| Bio/DB/GFF.pm | |||
|---|---|---|---|
| Criterion | Covered | Total | % |
| subroutine | 73 | 119 | 61.3 |
| pod | 67 | 79 | 84.8 |
| line | count | pod | subroutine |
|---|---|---|---|
| 597 | 3 | n/a | BEGIN |
| 599 | 3 | n/a | BEGIN |
| 600 | 3 | n/a | BEGIN |
| 601 | 3 | n/a | BEGIN |
| 602 | 3 | n/a | BEGIN |
| 603 | 3 | n/a | BEGIN |
| 604 | 3 | n/a | BEGIN |
| 606 | 3 | n/a | BEGIN |
| 716 | 5 | Yes | new |
| 806 | 25 | Yes | types |
| 836 | 0 | Yes | classes |
| 965 | 203 | Yes | segment |
| 976 | 203 | n/a | _multiple_return_args |
| 996 | 0 | No | abs_segment |
| 1001 | 224 | No | setup_segment_args |
| 1069 | 15 | Yes | features |
| 1129 | 0 | Yes | get_seq_stream |
| 1172 | 16 | Yes | get_feature_by_name |
| 1196 | 74 | n/a | __ANON__ |
| 1227 | 0 | Yes | get_feature_by_target |
| 1246 | 5 | Yes | get_feature_by_attribute |
| 1259 | 10 | n/a | __ANON__ |
| 1288 | 5 | Yes | get_feature_by_id |
| 1292 | 5 | n/a | __ANON__ |
| 1316 | 0 | Yes | get_feature_by_gid |
| 1320 | 0 | n/a | __ANON__ |
| 1347 | 0 | Yes | delete_fattribute_to_features |
| 1375 | 20 | Yes | delete_features |
| 1404 | 5 | Yes | delete_groups |
| 1478 | 21 | Yes | delete |
| 1533 | 195 | Yes | absolute |
| 1560 | 170 | Yes | strict_bounds_checking |
| 1580 | 0 | Yes | get_Seq_by_id |
| 1599 | 0 | Yes | get_Seq_by_accession |
| 1617 | 0 | Yes | get_Seq_by_acc |
| 1635 | 0 | Yes | get_Stream_by_name |
| 1655 | 0 | Yes | get_Stream_by_id |
| 1684 | 0 | Yes | get_Stream_by_group |
| 1707 | 0 | Yes | all_seqfeatures |
| 1744 | 5 | Yes | initialize |
| 1832 | 5 | Yes | load_gff |
| 1865 | 0 | Yes | load_gff_file |
| 1928 | 5 | Yes | load_fasta |
| 1960 | 0 | Yes | load_fasta_file |
| 1980 | 0 | Yes | load_sequence_string |
| 1989 | 10 | No | setup_argv |
| 1992 | 3 | n/a | BEGIN |
| 2038 | 0 | Yes | lock_on_load |
| 2061 | 0 | Yes | meta |
| 2085 | 5 | Yes | default_meta_values |
| 2106 | 8 | Yes | error |
| 2127 | 216 | Yes | debug |
| 2150 | 111 | Yes | automerge |
| 2194 | 20 | Yes | attributes |
| 2231 | 0 | Yes | fast_queries |
| 2259 | 20 | Yes | add_aggregator |
| 2303 | 106 | Yes | aggregators |
| 2327 | 5 | Yes | clear_aggregators |
| 2341 | 15 | Yes | preferred_groups |
| 2353 | 144 | n/a | _preferred_groups_hash |
| 2396 | 193 | Yes | abscoords |
| 2423 | 0 | Yes | default_aggregators |
| 2450 | 5 | Yes | do_load_gff |
| 2489 | 214 | n/a | _load_gff_line |
| 2571 | 5 | n/a | _load_sequence_start |
| 2578 | 10 | n/a | _load_sequence_finish |
| 2584 | 32950 | n/a | _load_sequence_line |
| 2618 | 5 | Yes | load_sequence |
| 2636 | 30330 | No | insert_sequence_chunk |
| 2651 | 30330 | No | dna_chunk_size |
| 2655 | 0 | No | insert_sequence |
| 2662 | 335 | No | default_class |
| 2672 | 165 | Yes | refclass |
| 2692 | 0 | Yes | setup_load |
| 2710 | 0 | Yes | finish_load |
| 2744 | 0 | Yes | load_gff_line |
| 2763 | 0 | Yes | do_initialize |
| 2800 | 120 | Yes | dna |
| 2811 | 0 | No | fetch_sequence |
| 2814 | 85 | No | features_in_range |
| 2868 | 0 | Yes | get_dna |
| 2965 | 0 | Yes | get_features |
| 2987 | 0 | n/a | _feature_by_name |
| 2993 | 0 | n/a | _feature_by_attribute |
| 3016 | 0 | n/a | _feature_by_id |
| 3069 | 85 | Yes | overlapping_features |
| 3094 | 0 | Yes | contained_features |
| 3113 | 0 | Yes | contained_in |
| 3140 | 0 | Yes | get_abscoords |
| 3174 | 0 | Yes | get_types |
| 3233 | 844 | Yes | make_feature |
| 3281 | 15 | No | make_aggregated_feature |
| 3325 | 168 | Yes | make_match_sub |
| 3328 | 0 | n/a | __ANON__ |
| 3379 | 594 | Yes | make_object |
| 3404 | 0 | Yes | do_attributes |
| 3421 | 2 | Yes | clone |
| 3467 | 100 | n/a | _features |
| 3488 | 15 | n/a | __ANON__ |
| 3489 | 270 | n/a | __ANON__ |
| 3501 | 470 | n/a | __ANON__ |
| 3539 | 0 | Yes | get_features_iterator |
| 3562 | 165 | Yes | split_group |
| 3589 | 99 | n/a | _split_gff2_group |
| 3676 | 71 | Yes | gff3_name_munging |
| 3689 | 66 | n/a | _split_gff3_group |
| 3742 | 66 | n/a | _gff3_name_munging |
| 3777 | 0 | n/a | _delete_features |
| 3783 | 5 | n/a | _delete_groups |
| 3789 | 0 | n/a | _delete |
| 3795 | 0 | n/a | _delete_fattribute_to_features |
| 3802 | 184 | No | unescape |
| 3809 | 2 | No | print_gff3_warning |
| 3827 | 3 | n/a | BEGIN |
| 3829 | 3 | n/a | BEGIN |
| 3832 | 0 | n/a | new |
| 3838 | 0 | n/a | next_seq |
| 3853 | 0 | n/a | new |
| 3858 | 0 | n/a | next_seq |