Bakta

This is the second v1.2 patch release (v1.2.2) providing a couple of improvements and bug fixes.

Compatible database scheme version: v3

Improvements:
- set BLAST_USAGE_REPORT environment variable to `false` forestalling `blastn` to hang for 90 secs if no internet connection is available
- add a check for duplicated input sequence IDs: https://github.com/oschwengers/bakta/commit/888bb9b06bda62f88d8a93e0dfbd85eb7cf50e3e (Thanks joyn-sromero)
- add further SQLite URI parameters to improve read-only access: https://github.com/oschwengers/bakta/commit/e658a2ea2e0f48434eade93198d9c6c346480cb2
- synchronize Conda environment dependencies and runtime dependency version checks: https://github.com/oschwengers/bakta/commit/95ef71fd40dbeb471a3c45e04bc389ccf2ca08df https://github.com/oschwengers/bakta/commit/c516656661eaedaa933c1689a0ec6dd4ddc8267b
- add AMRFinder protein hits to dbxref outputs: https://github.com/oschwengers/bakta/commit/505a2ce8743eb227e8422567f779d6d3c46b33b3

Bug fixes:
- fix `NA` issue on HMM-only AMRFinder hits: https://github.com/oschwengers/bakta/commit/71e2dac3c17136e55c258dff8cf2cfe700b2c670 https://github.com/oschwengers/bakta/commit/e9ff01cead6524c4c96a09fec1d8bd7df144d23e (Thanks taylorreiter)

This is the first patch release (v1.2.1) merely fixing a wrong former version tag (v1.1.2).

This is the second minor release (v1.2.0) introducing user provided proteins as well as many improvements.

This is the first v1.1 patch release (v1.1.1) providing a couple of improvements and minor bug fixes.

Compatible database scheme version: v3

Improvements:
- added a revision & refinement logic for gene symbols: https://github.com/oschwengers/bakta/commit/539137be5cd82b7b01960b09f1a69e2a6536ae17
- added further CDS product revision rules: https://github.com/oschwengers/bakta/commit/f8ec2aa69c9b01da542e0cd49a4878bb6281be3f https://github.com/oschwengers/bakta/commit/1fcca891087e16d0ab5b6844ac21a230901e09d4 https://github.com/oschwengers/bakta/commit/8915af7d5fc81e5e7d306bbc8e1e18ca4c717b10 https://github.com/oschwengers/bakta/commit/626981bb9a385f890c8f817f45d7d31e75d8f50b https://github.com/oschwengers/bakta/commit/321391b1d0a336541c03732a28c95e99ca4dc0b6 https://github.com/oschwengers/bakta/commit/0d93c2fd0edf1affa22c172fbe87045bc16ec16f https://github.com/oschwengers/bakta/issues/69 (Thanks michoug)

Bug fixes:
- fixed AMRFinderDB issue in docker shell script: https://github.com/oschwengers/bakta/commit/e8253616dd37ad55ff61df64a7494253351692a2
- fixed `None` values of CDS `rbs_motif` attributes: https://github.com/oschwengers/bakta/commit/0727b2551207e1bf57514f3824572f004a11fd9e
- skip CDS annotation if no CDS are predicted: https://github.com/oschwengers/bakta/commit/3787e01a2e44eb5c80d6a19d8350a6bce3732415
- fix several CDS product revision rules

This is the first minor release (v1.1) introducing several new features, many improvements and countless bug fixes.

This is the fourth v1.0 patch release (v1.0.4) fixing a couple of minor bugs and adding further minor improvements.