CHANGELOG.md

Changelog

All notable changes to HapLink.jl will be documented in this file.

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

Unreleased

1.1.0 - 2023-12-22

Changed

• Documentation improved (#62)
• Haplotype calling uses smallest possible bit depth (#61)
• Haplotype calling now uses sparse matrices (#60)
• FASTX.jl downgraded to v1 (#56)

1.0.0 - 2023-06-04

This release represents a big rewrite of HapLink

Added

• BAM index file finder (#35)
• VariationInfo type (#35)
• VariationPileup type (#35)
• VariationCall type (#35)
• HaplotypeCall type (#35)
• More rigorous haplotype combination finding algorithm (#35)
• significance function for haplotype chi-squared significance (#37)
• Earthfile for repeatable testing and documentation builds (#42/#45)
• Nix configuration (#41/#53)

Changed

• VCF parsing outsourced to VariantCallFormat.jl (#35)
• Codebase now uses Blue Style (#35)
• Variant calling and storage outsourced to SequenceVariation.jl (#35)
• [BREAKING] linkage now returns only the unweighted linkage disequilibrium, not a tuple of linkage disequilibrium and significance (#37)
• CLI now implemented in Comonicon.jl instead of ArgParse (#38/#47)
• haplink haplotypes now only outputs simulation-related settings if --simulated-reads flag is set (#40/#48)

Removed

• [BREAKING] myref2seq (functionality now present in BioAlignments.jl) (#35)
• Dependency on bam-readcount artifact (including x86-64 glibc Linux-specific code) (#35)
• Variant type (functionality now present in SequenceVariation.jl) (#35)
• Haplotype type (functionality now present in SequenceVariation.jl) (#35)

Fixed

• Linkage disequilibrium and chi-squared significance calculations corrected (#37)

0.7.1 - 2022-07-29

Fixed

• VCF output files no longer contain invalid characters (#30)

0.7.0 - 2022-04-28

Added

• haplink consensus command to generate consensus sequences from variant calls (#29)

Changed

• haplink haplotypes now calls haplotypes based on the consensus sequence (#30)

[0.6.1] - 2022-03-28

Fixed

• The CI scripts have been fixed

0.6.0 - 2022-03-28

Changed

• haplink haplotypes now requires a reference genome passed via --reference (PR#25)

0.5.1 - 2022-01-24

Added

• --seed parameter for fixing random seed

0.5.0 - 2022-01-12

Removed

• bam-readcount dependency

0.4.3 - 2021-12-30

Fixed

• Can now create and manipulate empty (reference) haplotypes

0.4.2 - 2021-12-29

Changed

• Use CHANGELOG for release notes on GitHub

0.4.1 - 2021-12-28

Changed

• Dockerfile now separated into multiple layers

Fixed

• Precompile script updated to use HapLink 0.4 output format

0.4.0 - 2021-12-28

Changed

• Output YAML schema changed to include more information

0.3.0 - 2021-12-28

Changed

• HapLink CLI functionality is now exposed as subcommands:
  • haplink variants
  • haplink haplotypes
  • haplink sequences
• Dockerfile version numbers extracted to environment variables

Removed

• make-haplotype-fastas command line/binary application
• haplink haplotypes no longer outputs in fasta format

0.2.0 - 2021-12-08

Added

• Julia Formatter to CI workflow
• Example files
• Precompile script
• Long reads/raw read haplotype finding

Changed

• Extacted the incidence matrix calculations to occurrence_matrix function
• Improved REPL printout for Haplotype type
• Haplotype read finder must now be passed as argument to haplotype finder

Removed

• Mac and Windows binary builds

0.1.2 - 2021-12-07

Changed

• Correct build workflow typo

0.1.1 - 2021-12-07

Changed

• Moved sequence manipulation functions to sequences.jl
• Moved haplotype finding functions to haplotypecalling.jl
• Moved variant calling functions to variantcalling.jl
• Improved binary building workflow

0.0.1 - 2021-12-06

Added

• New Julia Package via PkgTemplates.jl
• GitHub Issue Templates
• Code of Conduct
• Self-contained Dockerfile
• Logo artwork
• CLI programs
  • haplink
  • make-haplotype-fastas
• Types
  • Haplotype
  • Variant