Code

Upgrade treetime to v0.7#431

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trvrb merged 7 commits intomasternextstrain/augur:masterfrom tt07nextstrain/augur:tt07Copy head branch name to clipboardFeb 13, 2020

+83-101

Commits

Commits on Jan 3, 2020

• traits: use treetime's reconstruct_discrete_traits function instead of the parallel implementation that existed in augur traits.

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Commits on Jan 8, 2020

• ancestral: add mutually exclusive group --infer-ambiguous/keep-ambiguous with the latter being default (as it was for vcf, now also for fasta input).

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Commits on Jan 9, 2020

• v1-schema: allow nucleotide mutations to all valid IUPAC codes as we do in the v2-schema

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• ancestral: sanitize invalid nucleotide states that TreeTime treats as missing info by mapping them to 'N'

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Commits on Feb 9, 2020

• Merge remote-tracking branch 'origin/master' into tt07

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• refine: output skyline to json if inferred

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Commits on Feb 12, 2020

• Default to --infer-ambiguous

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