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 |
compute_path_interval(const PathPositionHandleGraph *graph, const Alignment &source, path_handle_t path_handle, const vector< path_chunk_t > &path_chunks) 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 |
dominated_path_chunk_diff | vg::Surjector | |
extract_linearized_path_graph(const PathPositionHandleGraph *graph, MutableHandleGraph *into, path_handle_t path_handle, size_t first, size_t last) const | vg::Surjector | protected |
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< path_handle_t, vector< tuple< size_t, size_t, int32_t >>> &connections_out) const | vg::Surjector | protected |
filter_redundant_path_chunks(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 vector< path_chunk_t > &path_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 |
graph | vg::Surjector | protected |
make_null_alignment(const Alignment &source) | vg::Surjector | protectedstatic |
make_null_mp_alignment(const multipath_alignment_t &source) | vg::Surjector | protectedstatic |
min_splice_length | vg::Surjector | |
parse_matrix(std::istream &matrix_stream) | vg::AlignerClient | static |
path_chunk_t typedef | 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, const vector< path_chunk_t > &path_chunks, pair< step_handle_t, step_handle_t > &path_range_out, bool allow_negative_scores, bool preserve_N_alignments=false, bool preserve_tail_indel_anchors=false) 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 | |
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 | |
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, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out) const | vg::Surjector | protected |
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, 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, Alignment *aln_out, multipath_alignment_t *mp_aln_out, const unordered_set< path_handle_t > &paths, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out, 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 |