Bakta

New features:
- add new `--compliant` option for INSDC genome submissions: https://github.com/oschwengers/bakta/issues/69 (Thanks michoug)
- introduce PSCCs (UniRef50) as a fallback if PSCs (UniRef90) are not detected, greatly improving the annotation of less represented species and metagenome-assembled genomes (MAGs): https://github.com/oschwengers/bakta/commit/84c808fb343cadb36b4afdbdd56dbf416b7512e3
- export nucleotide sequences: https://github.com/oschwengers/bakta/issues/57 (Thanks mcroxen)
- revise suspect CDS product names: https://github.com/oschwengers/bakta/commit/f85970b7a9b6a55336b91570955777c062f03852

Improvements:
- various improvements and fixes in GFF3, GenBank and EMBL files to adhere to INSDC specs: https://github.com/oschwengers/bakta/issues/69
- improve internal DB download: https://github.com/oschwengers/bakta/commit/bdd665aa87bcb14d7ddaba22744b45f9b700b74a
- use Diamond version v2.0.11 and its `--fast` option: https://github.com/oschwengers/bakta/commit/c82f4e21aae75ecc8d48146aab8499c5967d8b1b https://github.com/oschwengers/bakta/commit/19c95d802cd038500e53fdfa30353420c89f5480 (Thanks to bbuchfink for https://github.com/bbuchfink/diamond/issues/419)
- use stable CLI progress library [alive-progress](https://github.com/rsalmei/alive-progress) https://github.com/oschwengers/bakta/commit/0ac56256dda51e16fabce08b4500048bd1ea5d79
- improve GFF3 output regarding GFF3 specs: https://github.com/oschwengers/bakta/commit/697121f6192bbee883b3102578891d2de6beb2db
- store AMRFinderPlus DB within the Bakta DB directory: https://github.com/oschwengers/bakta/commit/04ff7b00c0b4b71738072710355a45a8f9fa8137 (Thanks to LuisFF)
- redirect BAKTA-TMP directory to AMRFinderPlus to prevent stale files: https://github.com/oschwengers/bakta/commit/26f81fcc82e1001ce2021011fcbb40416a9c11c2
- detect & mark tmRNA on sequence edges: https://github.com/oschwengers/bakta/commit/782f640f920368216920f9bf8d0ff4f219c3d91d
- adhere to translation table in tmRNA prediction: https://github.com/oschwengers/bakta/commit/450d6b7224469e4bf39cbad9ac24d3e9e3dbc9f1

Bug fixes:
- fix var name in Docker shell script: https://github.com/oschwengers/bakta/commit/e6bab09dba5ff9ea478242edb6b2863e5dd2e122 (Thanks joyn-sromero)
- fix inflated blastn thread numbers: https://github.com/oschwengers/bakta/commit/e9073e188c5888701bbcf5ab800058d191384463 (Thanks LuisFF)
- fix location of features on sequence edges: https://github.com/oschwengers/bakta/commit/34873e7bb91984a34d43d69bf2eb9b24573ab289
- fix BLAST+ tool name in GFF3: https://github.com/oschwengers/bakta/commit/efff065f212f9a627995291b0590f8bc6e55b9fb
and many more ...

Bug fixes:
- fix calculation of GC & N50 stats: https://github.com/oschwengers/bakta/commit/2829a24c7a01c94bcd4bf7d93319f2139b10765f (Thanks Matthew Croxen)
- fix a typo in GenBank/EMBL output: https://github.com/oschwengers/bakta/commit/1595133c2aede5a853397b0499c123676905d6e7 (Thanks davised)

Improvements:
- download/update AMRFinderPlus db upon Bakta db download/update: https://github.com/oschwengers/bakta/commit/94ccc695e2604dce19581d5bd1d2ed46f02d28c9
- add a short note to error msg if AMRFinderPlus db is not available: https://github.com/oschwengers/bakta/commit/750396feff7edb12c4e4c96e3c1ee2a15470adac
- add more sORF unit tests: https://github.com/oschwengers/bakta/commit/685a3bc045f4fec51d96f6d754989b5c9c31601b
- fix link to old db files: https://github.com/oschwengers/bakta/commit/140e34884ce555590cccef70bb8757562bcb463b (Thanks davised)
- readme updates & improvements

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)

This is the ninth minor release (v1.9) introducing user-provided feature regions and various minor improvements.

Compatible database scheme version: 5

New features
* Support _a priori_ user-provided feature regions via `--regions` either in Genbank or GFF3 format (currently, only `CDS` features are supported). CDS coordinates are imported, supersede _de novo_ predicted `CDS`, and are subject to the regular internal annotation workflow. To provide functional annotation, as well use `--proteins`: 216 245 247 250 259 (Thanks marade PengfanZhang simone-pignotti thorellk)

Improvements
* Extract & export CRISPR spacer & repeat sequences: 171 249 (Thanks alexweisberg)
* Add support for Pyrodigal v3: 240 244 (Thanks jsgounot)
* Replace HMMER with PyHMMER: 219 (Thanks jhahnfeld)
* Re-activate parallel pyrodigal gene prediction: 252 (Thanks althonos)
* Introduce auxiliary scripts: 246 251 (Thanks AhmedElsherbini)
* Add Podman wrapper script: bd50faabfe7a2cbad7c63f453baae854503a9d46
* Update dependencies to latest versions: 3260441ed181176c71e39125cb58a1e0df69b7dc 33c02f92305c51d3741172d3851bedc7463f83c8 a1d2ffeb465cc9afbb124fe903a877b3ef562d22 b2656722dd5199416b308291c6c7188ccd4f9f58 1a2c48ee177800e21d3ff3e2356fc253407ecd65

Fixes
* Fix PyPI CD: 231
* Add missing `--force` parameter to Docker wrapper script: f39434ed670d1310a144df9defcd3f556e36ffbf
* Fix wrong runtime report: 243

**Full Changelog**: https://github.com/oschwengers/bakta/compare/v1.8.2...v1.9.0