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.

align(Alignment &alignment, const HandleGraph &graph, const vector< handle_t > &topological_order, const vector< MaximalExactMatch > &mems, bool reverse_complemented) constvg::XdropAligner
align(Alignment &alignment, const HandleGraph &graph, const vector< MaximalExactMatch > &mems, bool reverse_complemented) constvg::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) constvg::XdropAlignerprivate
align_pinned(Alignment &alignment, const HandleGraph &g, bool pin_left) constvg::XdropAligner
align_pinned(Alignment &alignment, const HandleGraph &g, const vector< handle_t > &topological_order, bool pin_left) constvg::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) constvg::XdropAlignerprivate
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) constvg::XdropAlignerprivate
calculate_seed_position(const OrderedGraph &graph, const vector< MaximalExactMatch > &mems, size_t query_length, bool direction) constvg::XdropAlignerprivate
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) constvg::XdropAlignerprivate
full_length_bonusvg::XdropAlignerprivate
gap_extendvg::XdropAlignerprivate
gap_openvg::XdropAlignerprivate
max_gap_lengthvg::XdropAlignerprivate
operator=(XdropAligner const &)vg::XdropAligner
operator=(XdropAligner &&)vg::XdropAligner
push_edit(Mapping *mapping, uint8_t op, const char *alt, size_t len) constvg::XdropAlignerprivate
scan_seed_position(const OrderedGraph &graph, const string &query_seq, bool direction, dz_s *dz, vector< const dz_forefront_s * > &forefronts) constvg::XdropAlignerprivate
score_matrixvg::XdropAlignerprivate
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