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.github
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paper
scripts
- README.md
- beast-to-auspice-jsons-proof-of-principle.py
- compare-json-vcf.py
- diff_jsons.py
- diff_trees.py
- identify_emerging_clades.py
- json_tree_to_nexus.py
- plot_msa.py
- plot_tree.py
- prepared_json_to_fasta.py
- s3.py
- swap_colors.py
- traits_from_json.py
- tree_to_JSON.py
- verify_meta_json.py
tests
.coveragerc
.cramrc
.flake8
.gitignore
.mailmap
.pylintrc
.readthedocs.yml
CHANGES.md
CITATION.cff
DEPRECATED.md
LICENSE.nextstrain-cli
LICENSE.nextstrain-ncov-ingest
LICENSE.txt
MANIFEST.in
README.md
codecov.yml
mypy.ini
pyrightconfig.json
pytest.ini
run_tests.sh
setup.py

scripts

Replace usage of built-in extend action with ExtendOverwriteDefault

Jan 14, 2025

b01865f · Jan 14, 2025

Name		Name	Last commit message	Last commit date
parent directory ..
README.md		README.md	Reorganize tests directory	Sep 7, 2017
beast-to-auspice-jsons-proof-of-principle.py		beast-to-auspice-jsons-proof-of-principle.py	Remove unused imports	Sep 5, 2023
compare-json-vcf.py		compare-json-vcf.py	[ancestral] fix ambiguous site behaviour (VCF)	Jan 22, 2024
diff_jsons.py		diff_jsons.py	Replace usage of built-in extend action with ExtendOverwriteDefault	Jan 14, 2025
diff_trees.py		diff_trees.py	Allow repeating an option that takes multiple values	Apr 25, 2024
identify_emerging_clades.py		identify_emerging_clades.py	Update emerging clades script	Feb 28, 2021
json_tree_to_nexus.py		json_tree_to_nexus.py	Remove unused imports	Sep 5, 2023
plot_msa.py		plot_msa.py	Remove unused imports	Sep 5, 2023
plot_tree.py		plot_tree.py	Added scripts to plot MSA and auspice JSON tree for quality control.	May 11, 2018
prepared_json_to_fasta.py		prepared_json_to_fasta.py	Fix bugs in conversion of prepared JSONs to FASTA and metadata	Oct 4, 2018
s3.py		s3.py	Replace usage of built-in extend action with ExtendOverwriteDefault	Jan 14, 2025
swap_colors.py		swap_colors.py	Allow repeating an option that takes multiple values	Apr 25, 2024
traits_from_json.py		traits_from_json.py	Replace usage of built-in extend action with ExtendOverwriteDefault	Jan 14, 2025
tree_to_JSON.py		tree_to_JSON.py	Replace usage of built-in extend action with ExtendOverwriteDefault	Jan 14, 2025
verify_meta_json.py		verify_meta_json.py	Remove unused imports	Sep 5, 2023

README.md

Conversion scrips

Run from this directory.