Bakta

This is the first v1.10 patch release (v1.10.1).

Improvements
- Improved handling of draft genome in circular plots: 01189833cf70ca9f1fe9e72773f7521a7bf729f0
- Added N90 to genome statistics: 7abfa9aa59e791104f652db316267f1635f408c5

Fixes
- Fixed changed Micromamba parameter in Dockerfile: 342 345 (Thanks pamelacamejom / mjfos2r)
- Fixed INSDC `note` qualifiers: 346 (Thanks Dx-wmc)

This is the tenth minor release (v1.10) introducing user-provided HMMs, output file recovery, feature inference scores, and various improvements.

Compatible database scheme version: 5

Important
Since v1.10.0, Bakta requires Python `>=3.9`, uses [pyCirclize](https://github.com/moshi4/pyCirclize) instead of Circos, and discarded support of [DeepSig](https://github.com/BolognaBiocomp/deepsig)!

An important decision had to be made for this release regarding supported Python versions, external dependencies and features impacted by this. Both Circos and [DeepSig](https://github.com/BolognaBiocomp/deepsig) seem to be _out of support_ for a long time. Hence, Circos was replaced by [pyCirclize](https://github.com/moshi4/pyCirclize), a pure-Python actively-maintained library, enabling a couple of new features. As a result, Bakta's Python dependency had to be bumped to `>=3.9`, thus unfortunately loosing compatibility with [DeepSig](https://github.com/BolognaBiocomp/deepsig). Dropping an existing feature feels odd and wrong, but as a developer, sticking to unmaintained external software for too long constantly increases your daily pain level and slows down the project as a whole. This hasn't been an easy decision, but a necessary. So, If you depend on the detection of signaling peptides, please keep using Bakta `<=v1.9.4`.

New features
* Accept user-provided trusted HMMs via `--hmms`: 309 327 (Thanks StefDiV)
* Recover output files based on Bakta's comprehensive `JSON` output via `bakta_io`: 304 339 (Thanks cpauvert)
* Write annotation inference metrics to new `*.inference.tsv` file: 314 331 (Thanks jvera888 / gbouras13)
* Deactivate feature overlap filters via `--skip-filter` : 295 (Thanks Daniel-Tichy)

Improvements
* Support translation table `25`: 323 (Thanks ndombrowski)
* Export CRISPR and tRNA nucleotide sequences: 336 (Thanks YoungerRen)
* Replacement of Circos by [pyCirclize](https://github.com/moshi4/pyCirclize): #344 (Thanks acarafat / alexweisberg)
* Introduce `--label`, `--size` and `--dpi` parameters in `bakta_plot` to customize plots: 344
* Add fixes for common submission errors: 330 (Thanks kevinmyers)
* Improve INSDC compliance: 30b3928d62cab771f1b8f524946ba7c4aef9acf2 8ba8a146232861c28243b86f91624f4f455e042c
* Reduce the locus tag offset from 5 to 1 and allow specifications via `--locus-tag-increment`: 279 (Thanks 1996xjm)
* Revise internal/external designation of truncated features and (real) pseudogenes: 333
* Print msg if IPS and pseudogene detection is skipped using the db `light` version: 320 (Thanks flashton2003)
* Review internal main data structure: 338

Fixes
* Fix import of user-provided CDS spanning sequence edges: 324 332 (Thanks aekazakov)
* Fix translated protein sequences for CDS truncated at both sides: 340 (Thanks tpillone)
* Fix wrong truncation label: 341
* Fix import of user-provided regions in combination with a metadata replicon table: 326

**Full Changelog**: https://github.com/oschwengers/bakta/compare/v1.9.4...v1.10.0

This is the fourth v1.9 patch release (v1.9.4).

Fixes
- Fixed CDS gene translation in meta mode: 301 (Thanks ohickl)
- Fixed the CRISPR parser for short (<10 nt) spacer sequences: 299 302 (Thanks ohickl)
- Fixed Pyrodigal and Pyhmmer version detection: 294 (Thanks EricDeveaud)

Improvements
- Skip certain genes in user-provided regions: 288 303 (Thanks Dx-wmc)

This is the third v1.9 patch release (v1.9.3).

Fixes
- fixed a regex in the CRISPR parser skipping spacers in some special cases: c7478033265ccb2218582f9d3121825dbf7ce91a 265 (Thanks ZarulHanifah)
- fixed wrong Piler-CR CRISPR array stop position omitting the last spacer: 276
- tmp. pinned Diamond version to `v2.1.8` due to an upstream bug: 0dd84fb60d9fc03c280287af1d237da2fd7d74db

Improvements
- added parent ID to CRISPR repeat/spacer features in GFF3 outputs: ae71c09199981004db8c870d198e8ce11b2e60f8

This is the second v1.9 patch release (v1.9.2).

Fixes
- Changed tRNA pseudogene type to unknown in INSDC compliant mode: https://github.com/oschwengers/bakta/commit/bb8366aa9856994eca6687fd5325f09b278b4e6d
- Updated DB build scripts for v5.1: 270
- Allow uneven number of CRISPR spacers/repeats: 265 267 https://github.com/oschwengers/bakta/commit/7c1a7e88cf3e2c56174e9aa3ab39374ee53c3011 (Thanks ZarulHanifah, marade)
- Fixed wrong complete sequence inference for some cases: https://github.com/oschwengers/bakta/commit/231788bfb3a98dfcd1f2668e9d0a0b36f670a1b0 https://github.com/oschwengers/bakta/commit/24a43b9d137cc0d210f6a98ed526b3cc63d66e7e
- Fixed minor issues with DB downloads/updates: https://github.com/oschwengers/bakta/commit/4d609de8a2b553fcbd43b57222edfcc04a65362a https://github.com/oschwengers/bakta/commit/1a0413c6562a26b71b343701fdb28141dad4eb18 https://github.com/oschwengers/bakta/commit/ff836d166be82ebe6216b7961e65a68132c5df50

This is the first v1.9 patch release (v1.9.1).

Fixes

- Fixed a Python `KeyError` when both `--regions` and `--keep-contig-headers` are used: d3d7a98973e61d4f8fc5625ea41ee4984be4ec60 (Thanks thorellk)
- Fixed a bzip2 error in the Docker build process: 73ac39dd2bc3ee1063648ebc57322de038c37218 (Thanks lukasjelonek)