| anchored_filter(Alignment &aln) | vg::Filter | |
| avg_qual_filter(Alignment &aln) | vg::Filter | |
| breakend_filter(Alignment &aln_first, Alignment &aln_second) | vg::Filter | |
| coverage_filter(Alignment &aln) | vg::Filter | |
| deletion_filter(Alignment &aln_first, Alignment &aln_second) | vg::Filter | |
| depth_filter(Alignment &aln) | vg::Filter | |
| distance_between_positions(Position first, Position second) | vg::Filter | |
| do_remap | vg::Filter | |
| duplication_filter(Alignment &aln_first, Alignment &aln_second) | vg::Filter | |
| fill_node_to_position(string pathname) | vg::Filter | |
| Filter() | vg::Filter | |
| filter_matches | vg::Filter | |
| gcsa_ind | vg::Filter | |
| get_clipped_position(Alignment &a) | vg::Filter | |
| get_clipped_ref_position(Alignment &a) | vg::Filter | |
| get_clipped_seq(Alignment &a) | vg::Filter | |
| init_mapper() | vg::Filter | |
| insert_mean | vg::Filter | |
| insert_sd | vg::Filter | |
| insert_size_filter(Alignment &aln_first, Alignment &aln_second) | vg::Filter | |
| insertion_filter(Alignment &aln_first, Alignment &aln_second) | vg::Filter | |
| interchromosomal_filter(Alignment &aln_first, Alignment &aln_second) | vg::Filter | |
| inverse | vg::Filter | |
| inversion_filter(Alignment &aln_first, Alignment &aln_second) | vg::Filter | |
| is_left_clipped(Alignment &a) | vg::Filter | |
| lcp_ind | vg::Filter | |
| mark_smallVariant_alignments(Alignment &a, Alignment &b) | vg::Filter | |
| mark_sv_alignments(Alignment &a, Alignment &b) | vg::Filter | |
| max_path_length | vg::Filter | |
| min_avg_qual | vg::Filter | |
| min_cov | vg::Filter | |
| min_depth | vg::Filter | |
| min_percent_identity | vg::Filter | |
| min_qual | vg::Filter | |
| my_mapper | vg::Filter | |
| my_max_distance | vg::Filter | |
| my_path_position_graph | vg::Filter | |
| my_vg | vg::Filter | |
| node_to_position | vg::Filter | |
| one_end_anchored_filter(Alignment &aln_first, Alignment &aln_second) | vg::Filter | |
| pair_orientation_filter(Alignment &aln_first, Alignment &aln_second) | vg::Filter | |
| path_divergence_filter(Alignment &aln) | vg::Filter | |
| path_length_filter(Alignment &aln) | vg::Filter | |
| percent_identity_filter(Alignment &aln) | vg::Filter | |
| perfect_filter(Alignment &aln) | vg::Filter | |
| pos_to_edit_to_depth | vg::Filter | |
| pos_to_qual | vg::Filter | |
| qual_filter(Alignment &aln) | vg::Filter | |
| qual_offset | vg::Filter | |
| refactor_split_alignment(Alignment &a) | vg::Filter | |
| remap(Alignment &aln) | vg::Filter | |
| remap(string seq) | vg::Filter | |
| remove_clipped_portion(Alignment &a) | vg::Filter | |
| remove_failing_edits | vg::Filter | |
| reversing_filter(Alignment &aln) | vg::Filter | |
| set_avg(bool do_avg) | vg::Filter | |
| set_filter_matches(bool fm) | vg::Filter | |
| set_inverse(bool do_inv) | vg::Filter | |
| set_min_depth(int depth) | vg::Filter | |
| set_min_percent_identity(double pct_id) | vg::Filter | |
| set_min_qual(int qual) | vg::Filter | |
| set_my_path_position_graph(PathPositionHandleGraph *graph) | vg::Filter | |
| set_my_vg(vg::VG *vg) | vg::Filter | |
| set_remove_failing_edits(bool fm) | vg::Filter | |
| set_soft_clip_limit(int max_clip) | vg::Filter | |
| set_split_read_limit(int split_limit) | vg::Filter | |
| set_window_length(int window_length) | vg::Filter | |
| soft_clip_filter(Alignment &aln) | vg::Filter | |
| soft_clip_limit | vg::Filter | |
| split_read_filter(Alignment &aln) | vg::Filter | |
| split_read_limit | vg::Filter | |
| unmapped_filter(Alignment &aln) | vg::Filter | |
| use_avg | vg::Filter | |
| window_length | vg::Filter | |
| ~Filter() | vg::Filter | |
