vg
tools for working with variation graphs
|
This is the complete list of members for vg::XdropAligner, including all inherited members.
align(Alignment &alignment, const HandleGraph &graph, const vector< handle_t > &topological_order, const vector< MaximalExactMatch > &mems, bool reverse_complemented) const | vg::XdropAligner | |
align(Alignment &alignment, const HandleGraph &graph, const vector< MaximalExactMatch > &mems, bool reverse_complemented) const | vg::XdropAligner | |
align_downward(Alignment &alignment, const OrderedGraph &graph, const vector< graph_pos_s > &head_positions, bool left_to_right, dz_s *dz, vector< const dz_forefront_s * > &forefronts) const | vg::XdropAligner | private |
align_pinned(Alignment &alignment, const HandleGraph &g, bool pin_left) const | vg::XdropAligner | |
align_pinned(Alignment &alignment, const HandleGraph &g, const vector< handle_t > &topological_order, bool pin_left) const | vg::XdropAligner | |
calculate_and_save_alignment(Alignment &alignment, const OrderedGraph &graph, const vector< graph_pos_s > &head_positions, size_t tail_node_index, bool left_to_right, dz_s *dz, const vector< const dz_forefront_s * > &forefronts) const | vg::XdropAligner | private |
calculate_max_position(const OrderedGraph &graph, const graph_pos_s &seed_pos, size_t max_node_index, bool direction, dz_s *dz, const vector< const dz_forefront_s * > &forefronts) const | vg::XdropAligner | private |
calculate_seed_position(const OrderedGraph &graph, const vector< MaximalExactMatch > &mems, size_t query_length, bool direction) const | vg::XdropAligner | private |
extend(const OrderedGraph &graph, const dz_query_s *packed_query, const vector< graph_pos_s > &seed_positions, bool right_to_left, dz_s *dz, vector< const dz_forefront_s * > &forefronts) const | vg::XdropAligner | private |
full_length_bonus | vg::XdropAligner | private |
gap_extend | vg::XdropAligner | private |
gap_open | vg::XdropAligner | private |
max_gap_length | vg::XdropAligner | private |
operator=(XdropAligner const &) | vg::XdropAligner | |
operator=(XdropAligner &&) | vg::XdropAligner | |
push_edit(Mapping *mapping, uint8_t op, const char *alt, size_t len) const | vg::XdropAligner | private |
scan_seed_position(const OrderedGraph &graph, const string &query_seq, bool direction, dz_s *dz, vector< const dz_forefront_s * > &forefronts) const | vg::XdropAligner | private |
score_matrix | vg::XdropAligner | private |
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(const int8_t *_score_matrix, int8_t _gap_open, int8_t _gap_extension, int32_t _full_length_bonus, uint32_t _max_gap_length) | vg::XdropAligner | |
XdropAligner() | vg::XdropAligner | |
XdropAligner(XdropAligner const &) | vg::XdropAligner | |
XdropAligner(XdropAligner &&) | vg::XdropAligner | |
~XdropAligner(void) | vg::XdropAligner |