vg
tools for working with variation graphs
vg::BandedGlobalAligner< IntType >::BAMatrix Member List

This is the complete list of members for vg::BandedGlobalAligner< IntType >::BAMatrix, including all inherited members.

alignmentvg::BandedGlobalAligner< IntType >::BAMatrixprivate
AltTracebackStack classvg::BandedGlobalAligner< IntType >::BAMatrixfriend
BABuilder classvg::BandedGlobalAligner< IntType >::BAMatrixfriend
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
bottom_diagvg::BandedGlobalAligner< IntType >::BAMatrixprivate
cumulative_seq_lenvg::BandedGlobalAligner< IntType >::BAMatrixprivate
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
insert_colvg::BandedGlobalAligner< IntType >::BAMatrixprivate
insert_rowvg::BandedGlobalAligner< IntType >::BAMatrixprivate
matchvg::BandedGlobalAligner< IntType >::BAMatrixprivate
nodevg::BandedGlobalAligner< IntType >::BAMatrixprivate
print_band(const HandleGraph &graph, matrix_t which_mat)vg::BandedGlobalAligner< IntType >::BAMatrixprivate
print_full_matrices(const HandleGraph &graph)vg::BandedGlobalAligner< IntType >::BAMatrix
print_matrix(const HandleGraph &graph, matrix_t which_mat)vg::BandedGlobalAligner< IntType >::BAMatrixprivate
print_rectangularized_bands(const HandleGraph &graph)vg::BandedGlobalAligner< IntType >::BAMatrix
seedsvg::BandedGlobalAligner< IntType >::BAMatrixprivate
top_diagvg::BandedGlobalAligner< IntType >::BAMatrixprivate
traceback(const HandleGraph &graph, BABuilder &builder, AltTracebackStack &traceback_stack, matrix_t start_mat, 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
traceback_internal(const HandleGraph &graph, BABuilder &builder, AltTracebackStack &traceback_stack, int64_t start_row, int64_t start_col, matrix_t start_mat, bool in_lead_gap, 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 >::BAMatrixprivate
~BAMatrix()vg::BandedGlobalAligner< IntType >::BAMatrix