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	private
connected_components(const vector< vector< size_t >> &adj, const vector< vector< size_t >> &rev_adj, size_t *num_comps_out) const	vg::Surjector	private
extract_linearized_path_graph(const PathPositionHandleGraph graph, MutableHandleGraph into, path_handle_t path_handle, size_t first, size_t last) const	vg::Surjector	private
extract_overlapping_paths(const PathPositionHandleGraph *graph, const Alignment &source, const unordered_set< path_handle_t > &surjection_paths) const	vg::Surjector	private
find_constriction_edges(const vector< vector< size_t >> &adj) const	vg::Surjector	private
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	private
load_scoring_matrix(std::ifstream &matrix_stream)	vg::AlignerClient
make_null_alignment(const Alignment &source)	vg::Surjector	privatestatic
min_splice_length	vg::Surjector	private
path_chunk_t typedef	vg::Surjector
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, bool allow_negative_scores, bool preserve_N_alignments=false) const	vg::Surjector	private
regular_aligner	vg::AlignerClient	private
reverse_adjacencies(const vector< vector< size_t >> &adj) const	vg::Surjector	private
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
set_path_position(const PathPositionHandleGraph *graph, const Alignment &surjected, path_handle_t best_path_handle, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out) const	vg::Surjector	private
set_path_position_inexact(const PathPositionHandleGraph *graph, const Alignment &surjected, path_handle_t best_path_handle, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out) const	vg::Surjector	private
spliced_surject(const PathPositionHandleGraph *path_position_graph, const Alignment &source, const path_handle_t &path_handle, const vector< path_chunk_t > &path_chunks, const vector< pair< step_handle_t, step_handle_t >> &ref_chunks, bool allow_negative_scores) const	vg::Surjector	private
surject(const Alignment &source, const set< string > &path_names, 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 set< string > &path_names, bool allow_negative_scores=false, bool preserve_deletions=false) const	vg::Surjector
Surjector(const PathPositionHandleGraph *graph)	vg::Surjector
transitive_reduction(const vector< vector< size_t >> &adj) const	vg::Surjector	private