seqan / product_backlog

This repository is used as product backlog for all SeqAn relevant backlog items. This is intended to organise the work for the team.
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[Alignment Configuration] Change the align_cfg::max_error to align_cfg::min_score #182

Closed rrahn closed 4 years ago

rrahn commented 4 years ago

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:

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

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
rrahn commented 4 years ago

fixed by seqan/seqan3#2021