vg
tools for working with variation graphs
vg::XdropAligner Member List

This is the complete list of members for vg::XdropAligner, including all inherited members.

aa_matchvg::XdropAlignerprivate
align(Alignment &alignment, OrderedGraph const &graph, const vector< MaximalExactMatch > &mems, bool reverse_complemented)vg::XdropAligner
align(Alignment &alignment, Graph const &graph, const vector< MaximalExactMatch > &mems, bool reverse_complemented)vg::XdropAligner
align_downward(Alignment &alignment, OrderedGraph const &graph, graph_pos_s const &head_pos, bool left_to_right)vg::XdropAlignerprivate
align_pinned(Alignment &alignment, const HandleGraph &g, bool pin_left)vg::XdropAligner
align_pinned(Alignment &alignment, const HandleGraph &g, const vector< handle_t > &topological_order, bool pin_left)vg::XdropAligner
build_id_index_table(OrderedGraph const &graph)vg::XdropAlignerprivate
build_index_edge_table(OrderedGraph const &graph, uint32_t const seed_node_index, bool left_to_right)vg::XdropAlignerprivate
calculate_and_save_alignment(Alignment &alignment, OrderedGraph const &graph, graph_pos_s const &head_pos, size_t tail_node_index, bool left_to_right)vg::XdropAlignerprivate
calculate_max_position(OrderedGraph const &graph, graph_pos_s const &seed_pos, size_t max_node_index, bool direction)vg::XdropAlignerprivate
calculate_seed_position(OrderedGraph const &graph, vector< MaximalExactMatch > const &mems, size_t query_length, bool direction)vg::XdropAlignerprivate
comparevg::XdropAlignerprivate
dzvg::XdropAlignerprivate
edgevg::XdropAlignerprivate
extend(OrderedGraph const &graph, vector< uint64_t >::const_iterator begin, vector< uint64_t >::const_iterator end, dz_query_s const *packed_query, size_t seed_node_index, uint64_t seed_offset, bool right_to_left)vg::XdropAlignerprivate
forefrontsvg::XdropAlignerprivate
id_to_indexvg::XdropAlignerprivate
index_edgesvg::XdropAlignerprivate
index_edges_headvg::XdropAlignerprivate
operator=(XdropAligner const &)vg::XdropAligner
operator=(XdropAligner &&)vg::XdropAligner
push_edit(Mapping *mapping, uint8_t op, char const *alt, size_t len)vg::XdropAlignerprivate
scan_seed_position(OrderedGraph const &graph, std::string const &query_seq, bool direction)vg::XdropAlignerprivate
XdropAligner()vg::XdropAligner
XdropAligner(XdropAligner const &)vg::XdropAligner
XdropAligner(XdropAligner &&)vg::XdropAligner
XdropAligner(int8_t _match, int8_t _mismatch, int8_t _gap_open, int8_t _gap_extension, int32_t _full_length_bonus, uint32_t _max_gap_length)vg::XdropAligner
XdropAligner(int8_t const *_score_matrix, int8_t _gap_open, int8_t _gap_extension, int32_t _full_length_bonus, uint32_t _max_gap_length)vg::XdropAligner
~XdropAligner(void)vg::XdropAligner