Include distances and explicit aa muts by default#630
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We used to only include these annotations in auspice JSONs when `use_nextalign` was set to `true`. Now that nextalign is the default (and only) aligner, we should always include these annotations and allow users who never enabled nextalign to benefit from them.
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Description of proposed changes
We used to only include these annotations in auspice JSONs when
use_nextalignwas set totrue. Now that nextalign is the default (and only) aligner, we should always include these annotations and allow users who never enabled nextalign to benefit from them.Related issue(s)
Related to #615
Testing
What steps should be taken to test the changes you've proposed?
If you added or changed behavior in the codebase, did you update the tests, or do you need help with this?
Release checklist
If this pull request introduces new features, complete the following steps:
docs/change_log.mdin this pull request to document these changes by the date they were added.