| lib/Bio/BPWrapper/AlnManipulations.pm | |||
|---|---|---|---|
| Criterion | Covered | Total | % |
| subroutine | 55 | 73 | 75.3 |
| pod | 23 | 43 | 53.4 |
| line | count | pod | subroutine |
|---|---|---|---|
| 18 | 29 | n/a | BEGIN |
| 19 | 29 | n/a | BEGIN |
| 20 | 29 | n/a | BEGIN |
| 21 | 29 | n/a | BEGIN |
| 22 | 29 | n/a | BEGIN |
| 23 | 29 | n/a | BEGIN |
| 24 | 29 | n/a | BEGIN |
| 25 | 29 | n/a | BEGIN |
| 26 | 29 | n/a | BEGIN |
| 27 | 29 | n/a | BEGIN |
| 28 | 29 | n/a | BEGIN |
| 31 | 29 | n/a | BEGIN |
| 33 | 29 | n/a | BEGIN |
| 50 | 29 | n/a | BEGIN |
| 120 | 29 | Yes | initialize |
| 186 | 27 | No | can_handle |
| 191 | 26 | No | handle_opt |
| 203 | 0 | Yes | write_out_paml |
| 234 | 29 | Yes | write_out |
| 249 | 0 | No | phylip_non_interleaved |
| 271 | 0 | No | gap_char |
| 281 | 0 | No | pair_diff_ref |
| 323 | 0 | No | pair_diff |
| 377 | 0 | No | split_cdhit |
| 425 | 0 | No | trim_ends |
| 495 | 0 | No | gap_states |
| 544 | 0 | No | gap_states_matrix |
| 617 | 1 | Yes | print_avp_id |
| 629 | 1 | n/a | bootstrap |
| 645 | 1 | Yes | draw_codon_view |
| 718 | 1 | Yes | del_seqs |
| 729 | 1 | Yes | remove_gaps |
| 739 | 1 | Yes | print_length |
| 752 | 1 | Yes | print_match |
| 762 | 1 | Yes | print_num_seq |
| 775 | 1 | Yes | pick_seqs |
| 787 | 1 | Yes | change_ref |
| 812 | 1 | Yes | aln_slice |
| 830 | 1 | Yes | get_unique |
| 835 | 0 | n/a | _has_gap |
| 843 | 0 | n/a | _has_singleton |
| 858 | 0 | Yes | binary_informative |
| 897 | 0 | No | binary_ref |
| 952 | 1 | Yes | variable_sites |
| 993 | 1 | Yes | avg_id_by_win |
| 1016 | 1 | Yes | concat |
| 1066 | 90 | n/a | __gene_order |
| 1079 | 1 | No | conserved_blocks |
| 1141 | 1 | No | get_consensus |
| 1160 | 1 | Yes | dna_to_protein |
| 1164 | 1 | No | remove_gapped_cols_in_one_seq |
| 1184 | 1 | No | colnum_from_residue_pos |
| 1196 | 1 | Yes | list_ids |
| 1203 | 1 | No | permute_states |
| 1241 | 29 | n/a | BEGIN |
| 1242 | 1 | Yes | protein_to_dna |
| 1265 | 1 | Yes | sample_seqs |
| 1291 | 0 | Yes | shuffle_sites |
| 1327 | 0 | No | random_slice |
| 1335 | 1 | No | select_third_sites |
| 1362 | 0 | No | remove_third_sites |
| 1389 | 1 | No | upper_case |
| 1398 | 13 | n/a | _pad_display_id |
| 1407 | 2 | n/a | _print_positions |
| 1449 | 2 | n/a | _del_or_pick |
| 1464 | 1 | n/a | _get_gaps |
| 1477 | 210 | n/a | _paste_nt |
| 1484 | 210 | n/a | _get_a_site |
| 1507 | 0 | n/a | _seen_bases |
| 1517 | 210 | n/a | _is_constant |
| 1529 | 0 | n/a | _column_status |
| 1548 | 2 | n/a | _get_a_site_v2 |
| 1558 | 1 | n/a | _find_max_id_len |