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nextstrain / augur Public

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augur/clades.py: change clade assignment from mutations to sequences …#288

Merged

rneher merged 4 commits intomasternextstrain/augur:masterfrom fix_clade_assignmentnextstrain/augur:fix_clade_assignmentCopy head branch name to clipboard

May 25, 2019

+213-135

Conversation Commits4 (4)Checks Files changed

Commits

Commits on May 23, 2019

augur/clades.py: change clade assignment from mutations to sequences to avoid unassigned nodes when reference sequence with respect to which mutations are defined is not part of the build
rneher
committed
augur/clades.py: harmonize reference sequence handling to allow for similar patterns between fasta and vcf workflows. still needs testing
rneher
committed

Commits on May 24, 2019

augur/clades.py: clades now work with vcf (as before) and with fasta workflows were the optionally pull in the sequence of the root.
rneher
committed

Commits on May 25, 2019

augur/clades.py: add comments, fix line endings
rneher
committed

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