Flutile

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* Fix edge cases
* Pass filehandles to functions that print

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* Set caton82 antigenic sites exactly to the sites described in paper

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* Fix flake8 issues

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* Fix HA1 trimming for all subtypes
* Test agreement of flutile predicted HA1 with 50 randomly selected strains
for each subtype from genbank

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* Fix bug in dna2dna conversions and add tests

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* Don't spam .tmp temporary alignment files everywhere
* Add `--count` flag to aggregate counts in aadiff tables