fix: upper case root sequence for ancestral reconstruction

[rneher]

I ran into this issue when the root sequence was provided as lower case. All lower-to-upper case changes were attached to the root. This should fix it, but there might be better solutions.

[corneliusroemer]

Thanks! Seems like a strictly beneficial change, better solutions can be added later.

CI failing is because of monkeypox restructure, I will take mpox out of augur CI

[corneliusroemer]

Merging this then CI should work again: #1324

[corneliusroemer]

Added a test that failed before the fix so that alternative fixes are easy to test and we don't regress in the future.
5d8bc27

See: https://github.com/nextstrain/augur/actions/runs/6315326703/job/17147616573#step:9:20 for what the bug looks like

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 72.25%. Comparing base (2e993df) to head (c438653).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1323   +/-   ##
=======================================
  Coverage   72.25%   72.25%           
=======================================
  Files          79       79           
  Lines        8276     8276           
  Branches     1691     1691           
=======================================
  Hits         5980     5980           
  Misses       2011     2011           
  Partials      285      285           

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[victorlin]

I don't have enough background to understand why the change is needed. Is it because, for the purpose of ancestral reconstruction, "soft-masking" in the root sequence is irrelevant and should be ignored?

[corneliusroemer]

I didn't know about soft vs hard masking. Indeed, we don't ever treat upper and lower case nucleotides differently anywhere in augur - at least not as far as I'm aware.

[victorlin]

I think you're right - at least for augur index, sequences are lowercased.

[corneliusroemer]

This was actually resolved by @jameshadfield in 947e217 in an identical way so we can close this PR