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Feat/parse nextclade annotation#1263

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rneher wants to merge 16 commits intomasternextstrain/augur:masterfrom feat/parse-nextclade-annotationnextstrain/augur:feat/parse-nextclade-annotationCopy head branch name to clipboard

+3,329-660

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Commits on Jul 22, 2023

• feat: allow reconstruction of amino acid sequences

  Show description for 77608d5
  rneher

  committed
  77608d5

• rename argument, denoise output

  rneher

  committed
  5b5e7e3

• fix: make python 3.7 compatible

  rneher

  committed
  051ef41

• feat: allow to specify root-sequence for mutation reporting

  rneher

  committed
  7913547

• bring back mask

  rneher

  committed
  8faa4b1

• enable full sequences for nucleotides.

  rneher

  committed
  91f154b

Commits on Jul 24, 2023

• docs: add to changelog and comments

  rneher

  committed
  9764a34

Commits on Jul 26, 2023

• feat: make translation arguments a list, check consistency between annotation and translation

  rneher

  committed
  03ac136

• feat: add rudimentary json parser

  rneher

  committed
  29940ba

• doc: update parser comment to signal that json annotation allowed

  rneher

  committed
  9f1b1c2

Commits on Jul 27, 2023

• Update ancestral tests to reflect new expected output

  huddlej

  committed
  7c6ea87

• Standardize ancestral functional tests

  Show description for 7b6aa4e
  huddlej

  committed
  7b6aa4e

• Add functional test for amino acid sequence reconstruction

  Show description for 8d05f8d
  huddlej

  committed
  8d05f8d

Commits on Jul 29, 2023

• revert: make --translation argument a filename template again

  rneher

  committed
  ad51e1f

Commits on Jul 31, 2023

• Merge branch 'feat/aa-ancestral' into feat/parse-nextclade-annotation

  rneher

  committed
  fa934ac

Commits on Aug 1, 2023

• fix: account for annotations without explicit landmark features

  rneher

  committed
  bff657d