| alignment | vg::BandedGlobalAligner< IntType >::BAMatrix | private |
| AltTracebackStack class | vg::BandedGlobalAligner< IntType >::BAMatrix | friend |
| BABuilder class | vg::BandedGlobalAligner< IntType >::BAMatrix | friend |
| BAMatrix(Alignment &alignment, handle_t node, int64_t top_diag, int64_t bottom_diag, const vector< BAMatrix * > &seeds, int64_t cumulative_seq_len) | vg::BandedGlobalAligner< IntType >::BAMatrix | |
| BandedGlobalAligner class | vg::BandedGlobalAligner< IntType >::BAMatrix | friend |
| bottom_diag | vg::BandedGlobalAligner< IntType >::BAMatrix | private |
| cumulative_seq_len | vg::BandedGlobalAligner< IntType >::BAMatrix | private |
| fill_matrix(const HandleGraph &graph, int8_t *score_mat, int8_t *nt_table, int8_t gap_open, int8_t gap_extend, bool qual_adjusted, IntType min_inf) | vg::BandedGlobalAligner< IntType >::BAMatrix | |
| init_traceback_indexes(const HandleGraph &graph, int64_t &i, int64_t &j) | vg::BandedGlobalAligner< IntType >::BAMatrix | |
| insert_col | vg::BandedGlobalAligner< IntType >::BAMatrix | private |
| insert_row | vg::BandedGlobalAligner< IntType >::BAMatrix | private |
| match | vg::BandedGlobalAligner< IntType >::BAMatrix | private |
| node | vg::BandedGlobalAligner< IntType >::BAMatrix | private |
| print_band(const HandleGraph &graph, matrix_t which_mat) | vg::BandedGlobalAligner< IntType >::BAMatrix | private |
| print_full_matrices(const HandleGraph &graph) | vg::BandedGlobalAligner< IntType >::BAMatrix | |
| print_matrix(const HandleGraph &graph, matrix_t which_mat) | vg::BandedGlobalAligner< IntType >::BAMatrix | private |
| print_rectangularized_bands(const HandleGraph &graph) | vg::BandedGlobalAligner< IntType >::BAMatrix | |
| seeds | vg::BandedGlobalAligner< IntType >::BAMatrix | private |
| top_diag | vg::BandedGlobalAligner< IntType >::BAMatrix | private |
| traceback(const HandleGraph &graph, BABuilder &builder, AltTracebackStack &traceback_stack, int64_t &i, int64_t &j, matrix_t &mat, bool &in_lead_gap, const int8_t *score_mat, const int8_t *nt_table, const int8_t gap_open, const int8_t gap_extend, const bool qual_adjusted, IntType const min_inf) | vg::BandedGlobalAligner< IntType >::BAMatrix | |
| traceback_over_edge(const HandleGraph &graph, BABuilder &builder, AltTracebackStack &traceback_stack, int64_t &i, int64_t &j, matrix_t &mat, bool &in_lead_gap, int64_t &node_id, const int8_t *score_mat, const int8_t *nt_table, const int8_t gap_open, const int8_t gap_extend, const bool qual_adjusted, IntType const min_inf) | vg::BandedGlobalAligner< IntType >::BAMatrix | |
| ~BAMatrix() | vg::BandedGlobalAligner< IntType >::BAMatrix | |
