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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.
| align(Alignment &alignment, const HandleGraph &graph, const vector< MaximalExactMatch > &mems, bool reverse_complemented, int8_t full_length_bonus, uint16_t max_gap_length=default_xdrop_max_gap_length) | vg::DozeuInterface | |
| align(Alignment &alignment, const HandleGraph &graph, const vector< handle_t > &order, const vector< MaximalExactMatch > &mems, bool reverse_complemented, int8_t full_length_bonus, uint16_t max_gap_length=default_xdrop_max_gap_length) | vg::DozeuInterface | |
| align_downward(Alignment &alignment, const OrderedGraph &graph, const vector< graph_pos_s > &head_positions, bool left_to_right, vector< const dz_forefront_s * > &forefronts, int8_t full_length_bonus, uint16_t max_gap_length) | vg::DozeuInterface | protected |
| align_pinned(Alignment &alignment, const HandleGraph &g, bool pin_left, int8_t full_length_bonus, uint16_t max_gap_length=default_xdrop_max_gap_length) | vg::DozeuInterface | |
| 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, const vector< const dz_forefront_s * > &forefronts) | vg::DozeuInterface | protected |
| calculate_max_position(const OrderedGraph &graph, const graph_pos_s &seed_pos, size_t max_node_index, bool direction, const vector< const dz_forefront_s * > &forefronts) | vg::DozeuInterface | protected |
| calculate_seed_position(const OrderedGraph &graph, const vector< MaximalExactMatch > &mems, size_t query_length, bool direction) const | vg::DozeuInterface | protected |
| do_poa(const OrderedGraph &graph, const dz_query_s *packed_query, const vector< graph_pos_s > &seed_positions, bool right_to_left, vector< const dz_forefront_s * > &forefronts, uint16_t) | vg::DozeuInterface | protected |
| dz | vg::DozeuInterface | protected |
| extend(const dz_query_s *query, const dz_forefront_s **forefronts, size_t n_forefronts, const char *ref, int32_t rlen, uint32_t rid, uint16_t xt) | vg::XdropAligner | privatevirtual |
| flush() | vg::XdropAligner | privatevirtual |
| operator=(const XdropAligner &other) | vg::XdropAligner | |
| operator=(XdropAligner &&other) | vg::XdropAligner | |
| pack_query_forward(const char *seq, const uint8_t *qual, int8_t full_length_bonus, size_t len) | vg::XdropAligner | privatevirtual |
| pack_query_reverse(const char *seq, const uint8_t *qual, int8_t full_length_bonus, size_t len) | vg::XdropAligner | privatevirtual |
| push_edit(Mapping *mapping, uint8_t op, const char *alt, size_t len) const | vg::DozeuInterface | protected |
| scan(const dz_query_s *query, const dz_forefront_s **forefronts, size_t n_forefronts, const char *ref, int32_t rlen, uint32_t rid, uint16_t xt) | vg::XdropAligner | privatevirtual |
| scan_seed_position(const OrderedGraph &graph, const Alignment &alignment, bool direction, vector< const dz_forefront_s * > &forefronts, int8_t full_length_bonus, uint16_t max_gap_length) | vg::DozeuInterface | protected |
| trace(const dz_forefront_s *forefront) | vg::XdropAligner | privatevirtual |
| XdropAligner(const int8_t *_score_matrix, int8_t _gap_open, int8_t _gap_extension) | vg::XdropAligner | |
| XdropAligner()=default | vg::XdropAligner | |
| XdropAligner(const XdropAligner &other) | vg::XdropAligner | |
| XdropAligner(XdropAligner &&other) | vg::XdropAligner | |
| ~DozeuInterface()=default | vg::DozeuInterface | virtual |
| ~XdropAligner(void) | vg::XdropAligner |
1.8.17