SequenceVariation.jl/CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

Added

• translate functionality for Haplotypes (#31)
• More informative errors when constructing invalid Haplotypes (#34)

0.2.0 - 2023-01-10

Added

• Tutorial-type documentation (#28)
• Base.isless implementation for Edit and Variation (#32)

Changed

• Code now follows Blue style (#28)
• 💣 [BREAKING] Public and private API defined based on Blue style guidelines (#28)
• 💣 [BREAKING] Renamed type Variant to Haplotype (#20/#29)
• 💣 [BREAKING] Refactored reconstruct function to use Haplotype's reference sequence (#30)

Removed

• Windows and MacOS CI tests (#28)

0.1.4 - 2022-12-17

Fixed

• Soft clips at end of alignment causing invalid Variants (#25/#26)

0.1.3 - 2022-11-22

Changed

• Variations getter now returns type-parameterized vector (#23)

0.1.2 - 2022-10-04

Changed

• Updated dependency compats (#21)
  • BioAlignments: 2 -> 2,3
  • BioSequences: 2 -> 2,3
  • BioSymbols: 4 -> 4,5

0.1.1 - 2022-07-21

Added

• Constructor for Variant based on Variations (#18)

0.1.0 - 2022-07-14

Added

• Mutation types (Substitution, Deletion, Insertion)
• Variant type to store groups of mutations together
• Variation type to store and compare individual mutations
• reconstruct! function to build mutated sequences from Variants
• Variant constructor to automatically detect mutations from a BioAlignments.PairwiseAlignment
• Methods to get reference and alternate bases from a Variation