vg
tools for working with variation graphs
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This is the complete list of members for vg::XdropAligner, including all inherited members.
aa_match | vg::XdropAligner | private |
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::XdropAligner | private |
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::XdropAligner | private |
build_index_edge_table(OrderedGraph const &graph, uint32_t const seed_node_index, bool left_to_right) | vg::XdropAligner | private |
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::XdropAligner | private |
calculate_max_position(OrderedGraph const &graph, graph_pos_s const &seed_pos, size_t max_node_index, bool direction) | vg::XdropAligner | private |
calculate_seed_position(OrderedGraph const &graph, vector< MaximalExactMatch > const &mems, size_t query_length, bool direction) | vg::XdropAligner | private |
compare | vg::XdropAligner | private |
dz | vg::XdropAligner | private |
edge | vg::XdropAligner | private |
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::XdropAligner | private |
forefronts | vg::XdropAligner | private |
id_to_index | vg::XdropAligner | private |
index_edges | vg::XdropAligner | private |
index_edges_head | vg::XdropAligner | private |
operator=(XdropAligner const &) | vg::XdropAligner | |
operator=(XdropAligner &&) | vg::XdropAligner | |
push_edit(Mapping *mapping, uint8_t op, char const *alt, size_t len) | vg::XdropAligner | private |
scan_seed_position(OrderedGraph const &graph, std::string const &query_seq, bool direction) | vg::XdropAligner | private |
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 |