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 |
cluster_coverage_threshold | vg::MinimizerMapper | |
cluster_score_threshold | vg::MinimizerMapper | |
clusterer | 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_index | vg::MinimizerMapper | protected |
distance_limit | vg::MinimizerMapper | |
do_dp | vg::MinimizerMapper | |
extender | vg::MinimizerMapper | protected |
extension_score_threshold | vg::MinimizerMapper | |
extension_set_score_threshold | vg::MinimizerMapper | |
find_connecting_paths(const vector< GaplessExtension > &extended_seeds, size_t read_length) 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 |
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) const | vg::MinimizerMapper | protected |
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) 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 |
load_scoring_matrix(std::ifstream &matrix_stream) | vg::AlignerClient | |
map(Alignment &aln, AlignmentEmitter &alignment_emitter) | vg::MinimizerMapper | |
max_alignments | vg::MinimizerMapper | |
max_extensions | vg::MinimizerMapper | |
max_local_extensions | vg::MinimizerMapper | |
max_multimaps | vg::MinimizerMapper | |
minimizer_index | vg::MinimizerMapper | protected |
minimizer_score_fraction | vg::MinimizerMapper | |
MinimizerMapper(const gbwtgraph::GBWTGraph &graph, const gbwtgraph::DefaultMinimizerIndex &minimizer_index, MinimumDistanceIndex &distance_index, const PathPositionHandleGraph *path_graph=nullptr) | vg::MinimizerMapper | |
path_graph | vg::MinimizerMapper | protected |
process_until_threshold(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(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(const vector< Item > &items, const vector< Score > &scores, 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 |
sample_name | vg::MinimizerMapper | |
score_extension_group(const Alignment &aln, const vector< GaplessExtension > &extended_seeds, int gap_open_penalty, int gap_extend_penalty) | vg::MinimizerMapper | protectedstatic |
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 | |
to_path(const ImmutablePath &path) | vg::MinimizerMapper | protectedstatic |
track_correctness | vg::MinimizerMapper | |
track_provenance | vg::MinimizerMapper |