Closed tyleraland closed 8 years ago
To add to the specification: the threshold applies to reference sequences, not tax_ids. For example:
| hit | mismatches | species |
|-----+------------+---------|
| 1 | 0 | A |
| 2 | 3 | A |
| 3 | 0 | B |
| 4 | 2 | B |
| 5 | 2 | C |
| 6 | 2 | C |
if --closest=1, keep hits {1, 3} and the classification is A/B if --closest=2, keep hits {1, 3, 4, 5, 6} and the classification is A/B/C
Appears in 1.12
Noah/Steve requested additional reference sequence filtering for winnowing the names that appear in slash names: Sort references by number of mismatches from query and keep the top N names, where N is provided by the user and defaults to infinity.
Example: A sequence would normally be classified as A / B / C, where mismatches with A,B,C are 0,1,2 respectively. If given --closest 2, then C would be thrown away and our assigned name would be A* / B.