Before we had the align_cfg::max_error which was used to indicate the maximum errors for the edit alignment. But one can also translate it to min_score and thus make it applicable for non-edit scoring schemes as well.
Here is the proposed change of the interface:
seqan3::align_cfg::min_score [optional]
Produces an alignment result for every score which has at least min_score. (i.e. report results with min_score <= score)
Returns empty alignment results if the score could not be reached.
construction
seqan3::align_cfg::min_score min_score{-5};
later access and set
min_score.score = -5;
access by seqan::get:
auto && min_score = seqan3::get<seqan3::align_cfg::min_score>(config);
min_score.score = -5;
check if present:
config_t::template exists<seqan3::align_cfg::min_score>();
Acceptance Criteria
[ ] The alignment now works with align_cfg::min_score instead of align_cfg::max_error
Tasks
- [ ] Rename align_cfg::max_error to align_cfg::min_score and also change the access of the stored value.
- [ ] Update the documentation and snippets if applicable.
### Definition of Done
- [ ] Implementation and design approved
- [ ] Unit tests pass
- [ ] Test coverage = 100%
- [ ] Microbenchmarks added and/or affected microbenchmarks < 5% performance drop
- [ ] API documentation added
- [ ] Tutorial/teaching material added
- [ ] Test suite compiles in less than 30 seconds (on travis)
- [ ] Changelog entry added
Description
Before we had the align_cfg::max_error which was used to indicate the maximum errors for the edit alignment. But one can also translate it to min_score and thus make it applicable for non-edit scoring schemes as well. Here is the proposed change of the interface:
Acceptance Criteria
Tasks
- [ ] Rename align_cfg::max_error to align_cfg::min_score and also change the access of the stored value. - [ ] Update the documentation and snippets if applicable. ### Definition of Done - [ ] Implementation and design approved - [ ] Unit tests pass - [ ] Test coverage = 100% - [ ] Microbenchmarks added and/or affected microbenchmarks < 5% performance drop - [ ] API documentation added - [ ] Tutorial/teaching material added - [ ] Test suite compiles in less than 30 seconds (on travis) - [ ] Changelog entry added