Dnaapler

* Adds `-c/--custom_db` with `dnaapler all` to allow specifying custom databases with `dnaapler all`.

* Fixes bug where if the starting gene (`dnaA/terL/repA`) was on the reverse strand, and the top BLAST hit did not find the start codon, it would reorient the genome to begin at the end of the starting gene, not the start as desired i.e. the terL would be the last gene in the output, not the first. Thanks susiegriggo

* Updates `dnaapler citation` and documentation to include the JOSS citation

* With `dnaapler all`, adds the reoriented gene to the header (thanks ammaraziz 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 63 )

v0.5.0 is the JOSS Release, as published in the [Journal of Open-Source Software](https://joss.theoj.org/).

Add some changes with error and logging, and other minor improvements.

* Implements a modification to the logic for all cases where the top blastx hit alignment does not begin with a start codon. Instead of erroring (or skipping in `all`) as of v0.4.0 dnaapler will now choose the CDS (predicted by pyrodigal) that has the most overlap with the top hit alignment. Thanks simone-pignotti for this suggestion here 44 .
* Changes `dnaapler all` output FASTA name 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 CDS.