kbo-v0.5.1 (31 March 2025)

What's Changed

• Derive PartialEq for all Opts classes by @tmaklin in #54
• Remove WIP disclaimer from the GUI by @tmaklin in #54
• Link to https://maklin.fi/kbo for an example of the GUI by @tmaklin in #54

Full Changelog: v0.5.0...v0.5.1

kbo-v0.5.0 (24 March 2025)

This is an API breaking update:

• struct BuildOpts moved from index.rs to lib.rs.
• refine_translation has been renamed to fill_gaps and moved to gap_filling.rs.
• fill_gaps takes different parameters than refine_translation.

The output has also changed:

• Added nucleotide character 'N' for cases where a substitution is detected but the character is ambiguous.
• run_lengths and run_lengths_gapped now report start index as 0-based (previously 1-based).
• run_lengths and run_lengths_gapped have had multiple changes to counting gap characters.
• map now calls the new variant calling and gap filling code which affects the output.

What's Changed

• Implement variant calling by @jnalanko in #46
• Implement gap filling by @tmaklin in #45
• Add option to skip gap filling, variant calling, or formatting in map by @tmaklin in #48
• Rewrite run length encodings by @tmaklin in #49
• Update documentation for v0.5.0 by @tmaklin in #50
• Move build opts to lib by @tmaklin in #51

New Contributors

• @jnalanko made their first contribution in #46

Full Changelog: v0.4.2...v0.5.0

kbo-v0.4.2 (27 February 2025)

What's Changed

• Fix hardcoded k in translate_ms_vec by @tmaklin in #42

Full Changelog: v0.4.1...v0.4.2

kbo-v0.4.1 (09 January 2025)

What's Changed

• Update README.md by @tmaklin in #36
• Fix dollar signs in output by @tmaklin in #38

Full Changelog: v0.4.0...v0.4.1

kbo-v0.4.0 (18 November 2024)

What's Changed

• First public release by @tmaklin in #34

Changes in "First public release" #32

• Rename to kbo
• Add crate level documentation.
• Add gapped alignment to find.
• Return results as an RLE object from find.
• Build index in memory by default using the new bpks-mem feature in sbwt v0.3.4.
• Remove CLI from this repository (will move to a new kbo-cli repo).
• Minor bug fixes.

Full Changelog: v0.3.0...v0.4.0

sablast-v0.3.0 (31 October 2024)

What's Changed

• CLI development by @tmaklin in #28

CLI changes

• Gate building CLI behind the cli feature.
• Move cli code to src/cli.
• Expose max_error_probability in lib.rs and CLI.

This is a breaking update:

• sablast::matches now takes 4 parameters instead of 3.
• sablast::map now takes 4 parameters instead of 3.
• sablast::find now takes 4 parameters instead of 3.

Full Changelog: v0.2.0...v0.3.0

sablast-v0.2.0 (01 October 2024)

What's Changed

• Expose build parameters in all commands by @tmaklin in #27
• Implement sablast find for fasta references by @tmaklin in #27
• Clear todos from documentation by @tmaklin in #27
• Mark BuildOpts non-exhaustive (breaking change) by @tmaklin in #27.

Full Changelog: v0.1.1...v0.2.0

sablast-v0.1.1 (26 September 2024)

What's Changed

• Implement resolving SNPs in sablast map by @tmaklin in #26

Full Changelog: v0.1.0...v0.1.1

sablast-v0.1.0 (25 September 2024)

Basic functionality implemented by @tmaklin .

• find: Find some sequences in another and produce a list of their locations and quality similar to blast with -outfmt 6.
• map: Map a sequence to another and generate an alignment in the .aln format (same as ska map).
  ** map cannot currently distinguish between SNPs and 1bp insertions, so these are marked with a '-' in the result.
• build: Build the SBWT for a sequence for future use in find.

What's Changed

Development

• Finish implementation for derandomizing and translating matching statistics.
• Big refactor in an attempt to make the API (re)usable.

Features

• Implement map, find, and build.
  ** Old implementation of sablast map is now called sablast find.
  ** The function map has been renamed to matches.
• Use needletail to read input (fixes #1)
• Handle reverse complements in find by querying both strands separately.

Continuous integration

• Tests for most functions.
• Document most functions (use cargo doc to view)
• Workflow to find and comment on TODOs in pull requests.
• Workflow to turn TODOs merged to main into issues.

Full Changelog: v0.0.1...v0.1.0

sablast-v0.0.1 (19 September 2024)

Proof-of-concept for local alignment on SBWT using k-bounded matching statistics.

What's Changed

• Implement indexing and querying functionality by @tmaklin.
• Add workflow for building and releasing binaries by @tmaklin in #3

New Contributors

• @tmaklin made their first contribution in #3

Full Changelog: https://github.com/tmaklin/sablast/commits/v0.0.1