Vquest

Added

* FASTQ support ([37])

Changed

* Repository now at <https://github.com/ShawHahnLab/vquest> ([#36])

Fixed

* Usage example now matches packaged structure ([36])
* Requests to the IMGT server now use HTTPS ([34])

[37]: https://github.com/ShawHahnLab/vquest/pull/37
[36]: https://github.com/ShawHahnLab/vquest/pull/36
[34]: https://github.com/ressy/vquest/pull/34

Added

* `--outdir` argument to set output directory other than current working
directory ([24])
* `--no-collapse` argument (and updates to `request` function) to disable
automatic combining of results across batched submissions ([25])

Fixed

* Empty config files now result in the usual error message about required
options ([30])
* All command-line options now match V-QUEST option names ([28])

[30]: https://github.com/ressy/vquest/pull/30
[28]: https://github.com/ressy/vquest/pull/28
[25]: https://github.com/ressy/vquest/pull/25
[24]: https://github.com/ressy/vquest/pull/24

Fixed

* Don't include a trailing empty submission when submitting perfect multiples
of 50 sequences ([19])

[19]: https://github.com/ressy/vquest/pull/19

Fixed

* Removed a duplicate data directory from build/install process ([16])

[16]: https://github.com/ressy/vquest/pull/16

Changed

* Refactored top-level code into separate modules ([13])

Fixed

* Avoid trying to import dependencies at install time ([13])

[13]: https://github.com/ressy/vquest/pull/13

Added

* `--align` argument (via `airr_to_fasta` function) for extraction of sequence
alignment FASTA from AIRR results ([1])
* Error messages sent by the server are now raised as an exception containing
the server-provided message(s) ([7])

Changed

* Reorganized and expanded test code as its own package ([6])
* Added basic test of command-line usage ([10])
* Clarified wording on required options ([8])

Fixed

* Parse command-line options that should be integers from a finite list of
options as integers instead of strings ([5])

[10]: https://github.com/ressy/vquest/pull/10
[8]: https://github.com/ressy/vquest/pull/8
[7]: https://github.com/ressy/vquest/pull/7
[6]: https://github.com/ressy/vquest/pull/6
[5]: https://github.com/ressy/vquest/pull/5
[1]: https://github.com/ressy/vquest/pull/1