- Drop secondary references on repeated flank alignment failure - Add primary_ref, secondary_refs and excluded_refs to json run report
Changed
- Reduce complexity of Region find_primers() method - Use progress library - Add region and considered primers to progress message
Removed
- DIY progress bar
1.0.0
Added
- Use all reference sequences for primer generation - 3' distance-weighted mismatch scoring - Avoid stable heterodimers in same pool - Sort inputs by length, to make longest the primary by default (--no-sort reverts) - Inserts bed file output - Run report json output
Changed
- Infer mismatches from aligned references and primer coordinates - Merge mismatch and base primer scoring - Generate primers by digesting all references into K-mers at region flanks - Use own implementation of Primer3 base penalty algorithm - Update parameters for thermodyamic calculations - Rationalise the config file - Remove any remaining constants from the code base - Reduce code complexity - Consolidate exception handling - Improve candidate sorting to ensure deterministic output.
Removed
- primer3 FindPrimers function - Redundant classes - Redundant exceptions
0.3.0
Added
- Windows compatibility - Tests - Valid BED file strand column
Changed
- Use parasail for alignment - Improve stdout and logging - Improve code readability - Improved CLI - Candidate ranking improvements - Various bug fixes - Speed improvements
[1]: https://keepachangelog.com/en/1.0.0/ "Keep a Changelog" [2]: https://semver.org/spec/v2.0.0.html "Semantic Versioning"