Octofludb

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* Extended documentation in README
* Do not include gisaid data by default (replace `--no-gisaid` flag in
`octofludb pull` with `--include-gisaid`)
* Fix read error in `octofludb prep fasta`
* Remove the `octofludb make` subcommand
- moved `octofludb make masterlist` to `octofludb report masterlist`
- removed `const` and `subtypes`, just run SPARQL queries instead

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* Add motif generation to `pull`
* Add options to limit what data is updated with `pull`
* Add deletion commands

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* Bug fixes in octoFLU wrapper

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* Move imports to location of use (speeds usage mesages)
* Remove unused `clean` command
* Bug fixes

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* Remove `script` folder and all bash scripting
* Add `pull` subcommand for updating the database
* Add `classify` subcommand as a wrapper around octoFLU
* Add a config file that contains links to all data and the octoFLU reference

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* Fix subtype generation
* Fix bugs in init
* Add `report monthly --context` to pull sequences for comparisons
* Add support for the the SPARQL CONSTRUCT command
* Do not generate "unknown" triples