Releases: tmaklin/kbo
Releases · tmaklin/kbo
kbo-v0.4.0 (18 November 2024)
What's Changed
Changes in "First public release" #32
- Rename to
kbo
- Add crate level documentation.
- Add gapped alignment to
find
. - Return results as an
RLE
object fromfind
. - 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 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)
sablast-v0.1.1 (26 September 2024)
What's Changed
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
, andbuild
.
** Old implementation ofsablast map
is now calledsablast find
.
** The functionmap
has been renamed tomatches
. - 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
Full Changelog: https://github.com/tmaklin/sablast/commits/v0.0.1