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vg
tools for working with variation graphs
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This is the complete list of members for vg::Surjector, including all inherited members.
| adjust_alignments_for_base_quality | vg::AlignerClient | |
| AlignerClient(double gc_content_estimate=vg::default_gc_content) | vg::AlignerClient | protected |
| annotate_with_all_path_scores | vg::Surjector | |
| compute_path_interval(const PathPositionHandleGraph *graph, const Alignment &source, path_handle_t path_handle, bool rev_strand, const vector< path_chunk_t > &path_chunks, const vector< pair< step_handle_t, step_handle_t >> &ref_chunks, bool no_left_expansion, bool no_right_expansion) const | vg::Surjector | protected |
| connected_components(const vector< vector< size_t >> &adj, const vector< vector< size_t >> &rev_adj, size_t *num_comps_out) const | vg::Surjector | protected |
| cut_anchors(bool rev_strand, vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks, vector< tuple< size_t, size_t, int32_t >> &connections) const | vg::Surjector | protected |
| dominated_path_chunk_diff | vg::Surjector | |
| downsample_chunks(const string &src_sequence, vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks, vector< tuple< size_t, size_t, int32_t >> &connections) const | vg::Surjector | protected |
| downsample_coverage | vg::Surjector | |
| extract_overlapping_paths(const PathPositionHandleGraph *graph, const Alignment &source, const unordered_set< path_handle_t > &surjection_paths) const | vg::Surjector | protected |
| extract_overlapping_paths(const PathPositionHandleGraph *graph, const multipath_alignment_t &source, const unordered_set< path_handle_t > &surjection_paths, unordered_map< pair< path_handle_t, bool >, vector< tuple< size_t, size_t, int32_t >>> &connections_out) const | vg::Surjector | protected |
| filter_redundant_path_chunks(bool path_rev, vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks, vector< tuple< size_t, size_t, int32_t >> &connections) const | vg::Surjector | protected |
| find_constriction_bicliques(const vector< vector< size_t >> &adj, const string &src_sequence, const string &src_quality, vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks, const vector< tuple< size_t, size_t, int32_t >> &connections) const | vg::Surjector | protected |
| gc_content_estimate | vg::AlignerClient | private |
| get_aligner(bool have_qualities=true) const | vg::AlignerClient | protected |
| get_qual_adj_aligner() const | vg::AlignerClient | protected |
| get_regular_aligner() const | vg::AlignerClient | protected |
| get_score(const AlnType &aln) | vg::Surjector | protectedstatic |
| get_score(const Alignment &aln) | vg::Surjector | |
| get_score(const multipath_alignment_t &mp_aln) | vg::Surjector | |
| graph | vg::Surjector | protected |
| low_complexity_p_value | vg::Surjector | |
| make_null_alignment(const Alignment &source) | vg::Surjector | protectedstatic |
| make_null_mp_alignment(const string &src_sequence, const string &src_quality) | vg::Surjector | protectedstatic |
| max_anchors | vg::Surjector | |
| max_low_complexity_anchor_prune | vg::Surjector | |
| max_subgraph_bases | vg::Surjector | |
| max_tail_anchor_prune | vg::Surjector | |
| max_tail_length | vg::Surjector | |
| min_fold_coverage_for_downsample | vg::Surjector | |
| min_shift_for_prune | vg::Surjector | |
| min_splice_length | vg::Surjector | |
| min_splice_repair_length | vg::Surjector | |
| multi_surject(const Alignment &source, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool allow_negative_scores=false, bool preserve_deletions=false) const | vg::Surjector | |
| multi_surject(const Alignment &source, const unordered_set< path_handle_t > &paths, bool allow_negative_scores=false, bool preserve_deletions=false) const | vg::Surjector | |
| multi_surject(const multipath_alignment_t &source, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool allow_negative_scores=false, bool preserve_deletions=false) const | vg::Surjector | |
| pad_suspicious_anchors_to_length | vg::Surjector | |
| parse_matrix(std::istream &matrix_stream) | vg::AlignerClient | static |
| path_chunk_t typedef | vg::Surjector | |
| path_score_annotations(const unordered_map< pair< path_handle_t, bool >, pair< AlnType, pair< step_handle_t, step_handle_t >>> &surjections) const | vg::Surjector | protected |
| prune_suspicious_anchors | vg::Surjector | |
| prune_unconnectable(vector< vector< size_t >> &adj, vector< vector< tuple< size_t, int32_t, bool >>> &splice_adj, vector< size_t > &component, vector< vector< size_t >> &comp_groups, vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks) const | vg::Surjector | protected |
| qual_adj_aligner | vg::AlignerClient | private |
| realigning_surject(const PathPositionHandleGraph *graph, const Alignment &source, const path_handle_t &path_handle, bool rev_strand, const vector< path_chunk_t > &path_chunks, const vector< pair< step_handle_t, step_handle_t >> &ref_chunks, pair< step_handle_t, step_handle_t > &path_range_out, bool allow_negative_scores, bool preserve_N_alignments=false, bool sinks_are_anchors=false, bool sources_are_anchors=false, vector< pair< step_handle_t, step_handle_t >> *all_path_ranges_out=nullptr) const | vg::Surjector | protected |
| regular_aligner | vg::AlignerClient | private |
| remove_dominated_chunks(const string &src_sequence, const vector< vector< size_t >> &adj, vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks, vector< tuple< size_t, size_t, int32_t >> &connections) const | vg::Surjector | protected |
| reverse_adjacencies(const vector< vector< size_t >> &adj) const | vg::Surjector | 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 | virtual |
| set_alignment_scores(std::istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus) | vg::AlignerClient | virtual |
| set_alignment_scores(const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus) | vg::AlignerClient | virtual |
| set_path_position(const PathPositionHandleGraph *graph, const pos_t &init_surj_pos, const pos_t &final_surj_pos, const step_handle_t &range_begin, const step_handle_t &range_end, bool rev_strand, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out) const | vg::Surjector | protected |
| shift_prune_diff | vg::Surjector | |
| spliced_surject(const PathPositionHandleGraph *path_position_graph, const string &src_sequence, const string &src_quality, const int32_t src_mapping_quality, const path_handle_t &path_handle, bool rev_strand, vector< path_chunk_t > &path_chunks, vector< pair< step_handle_t, step_handle_t >> &ref_chunks, vector< tuple< size_t, size_t, int32_t >> &connections, pair< step_handle_t, step_handle_t > &path_range_out, bool allow_negative_scores, bool deletions_as_splices) const | vg::Surjector | protected |
| surject(const Alignment &source, const unordered_set< path_handle_t > &paths, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out, bool allow_negative_scores=false, bool preserve_deletions=false) const | vg::Surjector | |
| surject(const Alignment &source, const unordered_set< path_handle_t > &paths, bool allow_negative_scores=false, bool preserve_deletions=false) const | vg::Surjector | |
| surject(const multipath_alignment_t &source, const unordered_set< path_handle_t > &paths, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out, bool allow_negative_scores=false, bool preserve_deletions=false) const | vg::Surjector | |
| surject_internal(const Alignment *source_aln, const multipath_alignment_t *source_mp_aln, vector< Alignment > *alns_out, vector< multipath_alignment_t > *mp_alns_out, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool all_paths, bool allow_negative_scores, bool preserve_deletions) const | vg::Surjector | protected |
| Surjector(const PathPositionHandleGraph *graph) | vg::Surjector | |
| transitive_reduction(const vector< vector< size_t >> &adj) const | vg::Surjector | protected |
| warned_about_subgraph_size | vg::Surjector | mutable |
1.8.17