Primalscheme Versions Save

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

Notable changes

• Use parasail for alignment
• Windows compatible
• Improved stdout and logging
• Improved code readability
• Tests
• Improved CLI
• Candidate ranking improvements
• Valid BED file strand column
• Various bug fixes
• Speed improvements