(bool have_qualities=true) const | vg::AlignerClient | protected |
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) const | vg::MinimizerMapper | protected |
get_distance_limit(size_t read_length) const | vg::MinimizerMapper | inline |
get_fragment_length_mean() const | vg::MinimizerMapper | inline |
get_fragment_length_sample_size() const | vg::MinimizerMapper | inline |
get_fragment_length_stdev() const | vg::MinimizerMapper | inline |
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::MinimizerMapper | protectedstatic |
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::MinimizerMapper | protectedstatic |
get_qual_adj_aligner() const | vg::AlignerClient | protected |
get_regular_aligner() const | vg::AlignerClient | protected |
get_tail_forest(const GaplessExtension &extended_seed, size_t read_length, bool left_tails, size_t *longest_detectable_gap=nullptr) const | vg::MinimizerMapper | protected |
hard_hit_cap | vg::MinimizerMapper | |
hit_cap | vg::MinimizerMapper | |
immutable_path_from_length(const ImmutablePath &path) | vg::MinimizerMapper | protectedstatic |
ImmutablePath typedef | vg::MinimizerMapper | protected |
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_alignments | vg::MinimizerMapper | |
max_extensions | vg::MinimizerMapper | |
max_local_extensions | vg::MinimizerMapper | |
max_multimaps | vg::MinimizerMapper | |
max_rescue_attempts | vg::MinimizerMapper | |
min_extensions | vg::MinimizerMapper | |
minimizer_indexes | vg::MinimizerMapper | protected |
minimizer_score_fraction | vg::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_threshold | vg::MinimizerMapper | |
paired_distance_stdevs | vg::MinimizerMapper | |
paired_rescue_score_limit | vg::MinimizerMapper | |
parse_matrix(std::istream &matrix_stream) | vg::AlignerClient | static |
path_graph | vg::MinimizerMapper | protected |
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) const | vg::MinimizerMapper | protected |
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) const | vg::MinimizerMapper | protected |
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) const | vg::MinimizerMapper | protected |
qual_adj_aligner | vg::AlignerClient | private |
read_group | vg::MinimizerMapper | |
regular_aligner | vg::AlignerClient | private |
rescue_algorithm | vg::MinimizerMapper | |
rescue_dozeu enum value | vg::MinimizerMapper | |
rescue_gssw enum value | vg::MinimizerMapper | |
rescue_haplotypes enum value | vg::MinimizerMapper | |
rescue_none enum value | vg::MinimizerMapper | |
rescue_subgraph_stdevs | vg::MinimizerMapper | |
RescueAlgorithm enum name | vg::MinimizerMapper | |
sample_name | vg::MinimizerMapper | |
score_cluster(Cluster &cluster, size_t i, const std::vector< Minimizer > &minimizers, const std::vector< Seed > &seeds, size_t seq_length, Funnel &funnel) const | vg::MinimizerMapper | protected |
score_extension_group(const Alignment &aln, const vector< GaplessExtension > &extended_seeds, int gap_open_penalty, int gap_extend_penalty) | vg::MinimizerMapper | protectedstatic |
score_extensions(const std::vector< std::vector< GaplessExtension >> &extensions, const Alignment &aln, Funnel &funnel) const | vg::MinimizerMapper | protected |
score_extensions(const std::vector< std::pair< std::vector< GaplessExtension >, size_t >> &extensions, const Alignment &aln, Funnel &funnel) const | vg::MinimizerMapper | protected |
Seed typedef | vg::MinimizerMapper | protected |
seeds_in_subgraph(const std::vector< Minimizer > &minimizers, const std::unordered_set< id_t > &subgraph) const | vg::MinimizerMapper | protected |
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::MinimizerMapper | protectedstatic |
track_correctness | vg::MinimizerMapper | |
track_provenance | vg::MinimizerMapper | |
warned_about_bad_distribution | vg::MinimizerMapper | protected |
window_breaking_quality(const vector< Minimizer > &minimizers, vector< size_t > &broken, const string &sequence, const string &quality_bytes) | vg::MinimizerMapper | protectedstatic |