# History

# 0.5.2 (2024-01-24)

* Bumps version to include updated citation

# 0.5.1 (2024-01-09)

* With `dnaapler all`, adds the reoriented gene to the header (thanks @ammaraziz https://github.com/gbouras13/dnaapler/issues/67)
* Adds `--db` parameter to `dnaapler all`  allowing specifying a subset of genes to make up the database. In particular, if you have bacteria and plasmids, `--db dnaa,repa` should speed up Dnaapler's runtime quite a bit (thanks @oschwengers https://github.com/gbouras13/dnaapler/issues/63)

# 0.5.0 (2023-12-03)

* JOSS release with minor typos and bug fixes from v0.4

# 0.4.0 (2023-10-25)

* Implemented a modification to the logic for all cases where the top blastx hit alignment does not begin with a start codon. In this case, dnaapler will find the CDS according the pyrodigal that has the most overlap with the top hit alignment. Thanks @simone-pignotti for this suggestion [here](https://github.com/gbouras13/dnaapler/issues/44).
* Changes `dnaapler all` output FASTA to `_reoriented.fasta` instead of `_all_reoriented.fasta` for consistency with all other commands (except `dnaapler bulk`).
* Adds `-a` or `--autocomplete` option with `dnaapler all`.
* Adds `dnaapler largest` and `-a largest` as an option to orient your sequence beginning with the largest 

# 0.3.2 (2023-09-20)

* Changes `Orffinder` to `Genefinder`  to support `pyrodigal` v3.
* Updates dependency to `pyrodigal >=v3`.

# 0.3.1 (2023-09-01)

* Minor release to fix an error with dnaapler all #38 thanks @samnooij

# 0.3.0 (2023-08-18)

* `dnaapler all` subcommand added thanks @alexweisberg
* `dnaapler all` implements `--ignore` to ignore some contigs


# 0.2.0 (2023-08-08)

* `dnaapler nearest` subcommand added
* `dnaapler bulk` subcommand added
* dnaA database filtered to keep only bona-file dnaA genes (i.e. GN=dnaA)
* Adds `-e` parameter to vary BLAST evalue if desired
* Adds `-a` autocomplete parameter if user wants to reorient sequences with mystery or nearest methods in case the BLAST based method fails

# 0.1.0 (June 2023)

* Completely overhauled
* First stable released with pypi and conda 
* `dnaapler chromosome` added
* `dnaapler custom` added
* `dnaapler mystery` added 
* `dnaapler phage` added
* `dnaapler plasmid` added


# 0.0.1 (2022-10-12)

* First release (conda only `conda install -c gbouras dnaapler`)
